How mutation affects evolutionary games on graphs

PubMed Central

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

2011-01-01

Evolutionary dynamics are affected by population structure, mutation rates and update rules. Spatial or network structure facilitates the clustering of strategies, which represents a mechanism for the evolution of cooperation. Mutation dilutes this effect. Here we analyze how mutation influences evolutionary clustering on graphs. We introduce new mathematical methods to evolutionary game theory, specifically the analysis of coalescing random walks via generating functions. These techniques allow us to derive exact identity-by-descent (IBD) probabilities, which characterize spatial assortment on lattices and Cayley trees. From these IBD probabilities we obtain exact conditions for the evolution of cooperation and other game strategies, showing the dual effects of graph topology and mutation rate. High mutation rates diminish the clustering of cooperators, hindering their evolutionary success. Our model can represent either genetic evolution with mutation, or social imitation processes with random strategy exploration. PMID:21473871

An analysis of parameter sensitivities of preference-inspired co-evolutionary algorithms

NASA Astrophysics Data System (ADS)

Wang, Rui; Mansor, Maszatul M.; Purshouse, Robin C.; Fleming, Peter J.

2015-10-01

Many-objective optimisation problems remain challenging for many state-of-the-art multi-objective evolutionary algorithms. Preference-inspired co-evolutionary algorithms (PICEAs) which co-evolve the usual population of candidate solutions with a family of decision-maker preferences during the search have been demonstrated to be effective on such problems. However, it is unknown whether PICEAs are robust with respect to the parameter settings. This study aims to address this question. First, a global sensitivity analysis method - the Sobol' variance decomposition method - is employed to determine the relative importance of the parameters controlling the performance of PICEAs. Experimental results show that the performance of PICEAs is controlled for the most part by the number of function evaluations. Next, we investigate the effect of key parameters identified from the Sobol' test and the genetic operators employed in PICEAs. Experimental results show improved performance of the PICEAs as more preferences are co-evolved. Additionally, some suggestions for genetic operator settings are provided for non-expert users.

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.

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.

A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids.

PubMed

McGee, Matthew D; Borstein, Samuel R; Neches, Russell Y; Buescher, Heinz H; Seehausen, Ole; Wainwright, Peter C

2015-11-27

Evolutionary innovations, traits that give species access to previously unoccupied niches, may promote speciation and adaptive radiation. Here, we show that such innovations can also result in competitive inferiority and extinction. We present evidence that the modified pharyngeal jaws of cichlid fishes and several marine fish lineages, a classic example of evolutionary innovation, are not universally beneficial. A large-scale analysis of dietary evolution across marine fish lineages reveals that the innovation compromises access to energy-rich predator niches. We show that this competitive inferiority shaped the adaptive radiation of cichlids in Lake Tanganyika and played a pivotal and previously unrecognized role in the mass extinction of cichlid fishes in Lake Victoria after Nile perch invasion. Copyright © 2015, American Association for the Advancement of Science.

Thioredoxin and evolution

NASA Technical Reports Server (NTRS)

Buchanan, B. B.

1991-01-01

Comparisons of primary structure have revealed significant homology between the m type thioredoxins of chloroplasts and the thioredoxins from a variety of bacteria. Chloroplast thioredoxin f, by comparison, remains an enigma: certain residues are invariant with those of the other thioredoxins, but a phylogenetic relationship to bacterial or m thioredoxins seems distant. Knowledge of the evolutionary history of thioredoxin f is, nevertheless, of interest because of its role in photosynthesis. Therefore, we have attempted to gain information on the evolutionary history of chloroplast thioredoxin f, as well as m. Our goal was first to establish the utility of thioredoxin as a phylogenetic marker, and, if found suitable, to deduce the evolutionary histories of the chloroplast thioredoxins. To this end, we have constructed phylogenetic (minimal replacement) trees using computer analysis. The results show that the thioredoxins of bacteria and animals fall into distinct phylogenetic groups - the bacterial group resembling that derived from earlier 16s RNA analysis and the animal group showing a cluster consistent with known relationships. The chloroplast thioredoxins show a novel type of phylogenetic arrangement: one m type aligns with its counterpart of eukaryotic algae, cyanobacteria and other bacteria, whereas the second type (f type) tracks with animal thioredoxin. The results give new insight into the evolution of photosynthesis.

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.

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

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.

Evolutionary technology adoption in an oligopoly market with forward-looking firms

NASA Astrophysics Data System (ADS)

Lamantia, F.; Radi, D.

2018-05-01

In this paper, we propose an evolutionary oligopoly game of technology adoption in a market with isoelastic demand and two possible (linear) production technologies. While one technology is characterized by lower marginal costs, the magnitude of fixed costs entails that a technology does not necessarily dominate the other. Firms are forward-looking as they assess the profitability of employing either technology according to the corresponding expected profits. The dynamics of the system is studied through a piecewise-smooth map, for which we present a local stability analysis of equilibria and show the occurrence of smooth and border collision bifurcations. Global analysis of the model is also presented to show the coexistence of attractors and its economic significance. This investigation reveals that firms can fail to learn to adopt the more efficient technology.

Evolutionary technology adoption in an oligopoly market with forward-looking firms.

PubMed

Lamantia, F; Radi, D

2018-05-01

In this paper, we propose an evolutionary oligopoly game of technology adoption in a market with isoelastic demand and two possible (linear) production technologies. While one technology is characterized by lower marginal costs, the magnitude of fixed costs entails that a technology does not necessarily dominate the other. Firms are forward-looking as they assess the profitability of employing either technology according to the corresponding expected profits. The dynamics of the system is studied through a piecewise-smooth map, for which we present a local stability analysis of equilibria and show the occurrence of smooth and border collision bifurcations. Global analysis of the model is also presented to show the coexistence of attractors and its economic significance. This investigation reveals that firms can fail to learn to adopt the more efficient technology.

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

PubMed Central

Irie, Naoki; Kuratani, Shigeru

2011-01-01

One of the central issues in evolutionary developmental biology is how we can formulate the relationships between evolutionary and developmental processes. Two major models have been proposed: the 'funnel-like' model, in which the earliest embryo shows the most conserved morphological pattern, followed by diversifying later stages, and the 'hourglass' model, in which constraints are imposed to conserve organogenesis stages, which is called the phylotypic period. Here we perform a quantitative comparative transcriptome analysis of several model vertebrate embryos and show that the pharyngula stage is most conserved, whereas earlier and later stages are rather divergent. These results allow us to predict approximate developmental timetables between different species, and indicate that pharyngula embryos have the most conserved gene expression profiles, which may be the source of the basic body plan of vertebrates. PMID:21427719

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.

Evolution, the loss of diversity and the role of trade-offs.

PubMed

Best, Alex; Bowers, Roger; White, Andy

2015-06-01

We investigate how the loss of previously evolved diversity in host resistance to disease is dependent on the complexity of the underlying evolutionary trade-off. Working within the adaptive dynamics framework, using graphical tools (pairwise invasion plots, PIPs; trait evolution plots, TEPs) and algebraic analysis we consider polynomial trade-offs of increasing degree. Our focus is on the evolutionary trajectory of the dimorphic population after it has been attracted to an evolutionary branching point. We show that for sufficiently complex trade-offs (here, polynomials of degree three or higher) the resulting invasion boundaries can form closed 'oval' areas of invadability and strategy coexistence. If no attracting singular strategies exist within this region, then the population is destined to evolve outside of the region of coexistence, resulting in the loss of one strain. In particular, the loss of diversity in this model always occurs in such a way that the remaining strain is not attracted back to the branching point but to an extreme of the trade-off, meaning the diversity is lost forever. We also show similar results for a non-polynomial but complex trade-off, and for a different eco-evolutionary model. Our work further highlights the importance of trade-offs to evolutionary behaviour. Copyright © 2015 Elsevier Inc. All rights reserved.

Evolution of optimal Lévy-flight strategies in human mental searches

NASA Astrophysics Data System (ADS)

Radicchi, Filippo; Baronchelli, Andrea

2012-06-01

Recent analysis of empirical data [Radicchi, Baronchelli, and Amaral, PloS ONE1932-620310.1371/journal.pone.0029910 7, e029910 (2012)] showed that humans adopt Lévy-flight strategies when exploring the bid space in online auctions. A game theoretical model proved that the observed Lévy exponents are nearly optimal, being close to the exponent value that guarantees the maximal economical return to players. Here, we rationalize these findings by adopting an evolutionary perspective. We show that a simple evolutionary process is able to account for the empirical measurements with the only assumption that the reproductive fitness of the players is proportional to their search ability. Contrary to previous modeling, our approach describes the emergence of the observed exponent without resorting to any strong assumptions on the initial searching strategies. Our results generalize earlier research, and open novel questions in cognitive, behavioral, and evolutionary sciences.

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.

Structural characterization and evolutionary analysis of fish-specific TLR27.

PubMed

Wang, Jinlan; Zhang, Zheng; Liu, Jing; Li, Fang; Chang, Fen; Fu, Hui; Zhao, Jing; Yin, Deling

2015-08-01

Toll-like receptors (TLRs) are critical components of the innate immune response of fish. In a phylogenetic analysis, TLR27 from three fish species, which belongs to TLR family 1, clustered with TLR14/18 and TLR25 on the evolutionary tree. The ectodomain of TLR27 is predicted to include 19 leucine-rich repeat (LRR) modules. Structural modeling showed that the TLR27 ectodomain can be divided into three distinctive sections. The lack of conserved asparagines on the concave surface of the central subdomain causes a structural transition in the middle of the ectodomain, forming a distinct hydrophobic pocket at the border between the central subdomain and the C-terminal subdomain. We infer that, like other functionally characterized TLRs in family 1, the hydrophobic pocket located between LRR11 and LRR12 participates in ligand recognition by TLR27. An evolutionary analysis showed that the dN/dS value at the TLR27 locus was very low. Approximately one quarter of the total number of TLR27 sites are under significant negatively selection pressure, whereas only two sites are under positive selection. Consequently, TLR27 is highly evolutionarily conserved and probably plays an extremely important role in the innate immune systems of fishes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Females drive asymmetrical introgression from rare to common species in Darwin's tree finches.

PubMed

Peters, K J; Myers, S A; Dudaniec, R Y; O'Connor, J A; Kleindorfer, S

2017-11-01

The consequences of hybridization for biodiversity depend on the specific ecological and evolutionary context in which it occurs. Understanding patterns of gene flow among hybridizing species is crucial for determining the evolutionary trajectories of species assemblages. The recently discovered hybridization between two species of Darwin's tree finches (Camarhynchus parvulus and C. pauper) on Floreana Island, Galápagos, presents an exciting opportunity to investigate the mechanisms causing hybridization and its potential evolutionary consequences under conditions of recent habitat disturbance and the introduction of invasive pathogens. In this study, we combine morphological and genetic analysis with pairing observations to explore the extent, direction and drivers of hybridization and to test whether hybridization patterns are a result of asymmetrical pairing preference driven by females of the rarer species (C. pauper). We found asymmetrical introgression from the critically endangered, larger-bodied C. pauper to the common, smaller-bodied C. parvulus, which was associated with a lack of selection against heterospecific males by C. pauper females. Examination of pairing data showed that C. parvulus females paired assortatively, whereas C. pauper females showed no such pattern. This study shows how sex-specific drivers can determine the direction of gene flow in hybridizing species. Furthermore, our results suggest the existence of a hybrid swarm comprised of C. parvulus and hybrid birds. We discuss the influence of interspecific abundance differences and susceptibility to the invasive parasite Philornis downsi on the observed hybridization and recommend that the conservation of this iconic species group should be managed jointly rather than species-specific. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

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

Doves and hawks in economics revisited: An evolutionary quantum game theory based analysis of financial crises

NASA Astrophysics Data System (ADS)

Hanauske, Matthias; Kunz, Jennifer; Bernius, Steffen; König, Wolfgang

2010-11-01

The last financial and economic crisis demonstrated the dysfunctional long-term effects of aggressive behaviour in financial markets. Yet, evolutionary game theory predicts that under the condition of strategic dependence a certain degree of aggressive behaviour remains within a given population of agents. However, as a consequence of the financial crisis, it would be desirable to change the “rules of the game” in a way that prevents the occurrence of any aggressive behaviour and thereby also the danger of market crashes. The paper picks up this aspect. Through the extension of the well-known hawk-dove game by a quantum approach, we can show that dependent on entanglement, evolutionary stable strategies also can emerge, which are not predicted by the classical evolutionary game theory and where the total economic population uses a non-aggressive quantum strategy.

Evolutionary genomics and HIV restriction factors.

PubMed

Pyndiah, Nitisha; Telenti, Amalio; Rausell, Antonio

2015-03-01

To provide updated insights into innate antiviral immunity and highlight prototypical evolutionary features of well characterized HIV restriction factors. Recently, a new HIV restriction factor, Myxovirus resistance 2, has been discovered and the region/residue responsible for its activity identified using an evolutionary approach. Furthermore, IFI16, an innate immunity protein known to sense several viruses, has been shown to contribute to the defense to HIV-1 by causing cell death upon sensing HIV-1 DNA. Restriction factors against HIV show characteristic signatures of positive selection. Different patterns of accelerated sequence evolution can distinguish antiviral strategies--offense or defence--as well as the level of specificity of the antiviral properties. Sequence analysis of primate orthologs of restriction factors serves to localize functional domains and sites responsible for antiviral action. We use recent discoveries to illustrate how evolutionary genomic analyses help identify new antiviral genes and their mechanisms of action.

Analysis of convergence of an evolutionary algorithm with self-adaptation using a stochastic Lyapunov function.

PubMed

Semenov, Mikhail A; Terkel, Dmitri A

2003-01-01

This paper analyses the convergence of evolutionary algorithms using a technique which is based on a stochastic Lyapunov function and developed within the martingale theory. This technique is used to investigate the convergence of a simple evolutionary algorithm with self-adaptation, which contains two types of parameters: fitness parameters, belonging to the domain of the objective function; and control parameters, responsible for the variation of fitness parameters. Although both parameters mutate randomly and independently, they converge to the "optimum" due to the direct (for fitness parameters) and indirect (for control parameters) selection. We show that the convergence velocity of the evolutionary algorithm with self-adaptation is asymptotically exponential, similar to the velocity of the optimal deterministic algorithm on the class of unimodal functions. Although some martingale inequalities have not be proved analytically, they have been numerically validated with 0.999 confidence using Monte-Carlo simulations.

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

PubMed

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

2012-01-01

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

Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools.

PubMed

Franks, Steven J; Kane, Nolan C; O'Hara, Niamh B; Tittes, Silas; Rest, Joshua S

2016-08-01

There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome-wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late-season drought in California. These ancestor-descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (FST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome-wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

The evolutionary rate dynamically tracks changes in HIV-1 epidemics

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

Maljkovic-berry, Irina; Athreya, Gayathri; Daniels, Marcus

Large-sequence datasets provide an opportunity to investigate the dynamics of pathogen epidemics. Thus, a fast method to estimate the evolutionary rate from large and numerous phylogenetic trees becomes necessary. Based on minimizing tip height variances, we optimize the root in a given phylogenetic tree to estimate the most homogenous evolutionary rate between samples from at least two different time points. Simulations showed that the method had no bias in the estimation of evolutionary rates and that it was robust to tree rooting and topological errors. We show that the evolutionary rates of HIV-1 subtype B and C epidemics have changedmore » over time, with the rate of evolution inversely correlated to the rate of virus spread. For subtype B, the evolutionary rate slowed down and tracked the start of the HAART era in 1996. Subtype C in Ethiopia showed an increase in the evolutionary rate when the prevalence increase markedly slowed down in 1995. Thus, we show that the evolutionary rate of HIV-1 on the population level dynamically tracks epidemic events.« less

Comparison of the genetic relationship between nine Cephalopod species based on cluster analysis of karyotype evolutionary distance

PubMed Central

Wang, Jin-hai; Zheng, Xiao-dong

2017-01-01

Abstract Karyotype analysis was carried out on gill cells of three species of octopods using a conventional air-drying method. The karyotype results showed that all the three species have the same diploid chromosome number, 2n=60, but with different karyograms as 2n=38M+6SM+8ST+8T, FN (fundamental number)=104 (Cistopus chinensis Zheng et al., 2012), 2n=42M+6SM+4ST+8T, FN=108 (Octopus minor (Sasaki, 1920)) and 2n=32M+16SM+12T, FN=108 (Amphioctopus fangsiao (d’Orbigny, 1839–1841)). These findings were combined with data from earlier studies to infer the genetic relationships between nine species via cluster analysis using the karyotype evolutionary distance (De) and resemblance-near coefficient (λ). The resulting tree revealed a clear distinction between different families and orders which was substantially consistent with molecular phylogenies. The smallest intraspecific evolutionary distance (De=0.2013, 0.2399) and largest resemblance-near coefficient (λ=0.8184, 0.7871) appeared between O. minor and C. chinensis, and Sepia esculenta Hoyle, 1885 and S. lycidas Gray, 1849, respectively, indicating that these species have the closest relationship. The largest evolutionary gap appeared between species with complicated karyotypes and species with simple karyotypes. Cluster analysis of De and λ provides information to supplement traditional taxonomy and molecular systematics, and it would serve as an important auxiliary for routine phylogenetic study. PMID:29093799

Where is, in 2017, the evo in evo-devo (evolutionary developmental biology)?

PubMed

Diogo, Rui

2018-01-01

After the inaugural Pan-American-Evo-Devo meeting (2015, Berkeley), I showed how major concerns about evo-devo (Evolutionary Developmental Biology) research were demonstrated by a simple, non-biased quantitative analysis of the titles/abstracts of that meeting's talks. Here, I apply the same methodology to the titles/abstracts of the recent Pan-American-Evo-Devo meeting (2017, Calgary). The aim is to evaluate if the concerns raised by me in that paper and by other authors have been addressed and/or if there are other types of differences between the two meetings that may reflect trends within the field of evo-devo. This analysis shows that the proportion of presentations referring to "morphology", "organism", "selection", "adaptive", "phylogeny", and their derivatives was higher in the 2017 meeting, which therefore had a more "organismal" feel. However, there was a decrease in the use of "evolution"/its derivatives and of macroevolutionary terms related to the tempo and mode of evolution in the 2017 meeting. Moreover, the disproportionately high use of genetic/genomic terms clearly shows that evo-devo continues to be mainly focused on devo, and particularly on "Geno", that is, on molecular/genetic studies. Furthermore, the vast majority of animal evo-devo studies are focused only on hard tissues, which are just a small fraction of the whole organism-for example, only 15% of the tissue mass of the human body. The lack of an integrative approach is also evidenced by the lack of studies addressing conceptual/long-standing broader questions, including the links between ecology and particularly behavior and developmental/evolutionary variability and between evo-devo and evolutionary medicine. © 2018 Wiley Periodicals, Inc.

Evolutionary plasticity of plasma membrane interaction in DREPP family proteins.

PubMed

Vosolsobě, Stanislav; Petrášek, Jan; Schwarzerová, Kateřina

2017-05-01

The plant-specific DREPP protein family comprises proteins that were shown to regulate the actin and microtubular cytoskeleton in a calcium-dependent manner. Our phylogenetic analysis showed that DREPPs first appeared in ferns and that DREPPs have a rapid and plastic evolutionary history in plants. Arabidopsis DREPP paralogues called AtMDP25/PCaP1 and AtMAP18/PCaP2 are N-myristoylated, which has been reported as a key factor in plasma membrane localization. Here we show that N-myristoylation is neither conserved nor ancestral for the DREPP family. Instead, by using confocal microscopy and a new method for quantitative evaluation of protein membrane localization, we show that DREPPs rely on two mechanisms ensuring their plasma membrane localization. These include N-myristoylation and electrostatic interaction of a polybasic amino acid cluster. We propose that various plasma membrane association mechanisms resulting from the evolutionary plasticity of DREPPs are important for refining plasma membrane interaction of these signalling proteins under various conditions and in various cells. Copyright © 2017 Elsevier B.V. All rights reserved.

Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

PubMed Central

Dudley, Joel T.; Chen, Rong; Sanderford, Maxwell; Butte, Atul J.; Kumar, Sudhir

2012-01-01

Genome-wide disease association studies contrast genetic variation between disease cohorts and healthy populations to discover single nucleotide polymorphisms (SNPs) and other genetic markers revealing underlying genetic architectures of human diseases. Despite scores of efforts over the past decade, many reproducible genetic variants that explain substantial proportions of the heritable risk of common human diseases remain undiscovered. We have conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position. We propose a new measure for ranking SNPs that integrates evolutionary conservation scores and the P value (E-rank). Using published data from a large case-control study, we demonstrate that E-rank method prioritizes SNPs with a greater likelihood of bona fide and reproducible genetic disease associations, many of which may explain greater proportions of genetic variance. Therefore, long-term evolutionary histories of genomic positions offer key practical utility in reassessing data from existing disease association studies, and in the design and analysis of future studies aimed at revealing the genetic basis of common human diseases. PMID:22389448

Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle.

PubMed

Zhan, Xiangjiang; Pan, Shengkai; Wang, Junyi; Dixon, Andrew; He, Jing; Muller, Margit G; Ni, Peixiang; Hu, Li; Liu, Yuan; Hou, Haolong; Chen, Yuanping; Xia, Jinquan; Luo, Qiong; Xu, Pengwei; Chen, Ying; Liao, Shengguang; Cao, Changchang; Gao, Shukun; Wang, Zhaobao; Yue, Zhen; Li, Guoqing; Yin, Ye; Fox, Nick C; Wang, Jun; Bruford, Michael W

2013-05-01

As top predators, falcons possess unique morphological, physiological and behavioral adaptations that allow them to be successful hunters: for example, the peregrine is renowned as the world's fastest animal. To examine the evolutionary basis of predatory adaptations, we sequenced the genomes of both the peregrine (Falco peregrinus) and saker falcon (Falco cherrug), and we present parallel, genome-wide evidence for evolutionary innovation and selection for a predatory lifestyle. The genomes, assembled using Illumina deep sequencing with greater than 100-fold coverage, are both approximately 1.2 Gb in length, with transcriptome-assisted prediction of approximately 16,200 genes for both species. Analysis of 8,424 orthologs in both falcons, chicken, zebra finch and turkey identified consistent evidence for genome-wide rapid evolution in these raptors. SNP-based inference showed contrasting recent demographic trajectories for the two falcons, and gene-based analysis highlighted falcon-specific evolutionary novelties for beak development and olfaction and specifically for homeostasis-related genes in the arid environment-adapted saker.

Analysis of the expected density of internal equilibria in random evolutionary multi-player multi-strategy games.

PubMed

Duong, Manh Hong; Han, The Anh

2016-12-01

In this paper, we study the distribution and behaviour of internal equilibria in a d-player n-strategy random evolutionary game where the game payoff matrix is generated from normal distributions. The study of this paper reveals and exploits interesting connections between evolutionary game theory and random polynomial theory. The main contributions of the paper are some qualitative and quantitative results on the expected density, [Formula: see text], and the expected number, E(n, d), of (stable) internal equilibria. Firstly, we show that in multi-player two-strategy games, they behave asymptotically as [Formula: see text] as d is sufficiently large. Secondly, we prove that they are monotone functions of d. We also make a conjecture for games with more than two strategies. Thirdly, we provide numerical simulations for our analytical results and to support the conjecture. As consequences of our analysis, some qualitative and quantitative results on the distribution of zeros of a random Bernstein polynomial are also obtained.

Taking evolution seriously in political science.

PubMed

Lewis, Orion; Steinmo, Sven

2010-09-01

In this essay, we explore the epistemological and ontological assumptions that have been made to make political science "scientific." We show how political science has generally adopted an ontologically reductionist philosophy of science derived from Newtonian physics and mechanics. This mechanical framework has encountered problems and constraints on its explanatory power, because an emphasis on equilibrium analysis is ill-suited for the study of political change. We outline the primary differences between an evolutionary ontology of social science and the physics-based philosophy commonly employed. Finally, we show how evolutionary thinking adds insight into the study of political phenomena and research questions that are of central importance to the field, such as preference formation.

Sequence data - Magnitude and implications of some ambiguities.

NASA Technical Reports Server (NTRS)

Holmquist, R.; Jukes, T. H.

1972-01-01

A stochastic model is applied to the divergence of the horse-pig lineage from a common ansestor in terms of the alpha and beta chains of hemoglobin and fibrinopeptides. The results are compared with those based on the minimum mutation distance model of Fitch (1972). Buckwheat and cauliflower cytochrome c sequences are analyzed to demonstrate their ambiguities. A comparative analysis of evolutionary rates for various proteins of horses and pigs shows that errors of considerable magnitude are introduced by Glx and Asx ambiguities into evolutionary conclusions drawn from sequences of incompletely analyzed proteins.

Centrin diversity and basal body patterning across evolution: new insights from Paramecium

PubMed Central

Balavoine, Guillaume; Lemullois, Michel; Bouhouche, Khaled; Beisson, Janine; Koll, France

2017-01-01

ABSTRACT First discovered in unicellular eukaryotes, centrins play crucial roles in basal body duplication and anchoring mechanisms. While the evolutionary status of the founding members of the family, Centrin2/Vfl2 and Centrin3/cdc31 has long been investigated, the evolutionary origin of other members of the family has received less attention. Using a phylogeny of ciliate centrins, we identify two other centrin families, the ciliary centrins and the centrins present in the contractile filaments (ICL centrins). In this paper, we carry on the functional analysis of still not well-known centrins, the ICL1e subfamily identified in Paramecium, and show their requirement for correct basal body anchoring through interactions with Centrin2 and Centrin3. Using Paramecium as well as a eukaryote-wide sampling of centrins from completely sequenced genomes, we revisited the evolutionary story of centrins. Their phylogeny shows that the centrins associated with the ciliate contractile filaments are widespread in eukaryotic lineages and could be as ancient as Centrin2 and Centrin3. PMID:28432105

An evolutionary critique of cultural analysis in sociology.

PubMed

Crippen, T

1992-12-01

A noteworthy development that has transpired in American sociology in the past quarter century has been the increasingly sophisticated interest in the analysis of human cultural systems. Sadly, however, these analyses reveal that social scientists rarely appreciate the profoundly evolutionary aspects of human culture. The chief purpose of this essay is to address this shortcoming and to offer some tentative suggestions toward its rectification. The essay begins by briefly reviewing recent developments in the analysis of cultural systems, primarily by reference to the influential work of Wuthnow. Second, a common flaw in these approaches is addressed-namely, the absence of any recognition of the value of grounding sociocultural theory in an informed evolutionary framework-and the case is made that this shortcoming is avoidable, even within the context of the intellectual traditions of the social sciences. Third, the evolutionary foundations of human cultural behavior are explored in terms of an analysis of relevant theoretical and empirical developments in the evolutionary neurosciences. Fourth, the value of these insights is illustrated by reference to an evolutionary critique of a recent and thought-provoking contribution to the study of modern political culture-Douglas and Wildavsky's analysis ofRisk and Culture. Finally, the article concludes by emphasizing the value of and the necessity for incorporating evolutionary reasoning into the domain of sociocultural theory.

Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information

PubMed Central

Lopes, Anne; Sacquin-Mora, Sophie; Dimitrova, Viktoriya; Laine, Elodie; Ponty, Yann; Carbone, Alessandra

2013-01-01

Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis, are possible and realizable on hundreds of proteins with variate structures and interfaces. We demonstrated this on the 168 proteins of the Mintseris Benchmark 2.0. On the one hand, we evaluated the quality of the interaction signal and the contribution of docking information compared to evolutionary information showing that the combination of the two improves partner identification. On the other hand, since protein interactions usually occur in crowded environments with several competing partners, we realized a thorough analysis of the interactions of proteins with true partners but also with non-partners to evaluate whether proteins in the environment, competing with the true partner, affect its identification. We found three populations of proteins: strongly competing, never competing, and interacting with different levels of strength. Populations and levels of strength are numerically characterized and provide a signature for the behavior of a protein in the crowded environment. We showed that partner identification, to some extent, does not depend on the competing partners present in the environment, that certain biochemical classes of proteins are intrinsically easier to analyze than others, and that small proteins are not more promiscuous than large ones. Our approach brings to light that the knowledge of the binding site can be used to reduce the high computational cost of docking simulations with no consequence in the quality of the results, demonstrating the possibility to apply coarse-grain docking to datasets made of thousands of proteins. Comparison with all available large-scale analyses aimed to partner predictions is realized. We release the complete decoys set issued by coarse-grain docking simulations of both true and false interacting partners, and their evolutionary sequence analysis leading to binding site predictions. Download site: http://www.lgm.upmc.fr/CCDMintseris/ PMID:24339765

An evolutionary perspective on leaf economics: phylogenetics of leaf mass per area in vascular plants

PubMed Central

Flores, Olivier; Garnier, Eric; Wright, Ian J; Reich, Peter B; Pierce, Simon; Dìaz, Sandra; Pakeman, Robin J; Rusch, Graciela M; Bernard-Verdier, Maud; Testi, Baptiste; Bakker, Jan P; Bekker, Renée M; Cerabolini, Bruno E L; Ceriani, Roberta M; Cornu, Guillaume; Cruz, Pablo; Delcamp, Matthieu; Dolezal, Jiri; Eriksson, Ove; Fayolle, Adeline; Freitas, Helena; Golodets, Carly; Gourlet-Fleury, Sylvie; Hodgson, John G; Brusa, Guido; Kleyer, Michael; Kunzmann, Dieter; Lavorel, Sandra; Papanastasis, Vasilios P; Pérez-Harguindeguy, Natalia; Vendramini, Fernanda; Weiher, Evan

2014-01-01

In plant leaves, resource use follows a trade-off between rapid resource capture and conservative storage. This “worldwide leaf economics spectrum” consists of a suite of intercorrelated leaf traits, among which leaf mass per area, LMA, is one of the most fundamental as it indicates the cost of leaf construction and light-interception borne by plants. We conducted a broad-scale analysis of the evolutionary history of LMA across a large dataset of 5401 vascular plant species. The phylogenetic signal in LMA displayed low but significant conservatism, that is, leaf economics tended to be more similar among close relatives than expected by chance alone. Models of trait evolution indicated that LMA evolved under weak stabilizing selection. Moreover, results suggest that different optimal phenotypes evolved among large clades within which extremes tended to be selected against. Conservatism in LMA was strongly related to growth form, as were selection intensity and phenotypic evolutionary rates: woody plants showed higher conservatism in relation to stronger stabilizing selection and lower evolutionary rates compared to herbaceous taxa. The evolutionary history of LMA thus paints different evolutionary trajectories of vascular plant species across clades, revealing the coordination of leaf trait evolution with growth forms in response to varying selection regimes. PMID:25165520

Using creation science to demonstrate evolution: application of a creationist method for visualizing gaps in the fossil record to a phylogenetic study of coelurosaurian dinosaurs.

PubMed

Senter, P

2010-08-01

It is important to demonstrate evolutionary principles in such a way that they cannot be countered by creation science. One such way is to use creation science itself to demonstrate evolutionary principles. Some creation scientists use classic multidimensional scaling (CMDS) to quantify and visualize morphological gaps or continuity between taxa, accepting gaps as evidence of independent creation and accepting continuity as evidence of genetic relatedness. Here, I apply CMDS to a phylogenetic analysis of coelurosaurian dinosaurs and show that it reveals morphological continuity between Archaeopteryx, other early birds, and a wide range of nonavian coelurosaurs. Creation scientists who use CMDS must therefore accept that these animals are genetically related. Other uses of CMDS for evolutionary biologists include the identification of taxa with much missing evolutionary history and the tracing of the progressive filling of morphological gaps in the fossil record through successive years of discovery.

The Influence of Atomic Diffusion on Stellar Ages and Chemical Tagging

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

Dotter, Aaron; Conroy, Charlie; Cargile, Phillip

2017-05-10

In the era of large stellar spectroscopic surveys, there is an emphasis on deriving not only stellar abundances but also the ages for millions of stars. In the context of Galactic archeology, stellar ages provide a direct probe of the formation history of the Galaxy. We use the stellar evolution code MESA to compute models with atomic diffusion—with and without radiative acceleration—and extra mixing in the surface layers. The extra mixing consists of both density-dependent turbulent mixing and envelope overshoot mixing. Based on these models we argue that it is important to distinguish between initial, bulk abundances (parameters) and current,more » surface abundances (variables) in the analysis of individual stellar ages. In stars that maintain radiative regions on evolutionary timescales, atomic diffusion modifies the surface abundances. We show that when initial, bulk metallicity is equated with current, surface metallicity in isochrone age analysis, the resulting stellar ages can be systematically overestimated by up to 20%. The change of surface abundances with evolutionary phase also complicates chemical tagging, which is the concept that dispersed star clusters can be identified through unique, high-dimensional chemical signatures. Stars from the same cluster, but in different evolutionary phases, will show different surface abundances. We speculate that calibration of stellar models may allow us to estimate not only stellar ages but also initial abundances for individual stars. In the meantime, analyzing the chemical properties of stars in similar evolutionary phases is essential to minimize the effects of atomic diffusion in the context of chemical tagging.« less

The origins and evolutionary history of human non-coding RNA regulatory networks.

PubMed

Sherafatian, Masih; Mowla, Seyed Javad

2017-04-01

The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

Global distribution of NA1 genotype of respiratory syncytial virus and its evolutionary dynamics assessed from the past 11 years.

PubMed

Haider, Md Shakir Hussain; Deeba, Farah; Khan, Wajihul Hasan; Naqvi, Irshad H; Ali, Sher; Ahmed, Anwar; Broor, Shobha; Alsenaidy, Hytham A; Alsenaidy, Abdulrahman M; Dohare, Ravins; Parveen, Shama

2018-06-01

Respiratory syncytial virus (RSV) is a potent pathogen having global distribution. The main purpose of this study was to gain an insight into distribution pattern of the NA1 genotype of group A RSV across the globe together with its evolutionary dynamics. We focused on the second hypervariable region of the G protein gene and used the same for Phylogenetic, Bayesian and Network analyses. Eighteen percent of the samples collected from 500 symptomatic pediatric patients with acute respiratory tract infection (ARI) were found to be positive for RSV during 2011-15 from New Delhi, India. Of these, group B RSV was predominant and clustered into two different genotypes (BA and SAB4). Similarly, group A viruses clustered into two genotypes (NA1 and ON1). The data set from the group A viruses included 543 sequences from 23 different countries including 67 strains from India. The local evolutionary dynamics suggested consistent virus population of NA1 genotype in India during 2009 to 2014. The molecular clock analysis suggested that most recent common ancestor of group A and NA1 genotype have emerged in during the years 1953 and 2000, respectively. The global evolutionary rates of group A viruses and NA1 genotype were estimated to be 3.49 × 10 -3 (95% HPD, 2.90-4.17 × 10 -3 ) and 3.56 × 10 -3 (95% HPD, 2.91 × 10 -3 -4.18 × 10 -3 ) substitution/site/year, respectively. Analysis of the NA1 genotype of group A RSV reported during 11 years i.e. from 2004 to 2014 showed its dominance in 21 different countries across the globe reflecting its evolutionary dynamics. The Network analysis showed highly intricate but an inconsistent pattern of haplotypes of NA1 genotype circulating in the world. Present study seems to be first comprehensive attempt on global distribution and evolution of NA1 genotype augmenting the optimism towards the vaccine development. Copyright © 2018 Elsevier B.V. All rights reserved.

Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants1[W][OA

PubMed Central

Jiang, Wen-kai; Liu, Yun-long; Xia, En-hua; Gao, Li-zhi

2013-01-01

The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs. PMID:23396833

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

PubMed Central

Van Holle, Sofie; De Schutter, Kristof; Eggermont, Lore; Tsaneva, Mariya; Dang, Liuyi; Van Damme, Els J. M.

2017-01-01

Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins. PMID:28587095

Evolution of heliobacteria: implications for photosynthetic reaction center complexes

NASA Technical Reports Server (NTRS)

Vermaas, W. F.; Blankenship, R. E. (Principal Investigator)

1994-01-01

The evolutionary position of the heliobacteria, a group of green photosynthetic bacteria with a photosynthetic apparatus functionally resembling Photosystem I of plants and cyanobacteria, has been investigated with respect to the evolutionary relationship to Gram-positive bacteria and cyanobacteria. On the basis of 16S rRNA sequence analysis, the heliobacteria appear to be most closely related to Gram-positive bacteria, but also an evolutionary link to cyanobacteria is evident. Interestingly, a 46-residue domain including the putative sixth membrane-spanning region of the heliobacterial reaction center protein show rather strong similarity (33% identity and 72% similarity) to a region including the sixth membrane-spanning region of the CP47 protein, a chlorophyll-binding core antenna polypeptide of Photosystem II. The N-terminal half of the heliobacterial reaction center polypeptide shows a moderate sequence similarity (22% identity over 232 residues) with the CP47 protein, which is significantly more than the similarity with the Photosystem I core polypeptides in this region. An evolutionary model for photosynthetic reaction center complexes is discussed, in which an ancestral homodimeric reaction center protein (possibly resembling the heliobacterial reaction center protein) with 11 membrane-spanning regions per polypeptide has diverged to give rise to the core of Photosystem I, Photosystem II, and of the photosynthetic apparatus in green, purple, and heliobacteria.

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

PubMed

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

2013-11-01

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

Genetic diversity and variation of Chinese fir from Fujian province and Taiwan, China, based on ISSR markers

PubMed Central

Chen, Yu; Peng, Zhuqing; Wu, Chao; Ma, Zhihui; Ding, Guochang; Cao, Guangqiu; Ruan, Shaoning; Lin, Sizu

2017-01-01

Genetic diversity and variation among 11 populations of Chinese fir from Fujian province and Taiwan were assessed using inter-simple sequence repeat (ISSR) markers to reveal the evolutionary relationship in their distribution range in this report. Analysis of genetic parameters of the different populations showed that populations in Fujian province exhibited a greater level of genetic diversity than did the populations in Taiwan. Compared to Taiwan populations, significant limited gene flow were observed among Fujian populations. An UPGMA cluster analysis showed that the most individuals of Taiwan populations formed a single cluster, whereas 6 discrete clusters were formed by each population from Fujian. All populations were divided into 3 main groups and that all 5 populations from Taiwan were gathered into a subgroup combined with 2 populations, Dehua and Liancheng, formed one of the 3 main groups, which indicated relative stronger relatedness. It is supported by a genetic structure analysis. All those results are suggesting different levels of genetic diversity and variation of Chinese fir between Fujian and Taiwan, and indicating different patterns of evolutionary process and local environmental adaption. PMID:28406956

Genetic diversity and variation of Chinese fir from Fujian province and Taiwan, China, based on ISSR markers.

PubMed

Chen, Yu; Peng, Zhuqing; Wu, Chao; Ma, Zhihui; Ding, Guochang; Cao, Guangqiu; Ruan, Shaoning; Lin, Sizu

2017-01-01

Genetic diversity and variation among 11 populations of Chinese fir from Fujian province and Taiwan were assessed using inter-simple sequence repeat (ISSR) markers to reveal the evolutionary relationship in their distribution range in this report. Analysis of genetic parameters of the different populations showed that populations in Fujian province exhibited a greater level of genetic diversity than did the populations in Taiwan. Compared to Taiwan populations, significant limited gene flow were observed among Fujian populations. An UPGMA cluster analysis showed that the most individuals of Taiwan populations formed a single cluster, whereas 6 discrete clusters were formed by each population from Fujian. All populations were divided into 3 main groups and that all 5 populations from Taiwan were gathered into a subgroup combined with 2 populations, Dehua and Liancheng, formed one of the 3 main groups, which indicated relative stronger relatedness. It is supported by a genetic structure analysis. All those results are suggesting different levels of genetic diversity and variation of Chinese fir between Fujian and Taiwan, and indicating different patterns of evolutionary process and local environmental adaption.

Extrapolating Weak Selection in Evolutionary Games

PubMed Central

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

2013-01-01

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

Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica

PubMed Central

2011-01-01

Background Angiosperm mitochondrial genomes are more complex than those of other organisms. Analyses of the mitochondrial genome sequences of at least 11 angiosperm species have showed several common properties; these cannot easily explain, however, how the diverse mitotypes evolved within each genus or species. We analyzed the evolutionary relationships of Brassica mitotypes by sequencing. Results We sequenced the mitotypes of cam (Brassica rapa), ole (B. oleracea), jun (B. juncea), and car (B. carinata) and analyzed them together with two previously sequenced mitotypes of B. napus (pol and nap). The sizes of whole single circular genomes of cam, jun, ole, and car are 219,747 bp, 219,766 bp, 360,271 bp, and 232,241 bp, respectively. The mitochondrial genome of ole is largest as a resulting of the duplication of a 141.8 kb segment. The jun mitotype is the result of an inherited cam mitotype, and pol is also derived from the cam mitotype with evolutionary modifications. Genes with known functions are conserved in all mitotypes, but clear variation in open reading frames (ORFs) with unknown functions among the six mitotypes was observed. Sequence relationship analysis showed that there has been genome compaction and inheritance in the course of Brassica mitotype evolution. Conclusions We have sequenced four Brassica mitotypes, compared six Brassica mitotypes and suggested a mechanism for mitochondrial genome formation in Brassica, including evolutionary events such as inheritance, duplication, rearrangement, genome compaction, and mutation. PMID:21988783

Evolution Analysis of Simple Sequence Repeats in Plant Genome.

PubMed

Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

2015-01-01

Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1-3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution.

Open Reading Frame Phylogenetic Analysis on the Cloud

PubMed Central

2013-01-01

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

Genetic identification and evolutionary trends of the seagrass Halophila nipponica in temperate coastal waters of Korea.

PubMed

Kim, Young Kyun; Kim, Seung Hyeon; Yi, Joo Mi; Kang, Chang-Keun; Short, Frederick; Lee, Kun-Seop

2017-01-01

Although seagrass species in the genus Halophila are generally distributed in tropical or subtropical regions, H. nipponica has been reported to occur in temperate coastal waters of the northwestern Pacific. Because H. nipponica occurs only in the warm temperate areas influenced by the Kuroshio Current and shows a tropical seasonal growth pattern, such as severely restricted growth in low water temperatures, it was hypothesized that this temperate Halophila species diverged from tropical species in the relatively recent evolutionary past. We used a phylogenetic analysis of internal transcribed spacer (ITS) regions to examine the genetic variability and evolutionary trend of H. nipponica. ITS sequences of H. nipponica from various locations in Korea and Japan were identical or showed very low sequence divergence (less than 3-base pair, bp, difference), confirming that H. nipponica from Japan and Korea are the same species. Halophila species in the section Halophila, which have simple phyllotaxy (a pair of petiolate leaves at the rhizome node), were separated into five well-supported clades by maximum parsimony analysis. H. nipponica grouped with H. okinawensis and H. gaudichaudii from the subtropical regions in the same clade, the latter two species having quite low ITS sequence divergence from H. nipponica (7-15-bp). H. nipponica in Clade I diverged 2.95 ± 1.08 million years ago from species in Clade II, which includes H. ovalis. According to geographical distribution and genetic similarity, H. nipponica appears to have diverged from a tropical species like H. ovalis and adapted to warm temperate environments. The results of divergence time estimates suggest that the temperate H. nipponica is an older species than the subtropical H. okinawensis and H. gaudichaudii and they may have different evolutionary histories.

Genetic identification and evolutionary trends of the seagrass Halophila nipponica in temperate coastal waters of Korea

PubMed Central

Kim, Young Kyun; Kim, Seung Hyeon; Yi, Joo Mi; Kang, Chang-Keun; Short, Frederick; Lee, Kun-Seop

2017-01-01

Although seagrass species in the genus Halophila are generally distributed in tropical or subtropical regions, H. nipponica has been reported to occur in temperate coastal waters of the northwestern Pacific. Because H. nipponica occurs only in the warm temperate areas influenced by the Kuroshio Current and shows a tropical seasonal growth pattern, such as severely restricted growth in low water temperatures, it was hypothesized that this temperate Halophila species diverged from tropical species in the relatively recent evolutionary past. We used a phylogenetic analysis of internal transcribed spacer (ITS) regions to examine the genetic variability and evolutionary trend of H. nipponica. ITS sequences of H. nipponica from various locations in Korea and Japan were identical or showed very low sequence divergence (less than 3-base pair, bp, difference), confirming that H. nipponica from Japan and Korea are the same species. Halophila species in the section Halophila, which have simple phyllotaxy (a pair of petiolate leaves at the rhizome node), were separated into five well-supported clades by maximum parsimony analysis. H. nipponica grouped with H. okinawensis and H. gaudichaudii from the subtropical regions in the same clade, the latter two species having quite low ITS sequence divergence from H. nipponica (7–15-bp). H. nipponica in Clade I diverged 2.95 ± 1.08 million years ago from species in Clade II, which includes H. ovalis. According to geographical distribution and genetic similarity, H. nipponica appears to have diverged from a tropical species like H. ovalis and adapted to warm temperate environments. The results of divergence time estimates suggest that the temperate H. nipponica is an older species than the subtropical H. okinawensis and H. gaudichaudii and they may have different evolutionary histories. PMID:28505209

Transmissible cancers in an evolutionary context.

PubMed

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

2016-07-01

Cancer is an evolutionary and ecological process in which complex interactions between tumour cells and their environment share many similarities with organismal evolution. Tumour cells with highest adaptive potential have a selective advantage over less fit cells. Naturally occurring transmissible cancers provide an ideal model system for investigating the evolutionary arms race between cancer cells and their surrounding micro-environment and macro-environment. However, the evolutionary landscapes in which contagious cancers reside have not been subjected to comprehensive investigation. Here, we provide a multifocal analysis of transmissible tumour progression and discuss the selection forces that shape it. We demonstrate that transmissible cancers adapt to both their micro-environment and macro-environment, and evolutionary theories applied to organisms are also relevant to these unique diseases. The three naturally occurring transmissible cancers, canine transmissible venereal tumour (CTVT) and Tasmanian devil facial tumour disease (DFTD) and the recently discovered clam leukaemia, exhibit different evolutionary phases: (i) CTVT, the oldest naturally occurring cell line is remarkably stable; (ii) DFTD exhibits the signs of stepwise cancer evolution; and (iii) clam leukaemia shows genetic instability. While all three contagious cancers carry the signature of ongoing and fairly recent adaptations to selective forces, CTVT appears to have reached an evolutionary stalemate with its host, while DFTD and the clam leukaemia appear to be still at a more dynamic phase of their evolution. Parallel investigation of contagious cancer genomes and transcriptomes and of their micro-environment and macro-environment could shed light on the selective forces shaping tumour development at different time points: during the progressive phase and at the endpoint. A greater understanding of transmissible cancers from an evolutionary ecology perspective will provide novel avenues for the prevention and treatment of both contagious and non-communicable cancers. © 2016 The Authors. BioEssays published by WILEY Periodicals, Inc.

Spatial evolutionary epidemiology of spreading epidemics

PubMed Central

2016-01-01

Most spatial models of host–parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. PMID:27798295

Spatial evolutionary epidemiology of spreading epidemics.

PubMed

Lion, S; Gandon, S

2016-10-26

Most spatial models of host-parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. © 2016 The Author(s).

The evolutionary psychology of mate selection in Morocco : A multivariate analysis.

PubMed

Walter, A

1997-06-01

Patterns of mate preference in Morocco are investigated in order to test whether they support hypotheses advanced by David Buss and other evolutionary psychologists. Because of the custom of cousin marriage in Morocco, a multivariate model that included cosocialization data was developed for the purpose of testing the Westermarck hypothesis of inbreeding avoidance. Hence, two previously separate domains of research are unified in one design that permits the further exploration of questions pertaining to the domain specificity of psychological mechanisms. Multiple independent mate choice predictors were identified using logistic regression analysis. Results support the Westermarck hypothesis of inbreeding avoidance. Sleeping in the same room during childhood was found in both sexes to produce an aversion to marriage. Other evidence suggests that aversion to inbreeding extends further among females than males in that females but not males show an aversion to marriage to related individuals with whom they had daily social contact in early childhood. The evolutionary prediction that females differ from males concerning resource holding capacity was also supported. Females showed a preference for males whom they judged to have higher social status than theirs, while this criterion was unimportant for males. The predicted sex difference in preferred age of marriage partner was also supported. Contrary to previous findings, the predicted difference between the sexes with regard to physical attractiveness was not supported.

Phylogenetics and evolution of Trx SET genes in fully sequenced land plants.

PubMed

Zhu, Xinyu; Chen, Caoyi; Wang, Baohua

2012-04-01

Plant Trx SET proteins are involved in H3K4 methylation and play a key role in plant floral development. Genes encoding Trx SET proteins constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. To investigate the evolutionary history of the Trx SET gene family, we made a comprehensive evolutionary analysis on this gene family from 13 major representatives of green plants. A novel clustering (here named as cpTrx clade), which included the III-1, III-2, and III-4 orthologous groups, previously resolved was identified. Our analysis showed that plant Trx proteins possessed a variety of domain organizations and gene structures among paralogs. Additional domains such as PHD, PWWP, and FYR were early integrated into primordial SET-PostSET domain organization of cpTrx clade. We suggested that the PostSET domain was lost in some members of III-4 orthologous group during the evolution of land plants. At least four classes of gene structures had been formed at the early evolutionary stage of land plants. Three intronless orphan Trx SET genes from the Physcomitrella patens (moss) were identified, and supposedly, their parental genes have been eliminated from the genome. The structural differences among evolutionary groups of plant Trx SET genes with different functions were described, contributing to the design of further experimental studies.

Environmental survey meta-analysis reveals hidden diversity among unicellular opisthokonts.

PubMed

del Campo, Javier; Ruiz-Trillo, Iñaki

2013-04-01

The Opisthokonta clade includes Metazoa, Fungi, and several unicellular lineages, such as choanoflagellates, filastereans, ichthyosporeans, and nucleariids. To date, studies of the evolutionary diversity of opisthokonts have focused exclusively on metazoans, fungi, and, very recently, choanoflagellates. Thus, very little is known about diversity among the filastereans, ichthyosporeans, and nucleariids. To better understand the evolutionary diversity and ecology of the opisthokonts, here we analyze published environmental data from nonfungal unicellular opisthokonts and report 18S ribosomal DNA phylogenetic analyses. Our data reveal extensive diversity among all unicellular opisthokonts, except for the filastereans. We identify several clades that consist exclusively of environmental sequences, especially among ichthyosporeans and choanoflagellates. Moreover, we show that the ichthyosporeans represent a significant percentage of overall unicellular opisthokont diversity, with a greater ecological role in marine environments than previously believed. Our results provide a useful phylogenetic framework for future ecological and evolutionary studies of these poorly known lineages.

Recent advances in the evolutionary engineering of industrial biocatalysts.

PubMed

Winkler, James D; Kao, Katy C

2014-12-01

Evolutionary engineering has been used to improve key industrial strain traits, such as carbon source utilization, tolerance to adverse environmental conditions, and resistance to chemical inhibitors, for many decades due to its technical simplicity and effectiveness. The lack of need for prior genetic knowledge underlying the phenotypes of interest makes this a powerful approach for strain development for even species with minimal genotypic information. While the basic experimental procedure for laboratory adaptive evolution has remained broadly similar for many years, a range of recent advances show promise for improving the experimental workflows for evolutionary engineering by accelerating the pace of evolution, simplifying the analysis of evolved mutants, and providing new ways of linking desirable phenotypes to selectable characteristics. This review aims to highlight some of these recent advances and discuss how they may be used to improve industrially relevant microbial phenotypes. Copyright © 2014 Elsevier Inc. All rights reserved.

Comparative and Evolutionary Analysis of the HES/HEY Gene Family Reveal Exon/Intron Loss and Teleost Specific Duplication Events

PubMed Central

Ma, Zhaowu; Zhou, Yang; Abbood, Nibras Najm; Liu, Jianfeng; Su, Li; Jia, Haibo; Guo, An-Yuan

2012-01-01

Background HES/HEY genes encode a family of basic helix-loop-helix (bHLH) transcription factors with both bHLH and Orange domain. HES/HEY proteins are direct targets of the Notch signaling pathway and play an essential role in developmental decisions, such as the developments of nervous system, somitogenesis, blood vessel and heart. Despite their important functions, the origin and evolution of this HES/HEY gene family has yet to be elucidated. Methods and Findings In this study, we identified genes of the HES/HEY family in representative species and performed evolutionary analysis to elucidate their origin and evolutionary process. Our results showed that the HES/HEY genes only existed in metazoans and may originate from the common ancestor of metazoans. We identified HES/HEY genes in more than 10 species representing the main lineages. Combining the bHLH and Orange domain sequences, we constructed the phylogenetic trees by different methods (Bayesian, ML, NJ and ME) and classified the HES/HEY gene family into four groups. Our results indicated that this gene family had undergone three expansions, which were along with the origins of Eumetazoa, vertebrate, and teleost. Gene structure analysis revealed that the HES/HEY genes were involved in exon and/or intron loss in different species lineages. Genes of this family were duplicated in bony fishes and doubled than other vertebrates. Furthermore, we studied the teleost-specific duplications in zebrafish and investigated the expression pattern of duplicated genes in different tissues by RT-PCR. Finally, we proposed a model to show the evolution of this gene family with processes of expansion, exon/intron loss, and motif loss. Conclusions Our study revealed the evolution of HES/HEY gene family, the expression and function divergence of duplicated genes, which also provide clues for the research of Notch function in development. This study shows a model of gene family analysis with gene structure evolution and duplication. PMID:22808219

Comparative and evolutionary analysis of the HES/HEY gene family reveal exon/intron loss and teleost specific duplication events.

PubMed

Zhou, Mi; Yan, Jun; Ma, Zhaowu; Zhou, Yang; Abbood, Nibras Najm; Liu, Jianfeng; Su, Li; Jia, Haibo; Guo, An-Yuan

2012-01-01

HES/HEY genes encode a family of basic helix-loop-helix (bHLH) transcription factors with both bHLH and Orange domain. HES/HEY proteins are direct targets of the Notch signaling pathway and play an essential role in developmental decisions, such as the developments of nervous system, somitogenesis, blood vessel and heart. Despite their important functions, the origin and evolution of this HES/HEY gene family has yet to be elucidated. In this study, we identified genes of the HES/HEY family in representative species and performed evolutionary analysis to elucidate their origin and evolutionary process. Our results showed that the HES/HEY genes only existed in metazoans and may originate from the common ancestor of metazoans. We identified HES/HEY genes in more than 10 species representing the main lineages. Combining the bHLH and Orange domain sequences, we constructed the phylogenetic trees by different methods (Bayesian, ML, NJ and ME) and classified the HES/HEY gene family into four groups. Our results indicated that this gene family had undergone three expansions, which were along with the origins of Eumetazoa, vertebrate, and teleost. Gene structure analysis revealed that the HES/HEY genes were involved in exon and/or intron loss in different species lineages. Genes of this family were duplicated in bony fishes and doubled than other vertebrates. Furthermore, we studied the teleost-specific duplications in zebrafish and investigated the expression pattern of duplicated genes in different tissues by RT-PCR. Finally, we proposed a model to show the evolution of this gene family with processes of expansion, exon/intron loss, and motif loss. Our study revealed the evolution of HES/HEY gene family, the expression and function divergence of duplicated genes, which also provide clues for the research of Notch function in development. This study shows a model of gene family analysis with gene structure evolution and duplication.

SETI in vivo: testing the we-are-them hypothesis

NASA Astrophysics Data System (ADS)

Makukov, Maxim A.; Shcherbak, Vladimir I.

2018-04-01

After it was proposed that life on Earth might descend from seeding by an earlier extraterrestrial civilization motivated to secure and spread life, some authors noted that this alternative offers a testable implication: microbial seeds could be intentionally supplied with a durable signature that might be found in extant organisms. In particular, it was suggested that the optimal location for such an artefact is the genetic code, as the least evolving part of cells. However, as the mainstream view goes, this scenario is too speculative and cannot be meaningfully tested because encoding/decoding a signature within the genetic code is something ill-defined, so any retrieval attempt is doomed to guesswork. Here we refresh the seeded-Earth hypothesis in light of recent observations, and discuss the motivation for inserting a signature. We then show that `biological SETI' involves even weaker assumptions than traditional SETI and admits a well-defined methodological framework. After assessing the possibility in terms of molecular and evolutionary biology, we formalize the approach and, adopting the standard guideline of SETI that encoding/decoding should follow from first principles and be convention-free, develop a universal retrieval strategy. Applied to the canonical genetic code, it reveals a non-trivial precision structure of interlocked logical and numerical attributes of systematic character (previously we found these heuristically). To assess this result in view of the initial assumption, we perform statistical, comparison, interdependence and semiotic analyses. Statistical analysis reveals no causal connection of the result to evolutionary models of the genetic code, interdependence analysis precludes overinterpretation, and comparison analysis shows that known variations of the code lack any precision-logic structures, in agreement with these variations being post-LUCA (i.e. post-seeding) evolutionary deviations from the canonical code. Finally, semiotic analysis shows that not only the found attributes are consistent with the initial assumption, but that they make perfect sense from SETI perspective, as they ultimately maintain some of the most universal codes of culture.

Nursing professionalism: An evolutionary concept analysis

PubMed Central

Ghadirian, Fataneh; Salsali, Mahvash; Cheraghi, Mohammad Ali

2014-01-01

Background: Professionalism is an important feature of the professional jobs. Dynamic nature and the various interpretations of this term lead to multiple definitions of this concept. The aim of this paper is to identify the core attributes of the nursing professionalism. Materials and Methods: We followed Rodgers’ evolutionary method of concept analysis. Texts published in scientific databases about nursing professionalism between 1980 and 2011 were assessed. After applying the selection criteria, the final sample consisting of 4 books and 213 articles was selected, examined, and analyzed in depth. Two experts checked the process of analysis and monitored and reviewed them. Results: The analysis showed that nursing professionalism is determined by three attributes of cognitive, attitudinal, and psychomotor. In addition, the most important antecedents concepts were demographic, experiential, educational, environmental, and attitudinal factors. Conclusion: Nursing professionalism is an inevitable, complex, varied, and dynamic process. In this study, the importance, scope, and concept of professionalism in nursing, the concept of a beginning for further research and development, and expanding the nursing knowledge are explained and clarified. PMID:24554953

Phylogenetic Analysis Supports the Aerobic-Capacity Model for the Evolution of Endothermy.

PubMed

Nespolo, Roberto F; Solano-Iguaran, Jaiber J; Bozinovic, Francisco

2017-01-01

The evolution of endothermy is a controversial topic in evolutionary biology, although several hypotheses have been proposed to explain it. To a great extent, the debate has centered on the aerobic-capacity model (AC model), an adaptive hypothesis involving maximum and resting rates of metabolism (MMR and RMR, respectively; hereafter "metabolic traits"). The AC model posits that MMR, a proxy of aerobic capacity and sustained activity, is the target of directional selection and that RMR is also influenced as a correlated response. Associated with this reasoning are the assumptions that (1) factorial aerobic scope (FAS; MMR/RMR) and net aerobic scope (NAS; MMR - RMR), two commonly used indexes of aerobic capacity, show different evolutionary optima and (2) the functional link between MMR and RMR is a basic design feature of vertebrates. To test these assumptions, we performed a comparative phylogenetic analysis in 176 vertebrate species, ranging from fish and amphibians to birds and mammals. Using disparity-through-time analysis, we also explored trait diversification and fitted different evolutionary models to study the evolution of metabolic traits. As predicted, we found (1) a positive phylogenetic correlation between RMR and MMR, (2) diversification of metabolic traits exceeding that of random-walk expectations, (3) that a model assuming selection fits the data better than alternative models, and (4) that a single evolutionary optimum best fits FAS data, whereas a model involving two optima (one for ectotherms and another for endotherms) is the best explanatory model for NAS. These results support the AC model and give novel information concerning the mode and tempo of physiological evolution of vertebrates.

Gene fusion analysis in the battle against the African endemic sleeping sickness.

PubMed

Trimpalis, Philip; Koumandou, Vassiliki Lila; Pliakou, Evangelia; Anagnou, Nicholas P; Kossida, Sophia

2013-01-01

The protozoan Trypanosoma brucei causes African Trypanosomiasis or sleeping sickness in humans, which can be lethal if untreated. Most available pharmacological treatments for the disease have severe side-effects. The purpose of this analysis was to detect novel protein-protein interactions (PPIs), vital for the parasite, which could lead to the development of drugs against this disease to block the specific interactions. In this work, the Domain Fusion Analysis (Rosetta Stone method) was used to identify novel PPIs, by comparing T. brucei to 19 organisms covering all major lineages of the tree of life. Overall, 49 possible protein-protein interactions were detected, and classified based on (a) statistical significance (BLAST e-value, domain length etc.), (b) their involvement in crucial metabolic pathways, and (c) their evolutionary history, particularly focusing on whether a protein pair is split in T. brucei and fused in the human host. We also evaluated fusion events including hypothetical proteins, and suggest a possible molecular function or involvement in a certain biological process. This work has produced valuable results which could be further studied through structural biology or other experimental approaches so as to validate the protein-protein interactions proposed here. The evolutionary analysis of the proteins involved showed that, gene fusion or gene fission events can happen in all organisms, while some protein domains are more prone to fusion and fission events and present complex evolutionary patterns.

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 spatially structured host-parasite interactions.

PubMed

Lion, S; Gandon, S

2015-01-01

Spatial structure has dramatic effects on the demography and the evolution of species. A large variety of theoretical models have attempted to understand how local dispersal may shape the coevolution of interacting species such as host-parasite interactions. The lack of a unifying framework is a serious impediment for anyone willing to understand current theory. Here, we review previous theoretical studies in the light of a single epidemiological model that allows us to explore the effects of both host and parasite migration rates on the evolution and coevolution of various life-history traits. We discuss the impact of local dispersal on parasite virulence, various host defence strategies and local adaptation. Our analysis shows that evolutionary and coevolutionary outcomes crucially depend on the details of the host-parasite life cycle and on which life-history trait is involved in the interaction. We also discuss experimental studies that support the effects of spatial structure on the evolution of host-parasite interactions. This review highlights major similarities between some theoretical results, but it also reveals an important gap between evolutionary and coevolutionary models. We discuss possible ways to bridge this gap within a more unified framework that would reconcile spatial epidemiology, evolution and coevolution. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Genomic V exons from whole genome shotgun data in reptiles.

PubMed

Olivieri, D N; von Haeften, B; Sánchez-Espinel, C; Faro, J; Gambón-Deza, F

2014-08-01

Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged: one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia, and Aves. In this study, we determined the genomic variable (V) exons from whole genome shotgun sequencing (WGS) data in reptiles corresponding to the three main immunoglobulin (IG) loci and the four main T cell receptor (TR) loci. We show that Squamata lack the TRG and TRD genes, and snakes lack the IGKV genes. In representative species of Testudines and Crocodylia, the seven major IG and TR loci are maintained. As in mammals, genes of the IG loci can be grouped into well-defined IMGT clans through a multi-species phylogenetic analysis. We show that the reptilian IGHV and IGLV genes are distributed amongst the established mammalian clans, while their IGKV genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptilian and mammalian TRAV genes cluster into six common evolutionary clades (since IMGT clans have not been defined for TR). In contrast, the reptilian TRBV genes cluster into three clades, which have few mammalian members. In this locus, the V exon sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptilian clans. These sequences can be obtained in a freely available public repository (http://vgenerepertoire.org).

Genome-Wide Identification and Comparative Analysis of Albumin Family in Vertebrates

PubMed Central

Li, Shugang; Cao, Yiping; Geng, Fang

2017-01-01

Albumins are the most well-known globular proteins, and the most typical representatives are the serum albumins. However, less attention was paid to the albumin family, except for the human and bovine serum albumin. To characterize the features of albumin family, we have mined all the putative albumin proteins from the available genome sequences. The results showed that albumin is widely distributed in vertebrates, but not present in the bacteria and archaea. The phylogenetic analysis of vertebrate albumin family implied an evolutionary relationship between members of serum albumin, α-fetoprotein, vitamin D–binding protein, and afamin. Meanwhile, a new member from the albumin family was found, namely, extracellular matrix protein 1. The structural analysis revealed that the motifs for forming the internal disulfide bonds are highly conserved in the albumin family, despite the low overall sequence identity across the family. The domain arrangement of albumin proteins indicated that most of vertebrate albumins contain 3 characteristic domains, arising from 2 evolutionary patterns. And a significant trend has been observed that the albumin proteins in higher vertebrate species tend to possess more characteristic domains. This study has provided the fundamental information required for achieving a better understanding of the albumin distribution, phylogenetic relationship, characteristic motif, structure, and new insights into the evolutionary pattern. PMID:28680266

Evolutionary analysis of FAM83H in vertebrates.

PubMed

Huang, Wushuang; Yang, Mei; Wang, Changning; Song, Yaling

2017-01-01

Amelogenesis imperfecta is a group of disorders causing abnormalities in enamel formation in various phenotypes. Many mutations in the FAM83H gene have been identified to result in autosomal dominant hypocalcified amelogenesis imperfecta in different populations. However, the structure and function of FAM83H and its pathological mechanism have yet to be further explored. Evolutionary analysis is an alternative for revealing residues or motifs that are important for protein function. In the present study, we chose 50 vertebrate species in public databases representative of approximately 230 million years of evolution, including 1 amphibian, 2 fishes, 7 sauropsidas and 40 mammals, and we performed evolutionary analysis on the FAM83H protein. By sequence alignment, conserved residues and motifs were indicated, and the loss of important residues and motifs of five special species (Malayan pangolin, platypus, minke whale, nine-banded armadillo and aardvark) was discovered. A phylogenetic time tree showed the FAM83H divergent process. Positive selection sites in the C-terminus suggested that the C-terminus of FAM83H played certain adaptive roles during evolution. The results confirmed some important motifs reported in previous findings and identified some new highly conserved residues and motifs that need further investigation. The results suggest that the C-terminus of FAM83H contain key conserved regions critical to enamel formation and calcification.

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host–parasite interaction

PubMed Central

Jackson, Andrew P.; Otto, Thomas D.; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B.; Moussa, Ehab; Nair, Mridul; Reid, Adam J.; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A.; Weir, William; Wastling, Jonathan M.; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R.; Pain, Arnab

2014-01-01

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5′ ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. PMID:24799432

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

PubMed Central

Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

2011-01-01

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

Evolutionary paths of streptococcal and staphylococcal superantigens

PubMed Central

2012-01-01

Background Streptococcus pyogenes (GAS) harbors several superantigens (SAgs) in the prophage region of its genome, although speG and smez are not located in this region. The diversity of SAgs is thought to arise during horizontal transfer, but their evolutionary pathways have not yet been determined. We recently completed sequencing the entire genome of S. dysgalactiae subsp. equisimilis (SDSE), the closest relative of GAS. Although speG is the only SAg gene of SDSE, speG was present in only 50% of clinical SDSE strains and smez in none. In this study, we analyzed the evolutionary paths of streptococcal and staphylococcal SAgs. Results We compared the sequences of the 12–60 kb speG regions of nine SDSE strains, five speG+ and four speG–. We found that the synteny of this region was highly conserved, whether or not the speG gene was present. Synteny analyses based on genome-wide comparisons of GAS and SDSE indicated that speG is the direct descendant of a common ancestor of streptococcal SAgs, whereas smez was deleted from SDSE after SDSE and GAS split from a common ancestor. Cumulative nucleotide skew analysis of SDSE genomes suggested that speG was located outside segments of steeper slopes than the stable region in the genome, whereas the region flanking smez was unstable, as expected from the results of GAS. We also detected a previously undescribed staphylococcal SAg gene, selW, and a staphylococcal SAg -like gene, ssl, in the core genomes of all Staphylococcus aureus strains sequenced. Amino acid substitution analyses, based on dN/dS window analysis of the products encoded by speG, selW and ssl suggested that all three genes have been subjected to strong positive selection. Evolutionary analysis based on the Bayesian Markov chain Monte Carlo method showed that each clade included at least one direct descendant. Conclusions Our findings reveal a plausible model for the comprehensive evolutionary pathway of streptococcal and staphylococcal SAgs. PMID:22900646

Patterns of coordinated cortical remodeling during adolescence and their associations with functional specialization and evolutionary expansion.

PubMed

Sotiras, Aristeidis; Toledo, Jon B; Gur, Raquel E; Gur, Ruben C; Satterthwaite, Theodore D; Davatzikos, Christos

2017-03-28

During adolescence, the human cortex undergoes substantial remodeling to support a rapid expansion of behavioral repertoire. Accurately quantifying these changes is a prerequisite for understanding normal brain development, as well as the neuropsychiatric disorders that emerge in this vulnerable period. Past accounts have demonstrated substantial regional heterogeneity in patterns of brain development, but frequently have been limited by small samples and analytics that do not evaluate complex multivariate imaging patterns. Capitalizing on recent advances in multivariate analysis methods, we used nonnegative matrix factorization (NMF) to uncover coordinated patterns of cortical development in a sample of 934 youths ages 8-20, who completed structural neuroimaging as part of the Philadelphia Neurodevelopmental Cohort. Patterns of structural covariance (PSCs) derived by NMF were highly reproducible over a range of resolutions, and differed markedly from common gyral-based structural atlases. Moreover, PSCs were largely symmetric and showed correspondence to specific large-scale functional networks. The level of correspondence was ordered according to their functional role and position in the evolutionary hierarchy, being high in lower-order visual and somatomotor networks and diminishing in higher-order association cortex. Furthermore, PSCs showed divergent developmental associations, with PSCs in higher-order association cortex networks showing greater changes with age than primary somatomotor and visual networks. Critically, such developmental changes within PSCs were significantly associated with the degree of evolutionary cortical expansion. Together, our findings delineate a set of structural brain networks that undergo coordinated cortical thinning during adolescence, which is in part governed by evolutionary novelty and functional specialization.

Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis

PubMed Central

Ishikawa, Masakazu; Yuyama, Ikuko; Shimizu, Hiroshi; Nozawa, Masafumi; Ikeo, Kazuho; Gojobori, Takashi

2016-01-01

Endosymbiosis is an important evolutionary event for organisms, and there is widespread interest in understanding the evolution of endosymbiosis establishment. Hydra is one of the most suitable organisms for studying the evolution of endosymbiosis. Within the genus Hydra, H. viridissima and H. vulgaris show endosymbiosis with green algae. Previous studies suggested that the endosymbiosis in H. vulgaris took place much more recently than that in H. viridissima, noting that the establishment of the interaction between H. vulgaris and its algae is not as stable as in H. viridissima. To investigate the on-going process of endosymbiosis, we first compared growth and tolerance to starvation in symbiotic and aposymbiotic polyps of both species. The results revealed that symbiotic H. viridissima had a higher growth rate and greater tolerance to starvation than aposymbiotic polyps. By contrast, growth of symbiotic H. vulgaris was identical to that of aposymbiotic polyps, and symbiotic H. vulgaris was less tolerant to starvation. Moreover, our gene expression analysis showed a pattern of differential gene expression in H. viridissima similar to that in other endosymbiotically established organisms, and contrary to that observed in H. vulgaris. We also showed that H. viridissima could cope with oxidative stress that caused damage, such as cell death, in H. vulgaris. These observations support the idea that oxidative stress related genes play an important role in the on-going process of endosymbiosis evolution. The different evolutionary stages of endosymbiosis studied here provide a deeper insight into the evolutionary processes occurring toward a stable endosymbiosis. PMID:27324918

Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes

PubMed Central

Ekblom, Robert; French, Lisa; Slate, Jon; Burke, Terry

2010-01-01

Genes of the immune system are generally considered to evolve rapidly due to host–parasite coevolution. They are therefore of great interest in evolutionary biology and molecular ecology. In this study, we manually annotated 144 avian immune genes from the zebra finch (Taeniopygia guttata) genome and conducted evolutionary analyses of these by comparing them with their orthologs in the chicken (Gallus gallus). Genes classified as immune receptors showed elevated dN/dS ratios compared with other classes of immune genes. Immune genes in general also appear to be evolving more rapidly than other genes, as inferred from a higher dN/dS ratio compared with the rest of the genome. Furthermore, ten genes (of 27) for which sequence data were available from at least three bird species showed evidence of positive selection acting on specific codons. From transcriptome data of eight different tissues, we found evidence for expression of 106 of the studied immune genes, with primary expression of most of these in bursa, blood, and spleen. These immune-related genes showed a more tissue-specific expression pattern than other genes in the zebra finch genome. Several of the avian immune genes investigated here provide strong candidates for in-depth studies of molecular adaptation in birds. PMID:20884724

Impact of extracellularity on the evolutionary rate of mammalian proteins.

PubMed

Liao, Ben-Yang; Weng, Meng-Pin; Zhang, Jianzhi

2010-01-06

It is of fundamental importance to understand the determinants of the rate of protein evolution. Eukaryotic extracellular proteins are known to evolve faster than intracellular proteins. Although this rate difference appears to be due to the lower essentiality of extracellular proteins than intracellular proteins in yeast, we here show that, in mammals, the impact of extracellularity is independent from the impact of gene essentiality. Our partial correlation analysis indicated that the impact of extracellularity on mammalian protein evolutionary rate is also independent from those of tissue-specificity, expression level, gene compactness, and the number of protein-protein interactions and, surprisingly, is the strongest among all the factors we examined. Similar results were also found from principal component regression analysis. Our findings suggest that different rules govern the pace of protein sequence evolution in mammals and yeasts.

Polymorphism of CRISPR shows separated natural groupings of Shigella subtypes and evidence of horizontal transfer of CRISPR

PubMed Central

Yang, Chaojie; Li, Peng; Su, Wenli; Li, Hao; Liu, Hongbo; Yang, Guang; Xie, Jing; Yi, Shengjie; Wang, Jian; Cui, Xianyan; Wu, Zhihao; Wang, Ligui; Hao, Rongzhang; Jia, Leili; Qiu, Shaofu; Song, Hongbin

2015-01-01

Clustered, regularly interspaced, short palindromic repeats (CRISPR) act as an adaptive RNA-mediated immune mechanism in bacteria. They can also be used for identification and evolutionary studies based on polymorphisms within the CRISPR locus. We amplified and analyzed 6 CRISPR loci from 237 Shigella strains belonging to the 4 species groups, as well as 13 Escherichia coli strains. The CRISPR-associated (cas) gene sequence arrays of these strains were screened and compared. The CRISPR sequences from Shigella were conserved among subtypes, suggesting that CRISPR may represent a new identification tool for the detection and discrimination of Shigella species. Secondary structure analysis showed a different stem-loop structure at the terminal repeat, suggesting a distinct recognition mechanism in the formation of crRNA. In addition, the presence of “self-target” spacers and polymorphisms within CRISPR in Shigella indicated a selective pressure for inhibition of this system, which has the potential to damage “self DNA.” Homology analysis of spacers showed that CRISPR might be involved in the regulation of virulence transmission. Phylogenetic analysis based on CRISPR sequences from Shigella and E. coli indicated that although phenotypic properties maintain convergent evolution, the 4 Shigella species do not represent natural groupings. Surprisingly, comparative analysis of Shigella repeats with other species provided new evidence for CRISPR horizontal transfer. Our results suggested that CRISPR analysis is applicable for the detection of Shigella species and for investigation of evolutionary relationships. PMID:26327282

Polymorphism of CRISPR shows separated natural groupings of Shigella subtypes and evidence of horizontal transfer of CRISPR.

PubMed

Yang, Chaojie; Li, Peng; Su, Wenli; Li, Hao; Liu, Hongbo; Yang, Guang; Xie, Jing; Yi, Shengjie; Wang, Jian; Cui, Xianyan; Wu, Zhihao; Wang, Ligui; Hao, Rongzhang; Jia, Leili; Qiu, Shaofu; Song, Hongbin

2015-01-01

Clustered, regularly interspaced, short palindromic repeats (CRISPR) act as an adaptive RNA-mediated immune mechanism in bacteria. They can also be used for identification and evolutionary studies based on polymorphisms within the CRISPR locus. We amplified and analyzed 6 CRISPR loci from 237 Shigella strains belonging to the 4 species groups, as well as 13 Escherichia coli strains. The CRISPR-associated (cas) gene sequence arrays of these strains were screened and compared. The CRISPR sequences from Shigella were conserved among subtypes, suggesting that CRISPR may represent a new identification tool for the detection and discrimination of Shigella species. Secondary structure analysis showed a different stem-loop structure at the terminal repeat, suggesting a distinct recognition mechanism in the formation of crRNA. In addition, the presence of "self-target" spacers and polymorphisms within CRISPR in Shigella indicated a selective pressure for inhibition of this system, which has the potential to damage "self DNA." Homology analysis of spacers showed that CRISPR might be involved in the regulation of virulence transmission. Phylogenetic analysis based on CRISPR sequences from Shigella and E. coli indicated that although phenotypic properties maintain convergent evolution, the 4 Shigella species do not represent natural groupings. Surprisingly, comparative analysis of Shigella repeats with other species provided new evidence for CRISPR horizontal transfer. Our results suggested that CRISPR analysis is applicable for the detection of Shigella species and for investigation of evolutionary relationships.

Different evolutionary trajectories of vaccine-controlled and non-controlled avian infectious bronchitis viruses in commercial poultry

PubMed Central

Lee, Dong-Hun

2017-01-01

To determine the genetic and epidemiological relationship of infectious bronchitis virus (IBV) isolates from commercial poultry to attenuated live IBV vaccines we conducted a phylogenetic network analysis on the full-length S1 sequence for Arkansas (Ark), Massachusetts (Mass) and Delmarva/1639 (DMV/1639) type viruses isolated in 2015 from clinical cases by 3 different diagnostic laboratories. Phylogenetic network analysis of Ark isolates showed two predominant groups linked by 2 mutations, consistent with subpopulations found in commercial vaccines for this IBV type. In addition, a number of satellite groups surrounding the two predominant populations were observed for the Ark type virus, which is likely due to mutations associated with the nature of this vaccine to persist in flocks. The phylogenetic network analysis of Mass-type viruses shows two groupings corresponding to different manufacturers vaccine sequences. No satellite groups were observed for Mass-type viruses, which is consistent with no persistence of this vaccine type in the field. At the time of collection, no vaccine was being used for the DMV/1639 type viruses and phylogenetic network analysis showed a dispersed network suggesting no clear change in genetic distribution. Selection pressure analysis showed that the DMV/1639 and Mass-type strains were evolving under negative selection, whereas the Ark type viruses had evolved under positive selection. This data supports the hypothesis that live attenuated vaccine usage does play a role in the genetic profile of similar IB viruses in the field and phylogenetic network analysis can be used to identify vaccine and vaccine origin isolates, which is important for our understanding of the role live vaccines play in the evolutionary trajectory of those viruses. PMID:28472110

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.

Evolutionary speed of species invasions.

PubMed

García-Ramos, Gisela; Rodríguez, Diego

2002-04-01

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

Evolutionary Game Theory Analysis of Tumor Progression

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

Pheromone evolution and sexual behavior in Drosophila are shaped by male sensory exploitation of other males.

PubMed

Ng, Soon Hwee; Shankar, Shruti; Shikichi, Yasumasa; Akasaka, Kazuaki; Mori, Kenji; Yew, Joanne Y

2014-02-25

Animals exhibit a spectacular array of traits to attract mates. Understanding the evolutionary origins of sexual features and preferences is a fundamental problem in evolutionary biology, and the mechanisms remain highly controversial. In some species, females choose mates based on direct benefits conferred by the male to the female and her offspring. Thus, female preferences are thought to originate and coevolve with male traits. In contrast, sensory exploitation occurs when expression of a male trait takes advantage of preexisting sensory biases in females. Here, we document in Drosophila a previously unidentified example of sensory exploitation of males by other males through the use of the sex pheromone CH503. We use mass spectrometry, high-performance liquid chromatography, and behavioral analysis to demonstrate that an antiaphrodisiac produced by males of the melanogaster subgroup also is effective in distant Drosophila relatives that do not express the pheromone. We further show that species that produce the pheromone have become less sensitive to the compound, illustrating that sensory adaptation occurs after sensory exploitation. Our findings provide a mechanism for the origin of a sex pheromone and show that sensory exploitation changes male sexual behavior over evolutionary time.

The phylogenetic and evolutionary history of a novel alpha-globin-type gene in orangutans (Pongo pygmaeus).

PubMed

Steiper, Michael E; Wolfe, Nathan D; Karesh, William B; Kilbourn, Annelisa M; Bosi, Edwin J; Ruvolo, Maryellen

2006-07-01

The alpha-globin genes are implicated in human resistance to malaria, a disease caused by Plasmodium parasites. This study is the first to analyze DNA sequences from a novel alpha-globin-type gene in orangutans, a species affected by Plasmodium. Phylogenetic methods show that the gene is a duplication of an alpha-globin gene and is located 5' of alpha-2 globin. The alpha-globin-type gene is notable for having four amino acid replacements relative to the orangutan's alpha-1 and alpha-2 globin genes, with no synonymous differences. Pairwise K(a)/K(s) methods and likelihood ratio tests (LRTs) revealed that the evolutionary history of the alpha-globin-type gene has been marked by either neutral or positive evolution, but not purifying selection. A comparative analysis of the amino acid replacements of the alpha-globin-type gene with human hemoglobinopathies and hemoglobin structure showed that two of the four replaced sites are members of the same molecular bond, one that is crucial to the proper functioning of the hemoglobin molecule. This suggested an adaptive evolutionary change. Functionally, this locus may result in a thalassemia-like phenotype in orangutans, possibly as an adaptation to combat Plasmodium.

A millennial-scale chronicle of evolutionary responses to cultural eutrophication in Daphnia.

PubMed

Frisch, Dagmar; Morton, Philip K; Chowdhury, Priyanka Roy; Culver, Billy W; Colbourne, John K; Weider, Lawrence J; Jeyasingh, Punidan D

2014-03-01

For an accurate assessment of the anthropogenic impacts on evolutionary change in natural populations, we need long-term environmental, genetic and phenotypic data that predate human disturbances. Analysis of c. 1600 years of history chronicled in the sediments of South Center Lake, Minnesota, USA, revealed major environmental changes beginning c. 120 years ago coinciding with the initiation of industrialised agriculture in the catchment area. Population genetic structure, analysed using DNA from dormant eggs of the keystone aquatic herbivore, Daphnia pulicaria, suggested no change for c. 1500 years prior to striking shifts associated with anthropogenic environmental alterations. Furthermore, phenotypic assays on the oldest resurrected metazoan genotypes (potentially as old as c. 700 years) indicate significant shifts in phosphorus utilisation rates compared to younger genotypes. Younger genotypes show steeper reaction norms with high growth under high phosphorus (P), and low growth under low P, while 'ancient' genotypes show flat reaction norms, yet higher growth efficiency under low P. Using this resurrection ecology approach, environmental, genetic and phenotypic data spanning pre- and post-industrialised agricultural eras clearly reveal the evolutionary consequences of anthropogenic environmental change. © 2014 John Wiley & Sons Ltd/CNRS.

The Solute Carrier Families Have a Remarkably Long Evolutionary History with the Majority of the Human Families Present before Divergence of Bilaterian Species

PubMed Central

Höglund, Pär J.; Nordström, Karl J.V.; Schiöth, Helgi B.; Fredriksson, Robert

2011-01-01

The Solute Carriers (SLCs) are membrane proteins that regulate transport of many types of substances over the cell membrane. The SLCs are found in at least 46 gene families in the human genome. Here, we performed the first evolutionary analysis of the entire SLC family based on whole genome sequences. We systematically mined and analyzed the genomes of 17 species to identify SLC genes. In all, we identified 4,813 SLC sequences in these genomes, and we delineated the evolutionary history of each of the subgroups. Moreover, we also identified ten new human sequences not previously classified as SLCs, which most likely belong to the SLC family. We found that 43 of the 46 SLC families found in Homo sapiens were also found in Caenorhabditis elegans, whereas 42 of them were also found in insects. Mammals have a higher number of SLC genes in most families, perhaps reflecting important roles for these in central nervous system functions. This study provides a systematic analysis of the evolutionary history of the SLC families in Eukaryotes showing that the SLC superfamily is ancient with multiple branches that were present before early divergence of Bilateria. The results provide foundation for overall classification of SLC genes and are valuable for annotation and prediction of substrates for the many SLCs that have not been tested in experimental transport assays. PMID:21186191

Evolutionary distance from human homologs reflects allergenicity of animal food proteins.

PubMed

Jenkins, John A; Breiteneder, Heimo; Mills, E N Clare

2007-12-01

In silico analysis of allergens can identify putative relationships among protein sequence, structure, and allergenic properties. Such systematic analysis reveals that most plant food allergens belong to a restricted number of protein superfamilies, with pollen allergens behaving similarly. We have investigated the structural relationships of animal food allergens and their evolutionary relatedness to human homologs to define how closely a protein must resemble a human counterpart to lose its allergenic potential. Profile-based sequence homology methods were used to classify animal food allergens into Pfam families, and in silico analyses of their evolutionary and structural relationships were performed. Animal food allergens could be classified into 3 main families--tropomyosins, EF-hand proteins, and caseins--along with 14 minor families each composed of 1 to 3 allergens. The evolutionary relationships of each of these allergen superfamilies showed that in general, proteins with a sequence identity to a human homolog above approximately 62% were rarely allergenic. Single substitutions in otherwise highly conserved regions containing IgE epitopes in EF-hand parvalbumins may modulate allergenicity. These data support the premise that certain protein structures are more allergenic than others. Contrasting with plant food allergens, animal allergens, such as the highly conserved tropomyosins, challenge the capability of the human immune system to discriminate between foreign and self-proteins. Such immune responses run close to becoming autoimmune responses. Exploiting the closeness between animal allergens and their human homologs in the development of recombinant allergens for immunotherapy will need to consider the potential for developing unanticipated autoimmune responses.

Gap Gene Regulatory Dynamics Evolve along a Genotype Network

PubMed Central

Crombach, Anton; Wotton, Karl R.; Jiménez-Guri, Eva; Jaeger, Johannes

2016-01-01

Developmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as “system drift.” System drift is illustrated by the gap gene network—involved in segmental patterning—in dipteran insects. In the classic model organism Drosophila melanogaster and the nonmodel scuttle fly Megaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is essentially identical in both species. In this detailed modeling analysis of system drift, we use gene circuits which are fit to quantitative gap gene expression data in M. abdita and compare them with an equivalent set of models from D. melanogaster. The results of this comparative analysis show precisely how compensatory regulatory mechanisms achieve equivalent final patterns in both species. We discuss the larger implications of the work in terms of “genotype networks” and the ways in which the structure of regulatory networks can influence patterns of evolutionary change (evolvability). PMID:26796549

Where do health benefits of flavonoids come from? Insights from flavonoid targets and their evolutionary history.

PubMed

Lu, Ming-Feng; Xiao, Zheng-Tao; Zhang, Hong-Yu

2013-05-17

Flavonoid intake is negatively correlated with the incidence of some chronic diseases including cardiovascular diseases, type II diabetes, neurodegenerative diseases, and cancers. Thus, the molecular mechanisms underlying this correlation are of great interest. Although ample attention has been given to the free radical-scavenging potential of flavonoids, the poor bioavailability of exogenous flavonoids suggests that the direct antioxidant activity is unlikely responsible for their favorable effects. This study comprehensively analyzed flavonoid targets. The results show that the main functions of these targets are associated with cancers and cardiovascular and metabolic diseases. Moreover, evolutionary analysis of these targets showed that ~1000 of the targets have homologues in human gut bacterial metagenomes. Clusters of orthologous groups of proteins (COG) analysis indicated that most of these bacterial targets are associated with bacterial metabolism. Given that the metabolism of gut microbiota is coupled with the metabolism of the host, this finding implies that flavonoids exert their benefits by regulating gut microbes. Therefore, the health benefits of flavonoids are well explained by their targets rather than their direct antioxidant potential. Copyright © 2013 Elsevier Inc. All rights reserved.

Pathways to cognitive design.

PubMed

Wertz, Annie E; Moya, Cristina

2018-05-30

Despite a shared recognition that the design of the human mind and the design of human culture are tightly linked, researchers in the evolutionary social sciences tend to specialize in understanding one at the expense of the other. The disciplinary boundaries roughly correspond to research traditions that focus more on natural selection and those that focus more on cultural evolution. In this paper, we articulate how two research traditions within the evolutionary social sciences-evolutionary psychology and cultural evolution-approach the study of design. We focus our analysis on the design of cognitive mechanisms that are the result of the interplay of genetic and cultural evolution. We aim to show how the approaches of these two research traditions can complement each other, and provide a framework for developing a wider range of testable hypotheses about cognitive design. To do so, we provide concrete illustrations of how this integrated approach can be used to interrogate cognitive design using examples from our own work on plant and symbolic group boundary cognition. We hope this recognition of different pathways to design will broaden the hypothesis space in the evolutionary social sciences and encourage methodological pluralism in the investigation of the mind. Copyright © 2018 Elsevier B.V. All rights reserved.

Yellow Fever Virus Exhibits Slower Evolutionary Dynamics than Dengue Virus ▿ †

PubMed Central

Sall, Amadou A.; Faye, Ousmane; Diallo, Mawlouth; Firth, Cadhla; Kitchen, Andrew; Holmes, Edward C.

2010-01-01

Although yellow fever has historically been one of the most important viral infections of humans, relatively little is known about the evolutionary processes that shape its genetic diversity. Similarly, there is limited information on the molecular epidemiology of yellow fever virus (YFV) in Africa even though it most likely first emerged on this continent. Through an analysis of complete E gene sequences, including a newly acquired viral collection from Central and West Africa (Senegal, Cameroon, Central African Republic, Côte d'Ivoire, Mali, and Mauritania), we show that YFV exhibits markedly lower rates of evolutionary change than dengue virus, despite numerous biological similarities between these two viruses. From this observation, along with a lack of clock-like evolutionary behavior in YFV, we suggest that vertical transmission, itself characterized by lower replication rates, may play an important role in the evolution of YFV in its enzootic setting. Despite a reduced rate of nucleotide substitution, phylogenetic patterns and estimates of times to common ancestry in YFV still accord well with the dual histories of colonialism and the slave trade, with areas of sylvatic transmission (such as Kedougou, Senegal) acting as enzootic/epidemic foci. PMID:19889759

New insights into the phylogenetic relationships, character evolution, and phytogeographic patterns of Calceolaria (Calceolariaceae).

PubMed

Cosacov, Andrea; Sérsic, Alicia N; Sosa, Victoria; De-Nova, J Arturo; Nylinder, Stephan; Cocucci, Andrea A

2009-12-01

Biogeographical patterns and diversification processes in Andean and Patagonian flora are not yet well understood. Calceolaria is a highly diversified genus of these areas, representing one of the most specialized plant-pollinator systems because flowers produce nonvolatile oils, a very unusual floral reward. Phylogenetic analyses with molecular (ITS and matK) and morphological characters from 103 Calceolaria species were conducted to examine relationships, to understand biogeographic patterns, and to detect evolutionary patterns of floral and ecological characters. Total evidence analysis retrieved three major clades, which strongly correspond to the three previously recognized subgenera, although only subgenus Rosula was retrieved as a monophyletic group. A single historical event explains the expansion from the southern to central Andes, while different parallel evolutionary lines show a northward expansion from the central to northern Andes across the Huancabamba Deflection, an important geographical barrier in northern Peru. Polyploidy, acquisition of elaiophores, and a nototribic pollination mechanism are key aspects of the evolutionary history of Calceolaria. Pollination interactions were more frequently established with Centris than with Chalepogenus oil-collecting bee species. The repeated loss of the oil gland and shifts to pollen as the only reward suggest an evolutionary tendency from highly to moderately specialized pollination systems.

Evolutionary toxicology: Meta-analysis of evolutionary events in response to chemical stressors.

PubMed

M Oziolor, Elias; De Schamphelaere, Karel; Matson, Cole W

2016-12-01

The regulatory decision-making process regarding chemical safety is most often informed by evidence based on ecotoxicity tests that consider growth, reproduction and survival as end-points, which can be quantitatively linked to short-term population outcomes. Changes in these end-points resulting from chemical exposure can cause alterations in micro-evolutionary forces (mutation, drift, selection and gene flow) that control the genetic composition of populations. With multi-generation exposures, anthropogenic contamination can lead to a population with an altered genetic composition, which may respond differently to future stressors. These evolutionary changes are rarely discussed in regulatory or risk assessment frameworks, but the growing body of literature that documents their existence suggests that these important population-level impacts should be considered. In this meta-analysis we have compared existing contamination levels of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) that have been documented to be associated with evolutionary changes in resident aquatic organisms to regulatory benchmarks for these contaminants. The original intent of this project was to perform a meta-analysis on evolutionary events associated with PCB and PAH contamination. However, this effort was hindered by a lack of consistency in congener selection for "total" PCB or PAH measurements. We expanded this manuscript to include a discussion of methods used to determine PCB and PAH total contamination in addition to comparing regulatory guidelines and contamination that has caused evolutionary effects. Micro-evolutionary responses often lead populations onto unique and unpredictable trajectories. Therefore, to better understand the risk of population-wide alterations occurring, we need to improve comparisons of chemical contamination between affected locations. In this manuscript we offer several possibilities to unify chemical comparisons for PCBs and PAHs that would improve comparability among evolutionary toxicology investigations, and with regulatory guidelines. In addition, we identify studies documenting evolutionary change in the presence of PCB and PAH contamination levels below applicable regulatory benchmarks.

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

Evolution of the β-adrenoreceptors in vertebrates.

PubMed

Zavala, Kattina; Vandewege, Michael W; Hoffmann, Federico G; Opazo, Juan C

2017-01-01

The study of the evolutionary history of genes related to human disease lies at the interface of evolution and medicine. These studies provide the evolutionary context on which medical researchers should work, and are also useful in providing information to suggest further genetic experiments, especially in model species where genetic manipulations can be made. Here we studied the evolution of the β-adrenoreceptor gene family in vertebrates with the aim of adding an evolutionary framework to the already abundant physiological information. Our results show that in addition to the three already described vertebrate β-adrenoreceptor genes there is an additional group containing cyclostome sequences. We suggest that β-adrenoreceptors diversified as a product of the two whole genome duplications that occurred in the ancestor of vertebrates. Gene expression patterns are in general consistent across species, suggesting that expression dynamics were established early in the evolutionary history of vertebrates, and have been maintained since then. Finally, amino acid polymorphisms that are associated to pathological conditions in humans appear to be common in non-human mammals, suggesting that the phenotypic effects of these mutations depend on epistatic interaction with other positions. The evolutionary analysis of the β-adrenoreceptors delivers new insights about the diversity of these receptors in vertebrates, the evolution of the expression patterns and a comparative perspective regarding the polymorphisms that in humans are linked to pathological conditions. Copyright © 2016 Elsevier Inc. All rights reserved.

The evolution of parasite manipulation of host dispersal

PubMed Central

Lion, Sébastien; van Baalen, Minus; Wilson, William G

2006-01-01

We investigate the evolution of manipulation of host dispersal behaviour by parasites using spatially explicit individual-based simulations. We find that when dispersal is local, parasites always gain from increasing their hosts' dispersal rate, although the evolutionary outcome is determined by the costs-to-benefits ratio. However, when dispersal can be non-local, we show that parasites investing in an intermediate dispersal distance of their hosts are favoured even when the manipulation is not costly, due to the intrinsic spatial dynamics of the host–parasite interaction. Our analysis highlights the crucial importance of ecological spatial dynamics in evolutionary processes and reveals the theoretical possibility that parasites could manipulate their hosts' dispersal. PMID:16600882

Analysis of Evolutionary Processes of Species Jump in Waterfowl Parvovirus

PubMed Central

Fan, Wentao; Sun, Zhaoyu; Shen, Tongtong; Xu, Danning; Huang, Kehe; Zhou, Jiyong; Song, Suquan; Yan, Liping

2017-01-01

Waterfowl parvoviruses are classified into goose parvovirus (GPV) and Muscovy duck parvovirus (MDPV) according to their antigenic features and host preferences. A novel duck parvovirus (NDPV), identified as a new variant of GPV, is currently infecting ducks, thus causing considerable economic loss. This study analyzed the molecular evolution and population dynamics of the emerging parvovirus capsid gene to investigate the evolutionary processes concerning the host shift of NDPV. Two important amino acids changes (Asn-489 and Asn-650) were identified in NDPV, which may be responsible for host shift of NDPV. Phylogenetic analysis indicated that the currently circulating NDPV originated from the GPV lineage. The Bayesian Markov chain Monte Carlo tree indicated that the NDPV diverged from GPV approximately 20 years ago. Evolutionary rate analyses demonstrated that GPV evolved with 7.674 × 10-4 substitutions/site/year, and the data for MDPV was 5.237 × 10-4 substitutions/site/year, whereas the substitution rate in NDPV branch was 2.25 × 10-3 substitutions/site/year. Meanwhile, viral population dynamics analysis revealed that the GPV major clade, including NDPV, grew exponentially at a rate of 1.717 year-1. Selection pressure analysis showed that most sites are subject to strong purifying selection and no positively selected sites were found in NDPV. The unique immune-epitopes in waterfowl parvovirus were also estimated, which may be helpful for the prediction of antibody binding sites against NDPV in ducks. PMID:28352261

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

Multivariate genetic architecture of the Anolis dewlap reveals both shared and sex-specific features of a sexually dimorphic ornament.

PubMed

Cox, R M; Costello, R A; Camber, B E; McGlothlin, J W

2017-07-01

Darwin viewed the ornamentation of females as an indirect consequence of sexual selection on males and the transmission of male phenotypes to females via the 'laws of inheritance'. Although a number of studies have supported this view by demonstrating substantial between-sex genetic covariance for ornament expression, the majority of this work has focused on avian plumage. Moreover, few studies have considered the genetic basis of ornaments from a multivariate perspective, which may be crucial for understanding the evolution of sex differences in general, and of complex ornaments in particular. Here, we provide a multivariate, quantitative-genetic analysis of a sexually dimorphic ornament that has figured prominently in studies of sexual selection: the brightly coloured dewlap of Anolis lizards. Using data from a paternal half-sibling breeding experiment in brown anoles (Anolis sagrei), we show that multiple aspects of dewlap size and colour exhibit significant heritability and a genetic variance-covariance structure (G) that is broadly similar in males (G m ) and females (G f ). Whereas sexually monomorphic aspects of the dewlap, such as hue, exhibit significant between-sex genetic correlations (r mf ), sexually dimorphic features, such as area and brightness, exhibit reduced r mf values that do not differ from zero. Using a modified random skewers analysis, we show that the between-sex genetic variance-covariance matrix (B) should not strongly constrain the independent responses of males and females to sexually antagonistic selection. Our microevolutionary analysis is in broad agreement with macroevolutionary perspectives indicating considerable scope for the independent evolution of coloration and ornamentation in males and females. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

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

Chai, Juanjuan; Kora, Guruprasad; Ahn, Tae-Hyuk

2014-10-09

To supply some background, phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. Our results show a total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accuratemore » comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. In conclusion, our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.« less

Classification of Cowpox Viruses into Several Distinct Clades and Identification of a Novel Lineage

PubMed Central

Franke, Annika; Pfaff, Florian; Jenckel, Maria; Hoffmann, Bernd; Höper, Dirk; Antwerpen, Markus; Meyer, Hermann; Beer, Martin; Hoffmann, Donata

2017-01-01

Cowpox virus (CPXV) was considered as uniform species within the genus Orthopoxvirus (OPV). Previous phylogenetic analysis indicated that CPXV is polyphyletic and isolates may cluster into different clades with two of these clades showing genetic similarities to either variola (VARV) or vaccinia viruses (VACV). Further analyses were initiated to assess both the genetic diversity and the evolutionary background of circulating CPXVs. Here we report the full-length sequences of 20 CPXV strains isolated from different animal species and humans in Germany. A phylogenetic analysis of altogether 83 full-length OPV genomes confirmed the polyphyletic character of the species CPXV and suggested at least four different clades. The German isolates from this study mainly clustered into two CPXV-like clades, and VARV- and VACV-like strains were not observed. A single strain, isolated from a cotton-top tamarin, clustered distantly from all other CPXVs and might represent a novel and unique evolutionary lineage. The classification of CPXV strains into clades roughly followed their geographic origin, with the highest clade diversity so far observed for Germany. Furthermore, we found evidence for recombination between OPV clades without significant disruption of the observed clustering. In conclusion, this analysis markedly expands the number of available CPXV full-length sequences and confirms the co-circulation of several CPXV clades in Germany, and provides the first data about a new evolutionary CPXV lineage. PMID:28604604

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

PubMed Central

Munteanu, Andreea; Solé, Ricard V.

2008-01-01

Embryonic development is defined by the hierarchical dynamical process that translates genetic information (genotype) into a spatial gene expression pattern (phenotype) providing the positional information for the correct unfolding of the organism. The nature and evolutionary implications of genotype–phenotype mapping still remain key topics in evolutionary developmental biology (evo-devo). We have explored here issues of neutrality, robustness, and diversity in evo-devo by means of a simple model of gene regulatory networks. The small size of the system allowed an exhaustive analysis of the entire fitness landscape and the extent of its neutrality. This analysis shows that evolution leads to a class of robust genetic networks with an expression pattern characteristic of lateral inhibition. This class is a repertoire of distinct implementations of this key developmental process, the diversity of which provides valuable clues about its underlying causal principles. PMID:19023404

Exploring Evolutionary Patterns in Genetic Sequence: A Computer Exercise

ERIC Educational Resources Information Center

Shumate, Alice M.; Windsor, Aaron J.

2010-01-01

The increase in publications presenting molecular evolutionary analyses and the availability of comparative sequence data through resources such as NCBI's GenBank underscore the necessity of providing undergraduates with hands-on sequence analysis skills in an evolutionary context. This need is particularly acute given that students have been…

Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis.

PubMed

Ishikawa, Masakazu; Yuyama, Ikuko; Shimizu, Hiroshi; Nozawa, Masafumi; Ikeo, Kazuho; Gojobori, Takashi

2016-08-03

Endosymbiosis is an important evolutionary event for organisms, and there is widespread interest in understanding the evolution of endosymbiosis establishment. Hydra is one of the most suitable organisms for studying the evolution of endosymbiosis. Within the genus Hydra, H. viridissima and H. vulgaris show endosymbiosis with green algae. Previous studies suggested that the endosymbiosis in H. vulgaris took place much more recently than that in H. viridissima, noting that the establishment of the interaction between H. vulgaris and its algae is not as stable as in H. viridissima. To investigate the on-going process of endosymbiosis, we first compared growth and tolerance to starvation in symbiotic and aposymbiotic polyps of both species. The results revealed that symbiotic H. viridissima had a higher growth rate and greater tolerance to starvation than aposymbiotic polyps. By contrast, growth of symbiotic H. vulgaris was identical to that of aposymbiotic polyps, and symbiotic H. vulgaris was less tolerant to starvation. Moreover, our gene expression analysis showed a pattern of differential gene expression in H. viridissima similar to that in other endosymbiotically established organisms, and contrary to that observed in H. vulgaris We also showed that H. viridissima could cope with oxidative stress that caused damage, such as cell death, in H. vulgaris These observations support the idea that oxidative stress related genes play an important role in the on-going process of endosymbiosis evolution. The different evolutionary stages of endosymbiosis studied here provide a deeper insight into the evolutionary processes occurring toward a stable endosymbiosis. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.

PubMed

Jackson, Andrew P; Otto, Thomas D; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B; Moussa, Ehab; Nair, Mridul; Reid, Adam J; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A; Weir, William; Wastling, Jonathan M; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R; Pain, Arnab

2014-06-01

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5' ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Comparative evolutionary genomics of Corynebacterium with special reference to codon and amino acid usage diversities.

PubMed

Pal, Shilpee; Sarkar, Indrani; Roy, Ayan; Mohapatra, Pradeep K Das; Mondal, Keshab C; Sen, Arnab

2018-02-01

The present study has been aimed to the comparative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phylogenetic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium. Most of the optimal codons as well as translationally optimal codons are C ending i.e. RNY (R-purine, N-any nucleotide base, and Y-pyrimidine) and reveal translational selection pressure on codon bias of Corynebacterium. Amino acid usage is affected by hydrophobicity, aromaticity, protein energy cost, etc. Highly expressed genes followed the cost minimization hypothesis and are less diverged at their synonymous positions of codons. Functional analysis of core genes shows significant difference in pathogenic and non-pathogenic Corynebacterium. The study reveals close relationship between non-pathogenic and opportunistic pathogenic Corynebaterium as well as between molecular evolution and survival niches of the organism.

Multigenerational response to artificial selection for biased clutch sex ratios in Tigriopus californicus populations.

PubMed

Alexander, H J; Richardson, J M L; Anholt, B R

2014-09-01

Polygenic sex determination (PSD) is relatively rare and theoretically evolutionary unstable, yet has been reported across a range of taxa. Evidence for multilocus PSD is provided by (i) large between-family variance in sex ratio, (ii) paternal and maternal effects on family sex ratio and (iii) response to selection for family sex ratio. This study tests the polygenic hypothesis of sex determination in the harpacticoid copepod Tigriopus californicus using the criterion of response to selection. We report the first multigenerational quantitative evidence that clutch sex ratio responds to artificial selection in both directions (selection for male- and female-biased families) and in multiple populations of T. californicus. In the five of six lines that showed a response to selection, realized heritability estimated by multigenerational analysis ranged from 0.24 to 0.58. Divergence of clutch sex ratio between selection lines is rapid, with response to selection detectable within the first four generations of selection. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

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

Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions

PubMed Central

Laine, Elodie; Carbone, Alessandra

2015-01-01

Protein-protein interactions (PPIs) are essential to all biological processes and they represent increasingly important therapeutic targets. Here, we present a new method for accurately predicting protein-protein interfaces, understanding their properties, origins and binding to multiple partners. Contrary to machine learning approaches, our method combines in a rational and very straightforward way three sequence- and structure-based descriptors of protein residues: evolutionary conservation, physico-chemical properties and local geometry. The implemented strategy yields very precise predictions for a wide range of protein-protein interfaces and discriminates them from small-molecule binding sites. Beyond its predictive power, the approach permits to dissect interaction surfaces and unravel their complexity. We show how the analysis of the predicted patches can foster new strategies for PPIs modulation and interaction surface redesign. The approach is implemented in JET2, an automated tool based on the Joint Evolutionary Trees (JET) method for sequence-based protein interface prediction. JET2 is freely available at www.lcqb.upmc.fr/JET2. PMID:26690684

Stability of Zero-Sum Games in Evolutionary Game Theory

NASA Astrophysics Data System (ADS)

Knebel, Johannes; Krueger, Torben; Weber, Markus F.; Frey, Erwin

2014-03-01

Evolutionary game theory has evolved into a successful theoretical concept to study mechanisms that govern the evolution of ecological communities. On a mathematical level, this theory was formalized in the framework of the celebrated replicator equations (REs) and its stochastic generalizations. In our work, we analyze the long-time behavior of the REs for zero-sum games with arbitrarily many strategies, which are generalized versions of the children's game Rock-Paper-Scissors.[1] We demonstrate how to determine the strategies that survive and those that become extinct in the long run. Our results show that extinction of strategies is exponentially fast in generic setups, and that conditions for the survival can be formulated in terms of the Pfaffian of the REs' antisymmetric payoff matrix. Consequences for the stochastic dynamics, which arise in finite populations, are reflected by a generalized scaling law for the extinction time in the vicinity of critical reaction rates. Our findings underline the relevance of zero-sum games as a reference for the analysis of other models in evolutionary game theory.

Neurocranium versus Face: A Morphometric Approach with Classical Anthropometric Variables for Characterizing Patterns of Cranial Integration in Extant Hominoids and Extinct Hominins

PubMed Central

Pérez-Claros, Juan Antonio; Jiménez-Arenas, Juan Manuel; Palmqvist, Paul

2015-01-01

The relative importance of the two main cranial complexes, the neurocranium and the splanchnocranium, has been examined in the five species of extant hominoids and in a huge sample of extinct hominins using six standard craniometric variables that measure the length, width and height of each cranial module. Factor analysis and two-block partial least squares were used for establishing the major patterns of developmental and evolutionary integration between both cranial modules. The results obtained show that all extant hominoids (including the anatomically modern humans) share a conserved pattern of developmental integration, a result that agrees with previous studies. The pattern of evolutionary integration between both cranial modules in australopiths runs in parallel to developmental integration. In contrast, the pattern of evolutionary and developmental integration of the species of the genus Homo is the opposite, which is probably the consequence of distinctive selective regimes for both hominin groups. PMID:26177535

Neurocranium versus Face: A Morphometric Approach with Classical Anthropometric Variables for Characterizing Patterns of Cranial Integration in Extant Hominoids and Extinct Hominins.

PubMed

Pérez-Claros, Juan Antonio; Jiménez-Arenas, Juan Manuel; Palmqvist, Paul

2015-01-01

The relative importance of the two main cranial complexes, the neurocranium and the splanchnocranium, has been examined in the five species of extant hominoids and in a huge sample of extinct hominins using six standard craniometric variables that measure the length, width and height of each cranial module. Factor analysis and two-block partial least squares were used for establishing the major patterns of developmental and evolutionary integration between both cranial modules. The results obtained show that all extant hominoids (including the anatomically modern humans) share a conserved pattern of developmental integration, a result that agrees with previous studies. The pattern of evolutionary integration between both cranial modules in australopiths runs in parallel to developmental integration. In contrast, the pattern of evolutionary and developmental integration of the species of the genus Homo is the opposite, which is probably the consequence of distinctive selective regimes for both hominin groups.

FUSE Observations of He-rich sdB Stars

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

A hitchhikers guide to the Galápagos: co-phylogeography of Galápagos mockingbirds and their parasites

PubMed Central

2011-01-01

Background Parasites are evolutionary hitchhikers whose phylogenies often track the evolutionary history of their hosts. Incongruence in the evolutionary history of closely associated lineages can be explained through a variety of possible events including host switching and host independent speciation. However, in recently diverged lineages stochastic population processes, such as retention of ancestral polymorphism or secondary contact, can also explain discordant genealogies, even in fully co-speciating taxa. The relatively simple biogeographic arrangement of the Galápagos archipelago, compared with mainland biomes, provides a framework to identify stochastic and evolutionary informative components of genealogic data in these recently diverged organisms. Results Mitochondrial DNA sequences were obtained for four species of Galápagos mockingbirds and three sympatric species of ectoparasites - two louse and one mite species. These data were complemented with nuclear EF1α sequences in selected samples of parasites and with information from microsatellite loci in the mockingbirds. Mitochondrial sequence data revealed differences in population genetic diversity between all taxa and varying degrees of topological congruence between host and parasite lineages. A very low level of genetic variability and lack of congruence was found in one of the louse parasites, which was excluded from subsequent joint analysis of mitochondrial data. The reconciled multi-species tree obtained from the analysis is congruent with both the nuclear data and the geological history of the islands. Conclusions The gene genealogies of Galápagos mockingbirds and two of their ectoparasites show strong phylogeographic correlations, with instances of incongruence mostly explained by ancestral genetic polymorphism. A third parasite genealogy shows low levels of genetic diversity and little evidence of co-phylogeny with their hosts. These differences can mostly be explained by variation in life-history characteristics, primarily host specificity and dispersal capabilities. We show that pooling genetic data from organisms living in close ecological association reveals a more accurate phylogeographic history for these taxa. Our results have implications for the conservation and taxonomy of Galápagos mockingbirds and their parasites. PMID:21966954

Spatial phylogenetics of the vascular flora of Chile.

PubMed

Scherson, Rosa A; Thornhill, Andrew H; Urbina-Casanova, Rafael; Freyman, William A; Pliscoff, Patricio A; Mishler, Brent D

2017-07-01

Current geographic patterns of biodiversity are a consequence of the evolutionary history of the lineages that comprise them. This study was aimed at exploring how evolutionary features of the vascular flora of Chile are distributed across the landscape. Using a phylogeny at the genus level for 87% of the Chilean vascular flora, and a geographic database of sample localities, we calculated phylogenetic diversity (PD), phylogenetic endemism (PE), relative PD (RPD), and relative PE (RPE). Categorical Analyses of Neo- and Paleo-Endemism (CANAPE) were also performed, using a spatial randomization to assess statistical significance. A cluster analysis using range-weighted phylogenetic turnover was used to compare among grid cells, and with known Chilean bioclimates. PD patterns were concordant with known centers of high taxon richness and the Chilean biodiversity hotspot. In addition, several other interesting areas of concentration of evolutionary history were revealed as potential conservation targets. The south of the country shows areas of significantly high RPD and a concentration of paleo-endemism, and the north shows areas of significantly low PD and RPD, and a concentration of neo-endemism. Range-weighted phylogenetic turnover shows high congruence with the main macrobioclimates of Chile. Even though the study was done at the genus level, the outcome provides an accurate outline of phylogenetic patterns that can be filled in as more fine-scaled information becomes available. Copyright © 2017 Elsevier Inc. All rights reserved.

Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication.

PubMed

Shi, Tao; Dimitrov, Ivan; Zhang, Yinling; Tax, Frans E; Yi, Jing; Gou, Xiaoping; Li, Jia

2015-10-01

Traits related to grain and reproductive organs in grass crops have been under continuous directional selection during domestication. Barley is one of the oldest domesticated crops in human history. Thus genes associated with the grain and reproductive organs in barley may show evidence of dramatic evolutionary change. To understand how artificial selection contributes to protein evolution of biased genes in different barley organs, we used Digital Gene Expression analysis of six barley organs (grain, pistil, anther, leaf, stem and root) to identify genes with biased expression in specific organs. Pairwise comparisons of orthologs between barley and Brachypodium distachyon, as well as between highland and lowland barley cultivars mutually indicated that grain and pistil biased genes show relatively higher protein evolutionary rates compared with the median of all orthologs and other organ biased genes. Lineage-specific protein evolutionary rates estimation showed similar patterns with elevated protein evolution in barley grain and pistil biased genes, yet protein sequences generally evolve much faster in the lowland barley cultivar. Further functional annotations revealed that some of these grain and pistil biased genes with rapid protein evolution are related to nutrient biosynthesis and cell cycle/division. Our analyses provide insights into how domestication differentially shaped the evolution of genes specific to different organs of a crop species, and implications for future functional studies of domestication genes.

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

PubMed Central

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

2016-01-01

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

Learning: An Evolutionary Analysis

ERIC Educational Resources Information Center

Swann, Joanna

2009-01-01

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

Analysis of Students' Arguments on Evolutionary Theory

ERIC Educational Resources Information Center

Basel, Nicolai; Harms, Ute; Prechtl, Helmut

2013-01-01

A qualitative exploratory study was conducted to reveal students' argumentation skills in the context of the topic of evolution. Transcripts from problem-centred interviews on secondary students' beliefs about evolutionary processes of adaptation were analysed using a content analysis approach. For this purpose two categorical systems were…

Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom

NASA Astrophysics Data System (ADS)

Song, Xiaoming; Duan, Weike; Huang, Zhinan; Liu, Gaofeng; Wu, Peng; Liu, Tongkun; Li, Ying; Hou, Xilin

2015-09-01

In plants, flowering is the most important transition from vegetative to reproductive growth. The flowering patterns of monocots and eudicots are distinctly different, but few studies have described the evolutionary patterns of the flowering genes in them. In this study, we analysed the evolutionary pattern, duplication and expression level of these genes. The main results were as follows: (i) characterization of flowering genes in monocots and eudicots, including the identification of family-specific, orthologous and collinear genes; (ii) full characterization of CONSTANS-like genes in Brassica rapa (BraCOL genes), the key flowering genes; (iii) exploration of the evolution of COL genes in plant kingdom and construction of the evolutionary pattern of COL genes; (iv) comparative analysis of CO and FT genes between Brassicaceae and Grass, which identified several family-specific amino acids, and revealed that CO and FT protein structures were similar in B. rapa and Arabidopsis but different in rice; and (v) expression analysis of photoperiod pathway-related genes in B. rapa under different photoperiod treatments by RT-qPCR. This analysis will provide resources for understanding the flowering mechanisms and evolutionary pattern of COL genes. In addition, this genome-wide comparative study of COL genes may also provide clues for evolution of other flowering genes.

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

PubMed

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Racial classification in the evolutionary sciences: a comparative analysis.

PubMed

Billinger, Michael S

2007-01-01

Human racial classification has long been a problem for the discipline of anthropology, but much of the criticism of the race concept has focused on its social and political connotations. The central argument of this paper is that race is not a specifically human problem, but one that exists in evolutionary thought in general. This paper looks at various disciplinary approaches to racial or subspecies classification, extending its focus beyond the anthropological race concept by providing a comparative analysis of the use of racial classification in evolutionary biology, genetics, and anthropology.

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.

Evolutionary behaviour, trade-offs and cyclic and chaotic population dynamics.

PubMed

Hoyle, Andy; Bowers, Roger G; White, Andy

2011-05-01

Many studies of the evolution of life-history traits assume that the underlying population dynamical attractor is stable point equilibrium. However, evolutionary outcomes can change significantly in different circumstances. We present an analysis based on adaptive dynamics of a discrete-time demographic model involving a trade-off whose shape is also an important determinant of evolutionary behaviour. We derive an explicit expression for the fitness in the cyclic region and consequently present an adaptive dynamic analysis which is algebraic. We do this fully in the region of 2-cycles and (using a symbolic package) almost fully for 4-cycles. Simulations illustrate and verify our results. With equilibrium population dynamics, trade-offs with accelerating costs produce a continuously stable strategy (CSS) whereas trade-offs with decelerating costs produce a non-ES repellor. The transition to 2-cycles produces a discontinuous change: the appearance of an intermediate region in which branching points occur. The size of this region decreases as we move through the region of 2-cycles. There is a further discontinuous fall in the size of the branching region during the transition to 4-cycles. We extend our results numerically and with simulations to higher-period cycles and chaos. Simulations show that chaotic population dynamics can evolve from equilibrium and vice-versa.

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

PubMed Central

Pardo-Diaz, Carolina; Hanly, Joseph J.; Martin, Simon H.; Mallet, James; Dasmahapatra, Kanchon K.; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W. Owen; Jiggins, Chris D.

2016-01-01

An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation. PMID:26771987

Cancer Biomarkers from Genome-Scale DNA Methylation: Comparison of Evolutionary and Semantic Analysis Methods

PubMed Central

Valavanis, Ioannis; Pilalis, Eleftherios; Georgiadis, Panagiotis; Kyrtopoulos, Soterios; Chatziioannou, Aristotelis

2015-01-01

DNA methylation profiling exploits microarray technologies, thus yielding a wealth of high-volume data. Here, an intelligent framework is applied, encompassing epidemiological genome-scale DNA methylation data produced from the Illumina’s Infinium Human Methylation 450K Bead Chip platform, in an effort to correlate interesting methylation patterns with cancer predisposition and, in particular, breast cancer and B-cell lymphoma. Feature selection and classification are employed in order to select, from an initial set of ~480,000 methylation measurements at CpG sites, predictive cancer epigenetic biomarkers and assess their classification power for discriminating healthy versus cancer related classes. Feature selection exploits evolutionary algorithms or a graph-theoretic methodology which makes use of the semantics information included in the Gene Ontology (GO) tree. The selected features, corresponding to methylation of CpG sites, attained moderate-to-high classification accuracies when imported to a series of classifiers evaluated by resampling or blindfold validation. The semantics-driven selection revealed sets of CpG sites performing similarly with evolutionary selection in the classification tasks. However, gene enrichment and pathway analysis showed that it additionally provides more descriptive sets of GO terms and KEGG pathways regarding the cancer phenotypes studied here. Results support the expediency of this methodology regarding its application in epidemiological studies. PMID:27600245

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling.

PubMed

Wallbank, Richard W R; Baxter, Simon W; Pardo-Diaz, Carolina; Hanly, Joseph J; Martin, Simon H; Mallet, James; Dasmahapatra, Kanchon K; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W Owen; Jiggins, Chris D

2016-01-01

An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation.

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

Quantifying ecological impacts of mass extinctions with network analysis of fossil communities

PubMed Central

Muscente, A. D.; Prabhu, Anirudh; Zhong, Hao; Eleish, Ahmed; Meyer, Michael B.; Fox, Peter; Hazen, Robert M.; Knoll, Andrew H.

2018-01-01

Mass extinctions documented by the fossil record provide critical benchmarks for assessing changes through time in biodiversity and ecology. Efforts to compare biotic crises of the past and present, however, encounter difficulty because taxonomic and ecological changes are decoupled, and although various metrics exist for describing taxonomic turnover, no methods have yet been proposed to quantify the ecological impacts of extinction events. To address this issue, we apply a network-based approach to exploring the evolution of marine animal communities over the Phanerozoic Eon. Network analysis of fossil co-occurrence data enables us to identify nonrandom associations of interrelated paleocommunities. These associations, or evolutionary paleocommunities, dominated total diversity during successive intervals of relative community stasis. Community turnover occurred largely during mass extinctions and radiations, when ecological reorganization resulted in the decline of one association and the rise of another. Altogether, we identify five evolutionary paleocommunities at the generic and familial levels in addition to three ordinal associations that correspond to Sepkoski’s Cambrian, Paleozoic, and Modern evolutionary faunas. In this context, we quantify magnitudes of ecological change by measuring shifts in the representation of evolutionary paleocommunities over geologic time. Our work shows that the Great Ordovician Biodiversification Event had the largest effect on ecology, followed in descending order by the Permian–Triassic, Cretaceous–Paleogene, Devonian, and Triassic–Jurassic mass extinctions. Despite its taxonomic severity, the Ordovician extinction did not strongly affect co-occurrences of taxa, affirming its limited ecological impact. Network paleoecology offers promising approaches to exploring ecological consequences of extinctions and radiations. PMID:29686079

Efficient Allocation of Resources for Defense of Spatially Distributed Networks Using Agent-Based Simulation.

PubMed

Kroshl, William M; Sarkani, Shahram; Mazzuchi, Thomas A

2015-09-01

This article presents ongoing research that focuses on efficient allocation of defense resources to minimize the damage inflicted on a spatially distributed physical network such as a pipeline, water system, or power distribution system from an attack by an active adversary, recognizing the fundamental difference between preparing for natural disasters such as hurricanes, earthquakes, or even accidental systems failures and the problem of allocating resources to defend against an opponent who is aware of, and anticipating, the defender's efforts to mitigate the threat. Our approach is to utilize a combination of integer programming and agent-based modeling to allocate the defensive resources. We conceptualize the problem as a Stackelberg "leader follower" game where the defender first places his assets to defend key areas of the network, and the attacker then seeks to inflict the maximum damage possible within the constraints of resources and network structure. The criticality of arcs in the network is estimated by a deterministic network interdiction formulation, which then informs an evolutionary agent-based simulation. The evolutionary agent-based simulation is used to determine the allocation of resources for attackers and defenders that results in evolutionary stable strategies, where actions by either side alone cannot increase its share of victories. We demonstrate these techniques on an example network, comparing the evolutionary agent-based results to a more traditional, probabilistic risk analysis (PRA) approach. Our results show that the agent-based approach results in a greater percentage of defender victories than does the PRA-based approach. © 2015 Society for Risk Analysis.

Quantifying ecological impacts of mass extinctions with network analysis of fossil communities.

PubMed

Muscente, A D; Prabhu, Anirudh; Zhong, Hao; Eleish, Ahmed; Meyer, Michael B; Fox, Peter; Hazen, Robert M; Knoll, Andrew H

2018-05-15

Mass extinctions documented by the fossil record provide critical benchmarks for assessing changes through time in biodiversity and ecology. Efforts to compare biotic crises of the past and present, however, encounter difficulty because taxonomic and ecological changes are decoupled, and although various metrics exist for describing taxonomic turnover, no methods have yet been proposed to quantify the ecological impacts of extinction events. To address this issue, we apply a network-based approach to exploring the evolution of marine animal communities over the Phanerozoic Eon. Network analysis of fossil co-occurrence data enables us to identify nonrandom associations of interrelated paleocommunities. These associations, or evolutionary paleocommunities, dominated total diversity during successive intervals of relative community stasis. Community turnover occurred largely during mass extinctions and radiations, when ecological reorganization resulted in the decline of one association and the rise of another. Altogether, we identify five evolutionary paleocommunities at the generic and familial levels in addition to three ordinal associations that correspond to Sepkoski's Cambrian, Paleozoic, and Modern evolutionary faunas. In this context, we quantify magnitudes of ecological change by measuring shifts in the representation of evolutionary paleocommunities over geologic time. Our work shows that the Great Ordovician Biodiversification Event had the largest effect on ecology, followed in descending order by the Permian-Triassic, Cretaceous-Paleogene, Devonian, and Triassic-Jurassic mass extinctions. Despite its taxonomic severity, the Ordovician extinction did not strongly affect co-occurrences of taxa, affirming its limited ecological impact. Network paleoecology offers promising approaches to exploring ecological consequences of extinctions and radiations. Copyright © 2018 the Author(s). Published by PNAS.

Satellite DNA Sequences in Canidae and Their Chromosome Distribution in Dog and Red Fox.

PubMed

Vozdova, Miluse; Kubickova, Svatava; Cernohorska, Halina; Fröhlich, Jan; Rubes, Jiri

2016-01-01

Satellite DNA is a characteristic component of mammalian centromeric heterochromatin, and a comparative analysis of its evolutionary dynamics can be used for phylogenetic studies. We analysed satellite and satellite-like DNA sequences available in NCBI for 4 species of the family Canidae (red fox, Vulpes vulpes, VVU; domestic dog, Canis familiaris, CFA; arctic fox, Vulpes lagopus, VLA; raccoon dog, Nyctereutes procyonoides procyonoides, NPR) by comparative sequence analysis, which revealed 86-90% intraspecies and 76-79% interspecies similarity. Comparative fluorescence in situ hybridisation in the red fox and dog showed signals of the red fox satellite probe in canine and vulpine autosomal centromeres, on VVUY, B chromosomes, and in the distal parts of VVU9q and VVU10p which were shown to contain nucleolus organiser regions. The CFA satellite probe stained autosomal centromeres only in the dog. The CFA satellite-like DNA did not show any significant sequence similarity with the satellite DNA of any species analysed and was localised to the centromeres of 9 canine chromosome pairs. No significant heterochromatin block was detected on the B chromosomes of the red fox. Our results show extensive heterogeneity of satellite sequences among Canidae and prove close evolutionary relationships between the red and arctic fox. © 2017 S. Karger AG, Basel.

First principles prediction of amorphous phases using evolutionary algorithms

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

Nahas, Suhas, E-mail: shsnhs@iitk.ac.in; Gaur, Anshu, E-mail: agaur@iitk.ac.in; Bhowmick, Somnath, E-mail: bsomnath@iitk.ac.in

2016-07-07

We discuss the efficacy of evolutionary method for the purpose of structural analysis of amorphous solids. At present, ab initio molecular dynamics (MD) based melt-quench technique is used and this deterministic approach has proven to be successful to study amorphous materials. We show that a stochastic approach motivated by Darwinian evolution can also be used to simulate amorphous structures. Applying this method, in conjunction with density functional theory based electronic, ionic and cell relaxation, we re-investigate two well known amorphous semiconductors, namely silicon and indium gallium zinc oxide. We find that characteristic structural parameters like average bond length and bondmore » angle are within ∼2% of those reported by ab initio MD calculations and experimental studies.« less

Evolutionary Approach for Relative Gene Expression Algorithms

PubMed Central

Czajkowski, Marcin

2014-01-01

A Relative Expression Analysis (RXA) uses ordering relationships in a small collection of genes and is successfully applied to classiffication using microarray data. As checking all possible subsets of genes is computationally infeasible, the RXA algorithms require feature selection and multiple restrictive assumptions. Our main contribution is a specialized evolutionary algorithm (EA) for top-scoring pairs called EvoTSP which allows finding more advanced gene relations. We managed to unify the major variants of relative expression algorithms through EA and introduce weights to the top-scoring pairs. Experimental validation of EvoTSP on public available microarray datasets showed that the proposed solution significantly outperforms in terms of accuracy other relative expression algorithms and allows exploring much larger solution space. PMID:24790574

The mitochondrial genome of the ascalaphid owlfly Libelloides macaronius and comparative evolutionary mitochondriomics of neuropterid insects

PubMed Central

2011-01-01

Background The insect order Neuroptera encompasses more than 5,700 described species. To date, only three neuropteran mitochondrial genomes have been fully and one partly sequenced. Current knowledge on neuropteran mitochondrial genomes is limited, and new data are strongly required. In the present work, the mitochondrial genome of the ascalaphid owlfly Libelloides macaronius is described and compared with the known neuropterid mitochondrial genomes: Megaloptera, Neuroptera and Raphidioptera. These analyses are further extended to other endopterygotan orders. Results The mitochondrial genome of L. macaronius is a circular molecule 15,890 bp long. It includes the entire set of 37 genes usually present in animal mitochondrial genomes. The gene order of this newly sequenced genome is unique among Neuroptera and differs from the ancestral type of insects in the translocation of trnC. The L. macaronius genome shows the lowest A+T content (74.50%) among known neuropterid genomes. Protein-coding genes possess the typical mitochondrial start codons, except for cox1, which has an unusual ACG. Comparisons among endopterygotan mitochondrial genomes showed that A+T content and AT/GC-skews exhibit a broad range of variation among 84 analyzed taxa. Comparative analyses showed that neuropterid mitochondrial protein-coding genes experienced complex evolutionary histories, involving features ranging from codon usage to rate of substitution, that make them potential markers for population genetics/phylogenetics studies at different taxonomic ranks. The 22 tRNAs show variable substitution patterns in Neuropterida, with higher sequence conservation in genes located on the α strand. Inferred secondary structures for neuropterid rrnS and rrnL genes largely agree with those known for other insects. For the first time, a model is provided for domain I of an insect rrnL. The control region in Neuropterida, as in other insects, is fast-evolving genomic region, characterized by AT-rich motifs. Conclusions The new genome shares many features with known neuropteran genomes but differs in its low A+T content. Comparative analysis of neuropterid mitochondrial genes showed that they experienced distinct evolutionary patterns. Both tRNA families and ribosomal RNAs show composite substitution pathways. The neuropterid mitochondrial genome is characterized by a complex evolutionary history. PMID:21569260

The Current Status of the Philosophy of Biology

NASA Astrophysics Data System (ADS)

Takacs, Peter; Ruse, Michael

2013-01-01

The philosophy of biology today is one of the most exciting areas of philosophy. It looks critically across the life sciences, teasing out conceptual issues and difficulties bringing to bear the tools of philosophical analysis to achieve clarification and understanding. This essay surveys work in all of the major directions of research: evolutionary theory and the units/levels of selection; evolutionary developmental biology; reductionism; ecology; the species problem; teleology; evolutionary epistemology; evolutionary ethics; and progress. There is a comprehensive bibliography.

From genes to ecosystems: Measuring evolutionary diversity and community structure with Forest Inventory and Analysis (FIA) data

Treesearch

Kevin M. Potter

2009-01-01

Forest genetic sustainability is an important component of forest health because genetic diversity and evolutionary processes allow for the adaptation of species and for the maintenance of ecosystem functionality and resilience. Phylogenetic community analyses, a set of new statistical methods for describing the evolutionary relationships among species, offer an...

From Pleistocene to Holocene: the prehistory of southwest Asia in evolutionary context.

PubMed

Watkins, Trevor

2017-08-14

In this paper I seek to show how cultural niche construction theory offers the potential to extend the human evolutionary story beyond the Pleistocene, through the Neolithic, towards the kind of very large-scale societies in which we live today. The study of the human past has been compartmentalised, each compartment using different analytical vocabularies, so that their accounts are written in mutually incompatible languages. In recent years social, cognitive and cultural evolutionary theories, building on a growing body of archaeological evidence, have made substantial sense of the social and cultural evolution of the genus Homo. However, specialists in this field of studies have found it difficult to extend their kind of analysis into the Holocene human world. Within southwest Asia the three or four millennia of the Neolithic period at the beginning of the Holocene represents a pivotal point, which saw the transformation of human society in the emergence of the first large-scale, permanent communities, the domestication of plants and animals, and the establishment of effective farming economies. Following the Neolithic, the pace of human social, economic and cultural evolution continued to increase. By 5000 years ago, in parts of southwest Asia and northeast Africa there were very large-scale urban societies, and the first large-scale states (kingdoms). An extension of cultural niche construction theory enables us to extend the evolutionary narrative of the Pleistocene into the Holocene, opening the way to developing a single, long-term, evolutionary account of human history.

Evolution of nuclear ribosomal RNAs in kinetoplastid protozoa: perspectives on the age and origins of parasitism.

PubMed Central

Fernandes, A P; Nelson, K; Beverley, S M

1993-01-01

Molecular evolutionary relationships within the protozoan order Kinetoplastida were deduced from comparisons of the nuclear small and large subunit ribosomal RNA (rRNA) gene sequences. These studies show that relationships among the trypanosomatid protozoans differ from those previously proposed from studies of organismal characteristics or mitochondrial rRNAs. The genera Leishmania, Endotrypanum, Leptomonas, and Crithidia form a closely related group, which shows progressively more distant relationships to Phytomonas and Blastocrithidia, Trypanosoma cruzi, and lastly Trypanosoma brucei. The rooting of the trypanosomatid tree was accomplished by using Bodo caudatus (family Bodonidae) as an outgroup, a status confirmed by molecular comparisons with other eukaryotes. The nuclear rRNA tree agrees well with data obtained from comparisons of other nuclear genes. Differences with the proposed mitochondrial rRNA tree probably reflect the lack of a suitable outgroup for this tree, as the topologies are otherwise similar. Small subunit rRNA divergences within the trypanosomatids are large, approaching those among plants and animals, which underscores the evolutionary antiquity of the group. Analysis of the distribution of different parasitic life-styles of these species in conjunction with a probable timing of evolutionary divergences suggests that vertebrate parasitism arose multiple times in the trypanosomatids. PMID:8265597

Evolutionary Engineering in Chemostat Cultures for Improved Maltotriose Fermentation Kinetics in Saccharomyces pastorianus Lager Brewing Yeast

PubMed Central

Brickwedde, Anja; van den Broek, Marcel; Geertman, Jan-Maarten A.; Magalhães, Frederico; Kuijpers, Niels G. A.; Gibson, Brian; Pronk, Jack T.; Daran, Jean-Marc G.

2017-01-01

The lager brewing yeast Saccharomyces pastorianus, an interspecies hybrid of S. eubayanus and S. cerevisiae, ferments maltotriose, maltose, sucrose, glucose and fructose in wort to ethanol and carbon dioxide. Complete and timely conversion (“attenuation”) of maltotriose by industrial S. pastorianus strains is a key requirement for process intensification. This study explores a new evolutionary engineering strategy for improving maltotriose fermentation kinetics. Prolonged carbon-limited, anaerobic chemostat cultivation of the reference strain S. pastorianus CBS1483 on a maltotriose-enriched sugar mixture was used to select for spontaneous mutants with improved affinity for maltotriose. Evolved populations exhibited an up to 5-fold lower residual maltotriose concentration and a higher ethanol concentration than the parental strain. Uptake studies with 14C-labeled sugars revealed an up to 4.75-fold higher transport capacity for maltotriose in evolved strains. In laboratory batch cultures on wort, evolved strains showed improved attenuation and higher ethanol concentrations. These improvements were also observed in pilot fermentations at 1,000-L scale with high-gravity wort. Although the evolved strain exhibited multiple chromosomal copy number changes, analysis of beer made from pilot fermentations showed no negative effects on flavor compound profiles. These results demonstrate the potential of evolutionary engineering for strain improvement of hybrid, alloploid brewing strains. PMID:28943864

Evolutionary Engineering in Chemostat Cultures for Improved Maltotriose Fermentation Kinetics in Saccharomyces pastorianus Lager Brewing Yeast.

PubMed

Brickwedde, Anja; van den Broek, Marcel; Geertman, Jan-Maarten A; Magalhães, Frederico; Kuijpers, Niels G A; Gibson, Brian; Pronk, Jack T; Daran, Jean-Marc G

2017-01-01

The lager brewing yeast Saccharomyces pastorianus , an interspecies hybrid of S. eubayanus and S. cerevisiae , ferments maltotriose, maltose, sucrose, glucose and fructose in wort to ethanol and carbon dioxide. Complete and timely conversion ("attenuation") of maltotriose by industrial S. pastorianus strains is a key requirement for process intensification. This study explores a new evolutionary engineering strategy for improving maltotriose fermentation kinetics. Prolonged carbon-limited, anaerobic chemostat cultivation of the reference strain S. pastorianus CBS1483 on a maltotriose-enriched sugar mixture was used to select for spontaneous mutants with improved affinity for maltotriose. Evolved populations exhibited an up to 5-fold lower residual maltotriose concentration and a higher ethanol concentration than the parental strain. Uptake studies with 14 C-labeled sugars revealed an up to 4.75-fold higher transport capacity for maltotriose in evolved strains. In laboratory batch cultures on wort, evolved strains showed improved attenuation and higher ethanol concentrations. These improvements were also observed in pilot fermentations at 1,000-L scale with high-gravity wort. Although the evolved strain exhibited multiple chromosomal copy number changes, analysis of beer made from pilot fermentations showed no negative effects on flavor compound profiles. These results demonstrate the potential of evolutionary engineering for strain improvement of hybrid, alloploid brewing strains.

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

Analysis of the nicotinamide phosphoribosyltransferase family provides insight into vertebrate adaptation to different oxygen levels during the water-to-land transition.

PubMed

Fang, Chengchi; Guan, Lihong; Zhong, Zaixuan; Gan, Xiaoni; He, Shunping

2015-08-01

One of the most important events in vertebrate evolutionary history is the water-to-land transition, during which some morphological and physiological changes occurred in concert with the loss of specific genes in tetrapods. However, the molecular mechanisms underlying this transition have not been well explored. To explore vertebrate adaptation to different oxygen levels during the water-to-land transition, we performed comprehensive bioinformatics and experimental analysis aiming to investigate the NAMPT family in vertebrates. NAMPT, a rate-limiting enzyme in the salvage pathway of NAD+ biosynthesis, is critical for cell survival in a hypoxic environment, and a high level of NAMPT significantly augments oxidative stress in normoxic environments. Phylogenetic analysis showed that NAMPT duplicates arose from a second round whole-genome duplication event. NAMPTA existed in all classes of vertebrates, whereas NAMPTB was only found in fishes and not tetrapods. Asymmetric evolutionary rates and purifying selection were the main evolutionary forces involved. Although functional analysis identified several functionally divergent sites during NAMPT family evolution, in vitro experimental data demonstrated that NAMPTA and NAMPTB were functionally conserved for NAMPT enzymatic function in the NAD+ salvage pathway. In situ hybridization revealed broad NAMPTA and NAMPTB expression patterns, implying regulatory functions over a wide range of developmental processes. The morpholino-mediated knockdown data demonstrated that NAMPTA was more essential than NAMPTB for vertebrate embryo development. We propose that the retention of NAMPTB in water-breathing fishes and its loss in air-breathing tetrapods resulted from vertebrate adaptation to different oxygen levels during the water-to-land transition. © 2015 FEBS.

Evolutionary relationships of flying foxes (genus Pteropus) in the Philippines inferred from DNA sequences of cytochrome b gene.

PubMed

Bastian, S T; Tanaka, K; Anunciado, R V P; Natural, N G; Sumalde, A C; Namikawa, T

2002-04-01

Six flying fox species, genus Pteropus (four from the Philippines) were investigated using complete cytochrome b gene sequences (1140 bp) to infer their evolutionary relationships. The DNA sequences generated via polymerase chain reaction were analyzed using the neighbor-joining, parsimony, and maximum likelihood methods. We estimated that the first evolutionary event among these Pteropus species occurred approximately 13.90 +/- 1.49 MYA. Within this short period of evolutionary time we further hypothesized that the ancestors of the flying foxes found in the Philippines experienced a subsequent diversification forming two clusters in the topology. The first cluster is composed of P. pumilus (Philippine endemic), P. speciosus (restricted in western Mindanao) with P. scapulatus, while the second one comprised P. vampyrus and P. dasymallus species based on the analysis from first and second codon positions. Consistently, all phylogenetic analyses divulged close association of P. dasymallus with P. vampyrus contradicting the previous report categorizing P. dasymallus under subniger species group with P. pumilus. P. speciosus, and P. hypomelanus. The Philippine endemic species (P. pumilus) is closely linked with P. speciosus. The representative samples of P. vampyrus showed a large genetic distance of 1.87%. The large genetic distance between P. dasymallus and P. hypomelanus, P. pumilus and P. speciosus denotes a distinct species group.

A piecewise smooth model of evolutionary game for residential mobility and segregation

NASA Astrophysics Data System (ADS)

Radi, D.; Gardini, L.

2018-05-01

The paper proposes an evolutionary version of a Schelling-type dynamic system to model the patterns of residential segregation when two groups of people are involved. The payoff functions of agents are the individual preferences for integration which are empirically grounded. Differently from Schelling's model, where the limited levels of tolerance are the driving force of segregation, in the current setup agents benefit from integration. Despite the differences, the evolutionary model shows a dynamics of segregation that is qualitatively similar to the one of the classical Schelling's model: segregation is always a stable equilibrium, while equilibria of integration exist only for peculiar configurations of the payoff functions and their asymptotic stability is highly sensitive to parameter variations. Moreover, a rich variety of integrated dynamic behaviors can be observed. In particular, the dynamics of the evolutionary game is regulated by a one-dimensional piecewise smooth map with two kink points that is rigorously analyzed using techniques recently developed for piecewise smooth dynamical systems. The investigation reveals that when a stable internal equilibrium exists, the bimodal shape of the map leads to several different kinds of bifurcations, smooth, and border collision, in a complicated interplay. Our global analysis can give intuitions to be used by a social planner to maximize integration through social policies that manipulate people's preferences for integration.

Theoretical Analysis of Local Search and Simple Evolutionary Algorithms for the Generalized Travelling Salesperson Problem.

PubMed

Pourhassan, Mojgan; Neumann, Frank

2018-06-22

The generalized travelling salesperson problem is an important NP-hard combinatorial optimization problem for which meta-heuristics, such as local search and evolutionary algorithms, have been used very successfully. Two hierarchical approaches with different neighbourhood structures, namely a Cluster-Based approach and a Node-Based approach, have been proposed by Hu and Raidl (2008) for solving this problem. In this paper, local search algorithms and simple evolutionary algorithms based on these approaches are investigated from a theoretical perspective. For local search algorithms, we point out the complementary abilities of the two approaches by presenting instances where they mutually outperform each other. Afterwards, we introduce an instance which is hard for both approaches when initialized on a particular point of the search space, but where a variable neighbourhood search combining them finds the optimal solution in polynomial time. Then we turn our attention to analysing the behaviour of simple evolutionary algorithms that use these approaches. We show that the Node-Based approach solves the hard instance of the Cluster-Based approach presented in Corus et al. (2016) in polynomial time. Furthermore, we prove an exponential lower bound on the optimization time of the Node-Based approach for a class of Euclidean instances.

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.

Advances in computer simulation of genome evolution: toward more realistic evolutionary genomics analysis by approximate bayesian computation.

PubMed

Arenas, Miguel

2015-04-01

NGS technologies present a fast and cheap generation of genomic data. Nevertheless, ancestral genome inference is not so straightforward due to complex evolutionary processes acting on this material such as inversions, translocations, and other genome rearrangements that, in addition to their implicit complexity, can co-occur and confound ancestral inferences. Recently, models of genome evolution that accommodate such complex genomic events are emerging. This letter explores these novel evolutionary models and proposes their incorporation into robust statistical approaches based on computer simulations, such as approximate Bayesian computation, that may produce a more realistic evolutionary analysis of genomic data. Advantages and pitfalls in using these analytical methods are discussed. Potential applications of these ancestral genomic inferences are also pointed out.

Evolutionary domestication in Drosophila subobscura.

PubMed

Simões, P; Rose, M R; Duarte, A; Gonçalves, R; Matos, M

2007-03-01

The domestication of plants and animals is historically one of the most important topics in evolutionary biology. The evolutionary genetic changes arising from human cultivation are complex because of the effects of such varied processes as continuing natural selection, artificial selection, deliberate inbreeding, genetic drift and hybridization of different lineages. Despite the interest of domestication as an evolutionary process, few studies of multicellular sexual species have approached this topic using well-replicated experiments. Here we present a comprehensive study in which replicated evolutionary trajectories from several Drosophila subobscura populations provide a detailed view of the evolutionary dynamics of domestication in an outbreeding animal species. Our results show a clear evolutionary response in fecundity traits, but no clear pattern for adult starvation resistance and juvenile traits such as development time and viability. These results supply new perspectives on the confounding of adaptation with other evolutionary mechanisms in the process of domestication.

Introduction to the special issue: Tree invasions: towards a better understanding of their complex evolutionary dynamics.

PubMed

Hirsch, Heidi; Richardson, David M; Le Roux, Johannes J

2017-05-01

Many invasive plants show evidence of trait-based evolutionary change, but these remain largely unexplored for invasive trees. The increasing number of invasive trees and their tremendous impacts worldwide, however, illustrates the urgent need to bridge this knowledge gap to apply efficient management. Consequently, an interdisciplinary workshop, held in 2015 at Stellenbosch University in Stellenbosch, South Africa, brought together international researchers to discuss our understanding of evolutionary dynamics in invasive trees. The main outcome of this workshop is this Special Issue of AoB PLANTS . The collection of papers in this issue has helped to identify and assess the evolutionary mechanisms that are likely to influence tree invasions. It also facilitated expansion of the unified framework for biological invasions to incorporate key evolutionary processes. The papers cover a wide range of evolutionary mechanisms in tree genomes (adaptation), epigenomes (phenotypic plasticity) and their second genomes (mutualists), and show how such mechanisms can impact tree invasion processes and management. The special issue provides a comprehensive overview of the factors that promote and mitigate the invasive success of tree species in many parts of the world. It also shows that incorporating evolutionary concepts is crucial for understanding the complex drivers of tree invasions and has much potential to improve management. The contributions of the special issue also highlight many priorities for further work in the face of ever-increasing tree invasions; the complexity of this research needs calls for expanded interdisciplinary research collaborations.

Evolutionary Game Analysis of Government Regulation and Enterprise Emission from the Perspective of Environmental Tax

NASA Astrophysics Data System (ADS)

Mai, Yazong

2017-12-01

In the context of the upcoming implementation of the environmental tax policy, there is a need for a focus on the relationship between government regulation and corporate emissions. To achieve the real effect of environmental tax policy, government need to regulate the illegal emissions of enterprises. Based on the hypothesis of bounded rationality, this paper analyses the strategic set of government regulators and polluting enterprises in the implementation of environmental tax policy. By using the evolutionary game model, the utility function and payoff matrix of the both sides are constructed, and the evolutionary analysis and strategy adjustment of the environmental governance target and the actual profit of the stakeholders are carried out. Thus, the wrong behaviours could be corrected so that the equilibrium of the evolutionary system can be achieved gradually, which could also get the evolutionary stable strategies of the government and the polluting enterprises in the implementation of environmental tax policy.

Questioning Clerkship: Applying Popper's Evolutionary Analysis of Learning to Medical Student Training

ERIC Educational Resources Information Center

Chitpin, Jeremy Sebastian; Chitpin, Stephanie

2017-01-01

Purpose: Through a series of critical discussions on Karl Popper's evolutionary analysis of learning and the non-authoritarian values it promotes, the purpose of this paper is to advocate a Popperian approach for building medical student knowledge. Specifically, it challenges positivist assumptions that permeate the design and management of many…

Evolutionary computing for the design search and optimization of space vehicle power subsystems

NASA Technical Reports Server (NTRS)

Kordon, M.; Klimeck, G.; Hanks, D.

2004-01-01

Evolutionary computing has proven to be a straightforward and robust approach for optimizing a wide range of difficult analysis and design problems. This paper discusses the application of these techniques to an existing space vehicle power subsystem resource and performance analysis simulation in a parallel processing environment.

Metaphors--Messengers of Meaning: A Contribution to an Evolutionary Sociology of Science.

ERIC Educational Resources Information Center

Maasen, Sabine; Weingart, Peter

1995-01-01

Presents the idea that the central link between science and society is established by a diffusion of knowledge. Suggests knowledge transfers may be analyzed in a metaphorical context and that a metaphorical analysis should be combined with discourse analysis and central concepts of evolutionary theory. (50 references) (Author/AEF)

Evolutionary design optimization of traffic signals applied to Quito city.

PubMed

Armas, Rolando; Aguirre, Hernán; Daolio, Fabio; Tanaka, Kiyoshi

2017-01-01

This work applies evolutionary computation and machine learning methods to study the transportation system of Quito from a design optimization perspective. It couples an evolutionary algorithm with a microscopic transport simulator and uses the outcome of the optimization process to deepen our understanding of the problem and gain knowledge about the system. The work focuses on the optimization of a large number of traffic lights deployed on a wide area of the city and studies their impact on travel time, emissions and fuel consumption. An evolutionary algorithm with specialized mutation operators is proposed to search effectively in large decision spaces, evolving small populations for a short number of generations. The effects of the operators combined with a varying mutation schedule are studied, and an analysis of the parameters of the algorithm is also included. In addition, hierarchical clustering is performed on the best solutions found in several runs of the algorithm. An analysis of signal clusters and their geolocation, estimation of fuel consumption, spatial analysis of emissions, and an analysis of signal coordination provide an overall picture of the systemic effects of the optimization process.

Evolutionary design optimization of traffic signals applied to Quito city

PubMed Central

2017-01-01

This work applies evolutionary computation and machine learning methods to study the transportation system of Quito from a design optimization perspective. It couples an evolutionary algorithm with a microscopic transport simulator and uses the outcome of the optimization process to deepen our understanding of the problem and gain knowledge about the system. The work focuses on the optimization of a large number of traffic lights deployed on a wide area of the city and studies their impact on travel time, emissions and fuel consumption. An evolutionary algorithm with specialized mutation operators is proposed to search effectively in large decision spaces, evolving small populations for a short number of generations. The effects of the operators combined with a varying mutation schedule are studied, and an analysis of the parameters of the algorithm is also included. In addition, hierarchical clustering is performed on the best solutions found in several runs of the algorithm. An analysis of signal clusters and their geolocation, estimation of fuel consumption, spatial analysis of emissions, and an analysis of signal coordination provide an overall picture of the systemic effects of the optimization process. PMID:29236733

Adaptive elastic segmentation of brain MRI via shape-model-guided evolutionary programming.

PubMed

Pitiot, Alain; Toga, Arthur W; Thompson, Paul M

2002-08-01

This paper presents a fully automated segmentation method for medical images. The goal is to localize and parameterize a variety of types of structure in these images for subsequent quantitative analysis. We propose a new hybrid strategy that combines a general elastic template matching approach and an evolutionary heuristic. The evolutionary algorithm uses prior statistical information about the shape of the target structure to control the behavior of a number of deformable templates. Each template, modeled in the form of a B-spline, is warped in a potential field which is itself dynamically adapted. Such a hybrid scheme proves to be promising: by maintaining a population of templates, we cover a large domain of the solution space under the global guidance of the evolutionary heuristic, and thoroughly explore interesting areas. We address key issues of automated image segmentation systems. The potential fields are initially designed based on the spatial features of the edges in the input image, and are subjected to spatially adaptive diffusion to guarantee the deformation of the template. This also improves its global consistency and convergence speed. The deformation algorithm can modify the internal structure of the templates to allow a better match. We investigate in detail the preprocessing phase that the images undergo before they can be used more effectively in the iterative elastic matching procedure: a texture classifier, trained via linear discriminant analysis of a learning set, is used to enhance the contrast of the target structure with respect to surrounding tissues. We show how these techniques interact within a statistically driven evolutionary scheme to achieve a better tradeoff between template flexibility and sensitivity to noise and outliers. We focus on understanding the features of template matching that are most beneficial in terms of the achieved match. Examples from simulated and real image data are discussed, with considerations of algorithmic efficiency.

Evolutionary view of acyl-CoA diacylglycerol acyltransferase (DGAT), a key enzyme in neutral lipid biosynthesis.

PubMed

Turchetto-Zolet, Andreia C; Maraschin, Felipe S; de Morais, Guilherme L; Cagliari, Alexandro; Andrade, Cláudia M B; Margis-Pinheiro, Marcia; Margis, Rogerio

2011-09-20

Triacylglycerides (TAGs) are a class of neutral lipids that represent the most important storage form of energy for eukaryotic cells. DGAT (acyl-CoA: diacylglycerol acyltransferase; EC 2.3.1.20) is a transmembrane enzyme that acts in the final and committed step of TAG synthesis, and it has been proposed to be the rate-limiting enzyme in plant storage lipid accumulation. In fact, two different enzymes identified in several eukaryotic species, DGAT1 and DGAT2, are the main enzymes responsible for TAG synthesis. These enzymes do not share high DNA or protein sequence similarities, and it has been suggested that they play non-redundant roles in different tissues and in some species in TAG synthesis. Despite a number of previous studies on the DGAT1 and DGAT2 genes, which have emphasized their importance as potential obesity treatment targets to increase triacylglycerol accumulation, little is known about their evolutionary timeline in eukaryotes. The goal of this study was to examine the evolutionary relationship of the DGAT1 and DGAT2 genes across eukaryotic organisms in order to infer their origin. We have conducted a broad survey of fully sequenced genomes, including representatives of Amoebozoa, yeasts, fungi, algae, musses, plants, vertebrate and invertebrate species, for the presence of DGAT1 and DGAT2 gene homologs. We found that the DGAT1 and DGAT2 genes are nearly ubiquitous in eukaryotes and are readily identifiable in all the major eukaryotic groups and genomes examined. Phylogenetic analyses of the DGAT1 and DGAT2 amino acid sequences revealed evolutionary partitioning of the DGAT protein family into two major DGAT1 and DGAT2 clades. Protein secondary structure and hydrophobic-transmembrane analysis also showed differences between these enzymes. The analysis also revealed that the MGAT2 and AWAT genes may have arisen from DGAT2 duplication events. In this study, we identified several DGAT1 and DGAT2 homologs in eukaryote taxa. Overall, the data show that DGAT1 and DGAT2 are present in most eukaryotic organisms and belong to two different gene families. The phylogenetic and evolutionary analyses revealed that DGAT1 and DGAT2 evolved separately, with functional convergence, despite their wide molecular and structural divergence.

Evolutionary view of acyl-CoA diacylglycerol acyltransferase (DGAT), a key enzyme in neutral lipid biosynthesis

PubMed Central

2011-01-01

Background Triacylglycerides (TAGs) are a class of neutral lipids that represent the most important storage form of energy for eukaryotic cells. DGAT (acyl-CoA: diacylglycerol acyltransferase; EC 2.3.1.20) is a transmembrane enzyme that acts in the final and committed step of TAG synthesis, and it has been proposed to be the rate-limiting enzyme in plant storage lipid accumulation. In fact, two different enzymes identified in several eukaryotic species, DGAT1 and DGAT2, are the main enzymes responsible for TAG synthesis. These enzymes do not share high DNA or protein sequence similarities, and it has been suggested that they play non-redundant roles in different tissues and in some species in TAG synthesis. Despite a number of previous studies on the DGAT1 and DGAT2 genes, which have emphasized their importance as potential obesity treatment targets to increase triacylglycerol accumulation, little is known about their evolutionary timeline in eukaryotes. The goal of this study was to examine the evolutionary relationship of the DGAT1 and DGAT2 genes across eukaryotic organisms in order to infer their origin. Results We have conducted a broad survey of fully sequenced genomes, including representatives of Amoebozoa, yeasts, fungi, algae, musses, plants, vertebrate and invertebrate species, for the presence of DGAT1 and DGAT2 gene homologs. We found that the DGAT1 and DGAT2 genes are nearly ubiquitous in eukaryotes and are readily identifiable in all the major eukaryotic groups and genomes examined. Phylogenetic analyses of the DGAT1 and DGAT2 amino acid sequences revealed evolutionary partitioning of the DGAT protein family into two major DGAT1 and DGAT2 clades. Protein secondary structure and hydrophobic-transmembrane analysis also showed differences between these enzymes. The analysis also revealed that the MGAT2 and AWAT genes may have arisen from DGAT2 duplication events. Conclusions In this study, we identified several DGAT1 and DGAT2 homologs in eukaryote taxa. Overall, the data show that DGAT1 and DGAT2 are present in most eukaryotic organisms and belong to two different gene families. The phylogenetic and evolutionary analyses revealed that DGAT1 and DGAT2 evolved separately, with functional convergence, despite their wide molecular and structural divergence. PMID:21933415

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.

Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis.

PubMed

Liu, Ake; Wang, Yong; Zhang, Debao; Wang, Xuhua; Song, Huifang; Dang, Chunwang; Yao, Qin; Chen, Keping

2013-08-01

Helix-loop-helix (bHLH) proteins play essential regulatory roles in a variety of biological processes. These highly conserved proteins form a large transcription factor superfamily, and are commonly identified in large numbers within animal, plant, and fungal genomes. The bHLH domain has been well studied in many animal species, but has not yet been characterized in non-avian reptiles. In this study, we identified 102 putative bHLH genes in the genome of the green anole lizard, Anolis carolinensis. Based on phylogenetic analysis, these genes were classified into 43 families, with 43, 24, 16, 3, 10, and 3 members assigned into groups A, B, C, D, E, and F, respectively, and 3 members categorized as "orphans". Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with highly conserved patterns observed for introns and additional domains. Results from phylogenetic analysis of the H/E(spl) family suggest that genome and tandem gene duplications have contributed to this family's expansion. Our classification and evolutionary analysis has provided insights into the evolutionary diversification of animal bHLH genes, and should aid future studies on bHLH protein regulation of key growth and developmental processes.

Evolutionary trends in arvicolids and the endemic murid Mikrotia - New data and a critical overview

NASA Astrophysics Data System (ADS)

Maul, Lutz C.; Masini, Federico; Parfitt, Simon A.; Rekovets, Leonid; Savorelli, Andrea

2014-07-01

The study of evolutionary rates dates back to the work of Simpson and Haldane in the 1940s. Small mammals, especially Plio-Pleistocene arvicolids (voles and lemmings), are particularly suited for such studies because they have an unusually complete fossil record and exhibit significant evolutionary change through time. In recent decades, arvicolids have been the focus of intensive research devoted to the tempo and mode of evolutionary change and the identification of trends in dental evolution that can be used to correlate and date fossil sites. These studies have raised interesting questions about whether voles and lemmings had unique evolutionary trajectories, or show convergent evolutionary patterns with other hypsodont rodents. Here we review evolutionary patterns in selected arvicolid lineages and endemic Messinian murids (Mikrotia spp.) and discuss reasons for convergence in dental morphology in these two groups of hypsodont rodents. The results substantiate previously detected patterns, but the larger dataset shows that some trends are less regular than previous studies have suggested. With the exception of a pervasive and sustained trend towards increased hypsodonty, our results show that other features do not follow consistent patterns in all lineages, exhibiting a mosaic pattern comprising stasis, variable rate evolution and gradual unidirectional change through time. Evidence for higher evolutionary rates is found in lineages apparently undergoing adaptations to new ecological niches. In the case of Mikrotia, Microtus voles and the water vole (Mimomys-Arvicola) lineage, a shift to a fossorial lifestyle appears to have been an important driving force in their evolution. For other characters, different causes can be invoked; for example a shift to a semi-aquatic lifestyle may be responsible for the trend towards increasing size in Arvicola. Biochronological application of the data should take into account the complexity and biases of the data.

A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) haemagglutinin.

PubMed

Wagner, Andreas

2014-07-07

Networks of evolving genotypes can be constructed from the worldwide time-resolved genotyping of pathogens like influenza viruses. Such genotype networks are graphs where neighbouring vertices (viral strains) differ in a single nucleotide or amino acid. A rich trove of network analysis methods can help understand the evolutionary dynamics reflected in the structure of these networks. Here, I analyse a genotype network comprising hundreds of influenza A (H3N2) haemagglutinin genes. The network is rife with cycles that reflect non-random parallel or convergent (homoplastic) evolution. These cycles also show patterns of sequence change characteristic for strong and local evolutionary constraints, positive selection and mutation-limited evolution. Such cycles would not be visible on a phylogenetic tree, illustrating that genotype network analysis can complement phylogenetic analyses. The network also shows a distinct modular or community structure that reflects temporal more than spatial proximity of viral strains, where lowly connected bridge strains connect different modules. These and other organizational patterns illustrate that genotype networks can help us study evolution in action at an unprecedented level of resolution. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Regulatory Evolution and Theoretical Arguments in Evolutionary Biology

ERIC Educational Resources Information Center

Ioannidis, Stavros

2013-01-01

The "cis"-regulatory hypothesis is one of the most important claims of evolutionary developmental biology. In this paper I examine the theoretical argument for "cis"-regulatory evolution and its role within evolutionary theorizing. I show that, although the argument has some weaknesses, it acts as a useful example for the importance of current…

Hybrid zone studies: An interdisciplinary approach for the analysis of evolutionary processes

USGS Publications Warehouse

Scribner, Kim T.

1994-01-01

There has been considerable debate in the ecological and evolutionary literature over the relative importance and rate by which microevolutionary processes operating at the population level result in separation and differentiation of lineages and populations, and ultimately in speciation. Our understanding of evolutionary processes have need greatly enhances through the study of hybridization and hybrid zones. Indeed, hybrid zones have been described as “natural laboratories” (Barton, N. H., and G .M. Hewitt, 189. Adaptation, speciation, and hybrid zones. Nature 341:497-503) or as “windows on the evolutionary processes” (Harrison, R. G. 1990. Hybrid zones: windows on the evolutionary process. Oxford Surveys in Evolutionary Biology 7:69-128). Hybrid zones greatly facilitate analyses of evolutionary dynamics because differences in factors such as mating preference, fertility, and viability are likely to be magnified, making the consequences easier to document over short periods of time.

Genomic Diversity and Evolution of the Lyssaviruses

PubMed Central

Delmas, Olivier; Holmes, Edward C.; Talbi, Chiraz; Larrous, Florence; Dacheux, Laurent; Bouchier, Christiane; Bourhy, Hervé

2008-01-01

Lyssaviruses are RNA viruses with single-strand, negative-sense genomes responsible for rabies-like diseases in mammals. To date, genomic and evolutionary studies have most often utilized partial genome sequences, particularly of the nucleoprotein and glycoprotein genes, with little consideration of genome-scale evolution. Herein, we report the first genomic and evolutionary analysis using complete genome sequences of all recognised lyssavirus genotypes, including 14 new complete genomes of field isolates from 6 genotypes and one genotype that is completely sequenced for the first time. In doing so we significantly increase the extent of genome sequence data available for these important viruses. Our analysis of these genome sequence data reveals that all lyssaviruses have the same genomic organization. A phylogenetic analysis reveals strong geographical structuring, with the greatest genetic diversity in Africa, and an independent origin for the two known genotypes that infect European bats. We also suggest that multiple genotypes may exist within the diversity of viruses currently classified as ‘Lagos Bat’. In sum, we show that rigorous phylogenetic techniques based on full length genome sequence provide the best discriminatory power for genotype classification within the lyssaviruses. PMID:18446239

Complex adaptive systems and their relevance for nursing: An evolutionary concept analysis.

PubMed

Notarnicola, Ippolito; Petrucci, Cristina; De Jesus Barbosa, Maria Rosimar; Giorgi, Fabio; Stievano, Alessandro; Rocco, Gennaro; Lancia, Loreto

2017-06-01

This study aimed to analyse the concept of "complex adaptive systems." The construct is still nebulous in the literature, and a further explanation of the idea is needed to have a shared knowledge of it. A concept analysis was conducted utilizing Rodgers evolutionary method. The inclusive years of bibliographic search started from 2005 to 2015. The search was conducted at PubMed©, CINAHL© (EBSCO host©), Scopus©, Web of Science©, and Academic Search Premier©. Retrieved papers were critically analysed to explore the attributes, antecedents, and consequences of the concept. Moreover, surrogates, related terms, and a pattern recognition scheme were identified. The concept analysis showed that complex systems are adaptive and have the ability to process information. They can adapt to the environment and consequently evolve. Nursing is a complex adaptive system, and the nursing profession in practice exhibits complex adaptive system characteristics. Complexity science through complex adaptive systems provides new ways of seeing and understanding the mechanisms that underpin the nursing profession. © 2017 John Wiley & Sons Australia, Ltd.

Relative evolutionary rate inference in HyPhy with LEISR.

PubMed

Spielman, Stephanie J; Kosakovsky Pond, Sergei L

2018-01-01

We introduce LEISR (Likehood Estimation of Individual Site Rates, pronounced "laser"), a tool to infer relative evolutionary rates from protein and nucleotide data, implemented in HyPhy. LEISR is based on the popular Rate4Site (Pupko et al., 2002) approach for inferring relative site-wise evolutionary rates, primarily from protein data. We extend the original method for more general use in several key ways: (i) we increase the support for nucleotide data with additional models, (ii) we allow for datasets of arbitrary size, (iii) we support analysis of site-partitioned datasets to correct for the presence of recombination breakpoints, (iv) we produce rate estimates at all sites rather than at just a subset of sites, and (v) we implemented LEISR as MPI-enabled to support rapid, high-throughput analysis. LEISR is available in HyPhy starting with version 2.3.8, and it is accessible as an option in the HyPhy analysis menu ("Relative evolutionary rate inference"), which calls the HyPhy batchfile LEISR.bf.

Upon accounting for the impact of isoenzyme loss, gene deletion costs anticorrelate with their evolutionary rates

DOE PAGES

Jacobs, Christopher; Lambourne, Luke; Xia, Yu; ...

2017-01-20

Here, 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"º and the same gene's historical importance asmore » 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.« less

Upon accounting for the impact of isoenzyme loss, gene deletion costs anticorrelate with their evolutionary rates

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

Jacobs, Christopher; Lambourne, Luke; Xia, Yu

Here, 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"º and the same gene's historical importance asmore » 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.« less

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.

Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

DOE PAGES

Xue, Hong; Cordero, Otto X.; Camas, Francisco M.; ...

2015-05-05

Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells.more » Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.« less

Evolutionary dynamics of ecological niche in three Rhinogobio fishes from the upper Yangtze River inferred from morphological traits

PubMed Central

Wang, Meirong; Liu, Fei; Lin, Pengcheng; Yang, Shaorong; Liu, Huanzhang

2015-01-01

In the past decades, it has been debated whether ecological niche should be conserved among closely related species (phylogenetic niche conservatism, PNC) or largely divergent (traditional ecological niche theory and ecological speciation) and whether niche specialist and generalist might remain in equilibrium or niche generalist could not appear. In this study, we employed morphological traits to describe ecological niche and test whether different niche dimensions exhibit disparate evolutionary patterns. We conducted our analysis on three Rhinogobio fish species (R. typus,R. cylindricus, and R. ventralis) from the upper Yangtze River, China. Among the 32 measured morphological traits except body length, PCA extracted the first four principal components with their loading scores >1.000. To find the PNC among species, Mantel tests were conducted with the Euclidean distances calculated from the four principal components (representing different niche dimensions) against the pairwise distances calculated from mitochondrial cytochrome b sequence variations. The results showed that the second and the third niche dimension, both related to swimming ability and behavior, exhibited phylogenetic conservatism. Further comparison on niche breadth among these three species revealed that the fourth dimension of R. typus showed the greatest width, indicating that this dimension exhibited niche generalism. In conclusion, our results suggested that different niche dimensions could show different evolutionary dynamic patterns: they may exhibit PNC or not, and some dimensions may evolve generalism. PMID:25691981

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis.

PubMed

Kumar, Sudhir; Stecher, Glen; Peterson, Daniel; Tamura, Koichiro

2012-10-15

There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis. http://www.megasoftware.net/.

Ecological and evolutionary consequences of niche construction for its agent.

PubMed

Kylafis, Grigoris; Loreau, Michel

2008-10-01

Niche construction can generate ecological and evolutionary feedbacks that have been underinvestigated so far. We present an eco-evolutionary model that incorporates the process of niche construction to reveal its effects on the ecology and evolution of the niche-constructing agent. We consider a simple plant-soil nutrient ecosystem in which plants have the ability to increase the input of inorganic nutrient as an example of positive niche construction. On an ecological time scale, the model shows that niche construction allows the persistence of plants under infertile soil conditions that would otherwise lead to their extinction. This expansion of plants' niche, however, requires a high enough rate of niche construction and a high enough initial plant biomass to fuel the positive ecological feedback between plants and their soil environment. On an evolutionary time scale, we consider that the rates of niche construction and nutrient uptake coevolve in plants while a trade-off constrains their values. Different evolutionary outcomes are possible depending on the shape of the trade-off. We show that niche construction results in an evolutionary feedback between plants and their soil environment such that plants partially regulate soil nutrient content. The direct benefit accruing to plants, however, plays a crucial role in the evolutionary advantage of niche construction.

Evolutionary origins of leadership and followership.

PubMed

Van Vugt, Mark

2006-01-01

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

A theoretical comparison of evolutionary algorithms and simulated annealing

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

Hart, W.E.

1995-08-28

This paper theoretically compares the performance of simulated annealing and evolutionary algorithms. Our main result is that under mild conditions a wide variety of evolutionary algorithms can be shown to have greater performance than simulated annealing after a sufficiently large number of function evaluations. This class of EAs includes variants of evolutionary strategie and evolutionary programming, the canonical genetic algorithm, as well as a variety of genetic algorithms that have been applied to combinatorial optimization problems. The proof of this result is based on a performance analysis of a very general class of stochastic optimization algorithms, which has implications formore » the performance of a variety of other optimization algorithm.« less

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.

PubMed

Xu, Weijia; Ozer, Stuart; Gutell, Robin R

2009-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA

PubMed Central

Xu, Weijia; Ozer, Stuart; Gutell, Robin R.

2010-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure. PMID:20502534

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

Preserving the evolutionary potential of floras in biodiversity hotspots.

PubMed

Forest, Félix; Grenyer, Richard; Rouget, Mathieu; Davies, T Jonathan; Cowling, Richard M; Faith, Daniel P; Balmford, Andrew; Manning, John C; Procheş, Serban; van der Bank, Michelle; Reeves, Gail; Hedderson, Terry A J; Savolainen, Vincent

2007-02-15

One of the biggest challenges for conservation biology is to provide conservation planners with ways to prioritize effort. Much attention has been focused on biodiversity hotspots. However, the conservation of evolutionary process is now also acknowledged as a priority in the face of global change. Phylogenetic diversity (PD) is a biodiversity index that measures the length of evolutionary pathways that connect a given set of taxa. PD therefore identifies sets of taxa that maximize the accumulation of 'feature diversity'. Recent studies, however, concluded that taxon richness is a good surrogate for PD. Here we show taxon richness to be decoupled from PD, using a biome-wide phylogenetic analysis of the flora of an undisputed biodiversity hotspot--the Cape of South Africa. We demonstrate that this decoupling has real-world importance for conservation planning. Finally, using a database of medicinal and economic plant use, we demonstrate that PD protection is the best strategy for preserving feature diversity in the Cape. We should be able to use PD to identify those key regions that maximize future options, both for the continuing evolution of life on Earth and for the benefit of society.

The genomic and epidemiological dynamics of human influenza A virus.

PubMed

Rambaut, Andrew; Pybus, Oliver G; Nelson, Martha I; Viboud, Cecile; Taubenberger, Jeffery K; Holmes, Edward C

2008-05-29

The evolutionary interaction between influenza A virus and the human immune system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in A/H1N1, indicative of weaker antigenic drift. These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions.

Evolutionary Bi-objective Optimization for Bulldozer and Its Blade in Soil Cutting

NASA Astrophysics Data System (ADS)

Sharma, Deepak; Barakat, Nada

2018-02-01

An evolutionary optimization approach is adopted in this paper for simultaneously achieving the economic and productive soil cutting. The economic aspect is defined by minimizing the power requirement from the bulldozer, and the soil cutting is made productive by minimizing the time of soil cutting. For determining the power requirement, two force models are adopted from the literature to quantify the cutting force on the blade. Three domain-specific constraints are also proposed, which are limiting the power from the bulldozer, limiting the maximum force on the bulldozer blade and achieving the desired production rate. The bi-objective optimization problem is solved using five benchmark multi-objective evolutionary algorithms and one classical optimization technique using the ɛ-constraint method. The Pareto-optimal solutions are obtained with the knee-region. Further, the post-optimal analysis is performed on the obtained solutions to decipher relationships among the objectives and decision variables. Such relationships are later used for making guidelines for selecting the optimal set of input parameters. The obtained results are then compared with the experiment results from the literature that show a close agreement among them.

Functional and evolutionary relationships between bacteriorhodopsin and halorhodopsin in the archaebacterium, halobacterium halobium

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1986-01-01

The archaebacteria occupy a unique place in phylogenetic trees constructed from analyses of sequences from key informational macromolecules, and their study continues to yield interesting ideas on the early evolution and divergence of biological forms. It is now known that the halobacteria among these species contain various retinal-proteins, resembling eukaryotic rhodopsins, but with different functions. Two of these pigments, located in the cytoplasmic membranes of the bacteria, are bacteriorhodopsin (a light-driven proton pump) and halorhodopsin (a light-driven chloride pump). Comparison of these systems is expected to reveal structure/function relationships in these simple (primitive?) energy transducing membrane components and evolutionary relationships which had produced the structural features which allow the divergent functions. Findings indicate that very different primary structures are needed for these proteins to accomplish their different functions. Indeed, analysis of partial amino acid sequences from halo-opsin shows already that few if any long segments exist which are homologous to bacterio-opsin. Either these proteins diverged a very long time ago to allow for the observed differences, or the evolutionary clock in the halobacteria runs faster than usual.

Genetic architecture of hybrid male sterility in Drosophila: analysis of intraspecies variation for interspecies isolation.

PubMed

Reed, Laura K; LaFlamme, Brooke A; Markow, Therese A

2008-08-27

The genetic basis of postzygotic isolation is a central puzzle in evolutionary biology. Evolutionary forces causing hybrid sterility or inviability act on the responsible genes while they still are polymorphic, thus we have to study these traits as they arise, before isolation is complete. Isofemale strains of D. mojavensis vary significantly in their production of sterile F(1) sons when females are crossed to D. arizonae males. We took advantage of the intraspecific polymorphism, in a novel design, to perform quantitative trait locus (QTL) mapping analyses directly on F(1) hybrid male sterility itself. We found that the genetic architecture of the polymorphism for hybrid male sterility (HMS) in the F(1) is complex, involving multiple QTL, epistasis, and cytoplasmic effects. The role of extensive intraspecific polymorphism, multiple QTL, and epistatic interactions in HMS in this young species pair shows that HMS is arising as a complex trait in this system. Directional selection alone would be unlikely to maintain polymorphism at multiple loci, thus we hypothesize that directional selection is unlikely to be the only evolutionary force influencing postzygotic isolation.

Evolutionary Perspective on Collective Decision Making

NASA Astrophysics Data System (ADS)

Farrell, Dene; Sayama, Hiroki; Dionne, Shelley D.; Yammarino, Francis J.; Wilson, David Sloan

Team decision making dynamics are investigated from a novel perspective by shifting agency from decision makers to representations of potential solutions. We provide a new way to navigate social dynamics of collective decision making by interpreting decision makers as constituents of an evolutionary environment of an ecology of evolving solutions. We demonstrate distinct patterns of evolution with respect to three forms of variation: (1) Results with random variations in utility functions of individuals indicate that groups demonstrating minimal internal variation produce higher true utility values of group solutions and display better convergence; (2) analysis of variations in behavioral patterns within a group shows that a proper balance between selective and creative evolutionary forces is crucial to producing adaptive solutions; and (3) biased variations of the utility functions diminish the range of variation for potential solution utility, leaving only the differential of convergence performance static. We generally find that group cohesion (low random variation within a group) and composition (appropriate variation of behavioral patterns within a group) are necessary for a successful navigation of the solution space, but performance in both cases is susceptible to group level biases.

True-Triaxial Experimental Study of the Evolutionary Features of the Acoustic Emissions and Sounds of Rockburst Processes

NASA Astrophysics Data System (ADS)

Su, Guoshao; Shi, Yanjiong; Feng, Xiating; Jiang, Jianqing; Zhang, Jie; Jiang, Quan

2018-02-01

Rockbursts are markedly characterized by the ejection of rock fragments from host rocks at certain speeds. The rockburst process is always accompanied by acoustic signals that include acoustic emissions (AE) and sounds. A deep insight into the evolutionary features of AE and sound signals is important to improve the accuracy of rockburst prediction. To investigate the evolutionary features of AE and sound signals, rockburst tests on granite rock specimens under true-triaxial loading conditions were performed using an improved rockburst testing system, and the AE and sounds during rockburst development were recorded and analyzed. The results show that the evolutionary features of the AE and sound signals were obvious and similar. On the eve of a rockburst, a `quiescent period' could be observed in both the evolutionary process of the AE hits and the sound waveform. Furthermore, the time-dependent fractal dimensions of the AE hits and sound amplitude both showed a tendency to continuously decrease on the eve of the rockbursts. In addition, on the eve of the rockbursts, the main frequency of the AE and sound signals both showed decreasing trends, and the frequency spectrum distributions were both characterized by low amplitudes, wide frequency bands and multiple peak shapes. Thus, the evolutionary features of sound signals on the eve of rockbursts, as well as that of AE signals, can be used as beneficial information for rockburst prediction.

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

How Many Kinds of Birds Are There and Why Does It Matter?

PubMed

Barrowclough, George F; Cracraft, Joel; Klicka, John; Zink, Robert M

2016-01-01

Estimates of global species diversity have varied widely, primarily based on variation in the numbers derived from different inventory methods of arthropods and other small invertebrates. Within vertebrates, current diversity metrics for fishes, amphibians, and reptiles are known to be poor estimators, whereas those for birds and mammals are often assumed to be relatively well established. We show that avian evolutionary diversity is significantly underestimated due to a taxonomic tradition not found in most other taxonomic groups. Using a sample of 200 species taken from a list of 9159 biological species determined primarily by morphological criteria, we applied a diagnostic, evolutionary species concept to a morphological and distributional data set that resulted in an estimate of 18,043 species of birds worldwide, with a 95% confidence interval of 15,845 to 20,470. In a second, independent analysis, we examined intraspecific genetic data from 437 traditional avian species, finding an average of 2.4 evolutionary units per species, which can be considered proxies for phylogenetic species. Comparing recent lists of species to that used in this study (based primarily on morphology) revealed that taxonomic changes in the past 25 years have led to an increase of only 9%, well below what our results predict. Therefore, our molecular and morphological results suggest that the current taxonomy of birds understimates avian species diversity by at least a factor of two. We suggest that a revised taxonomy that better captures avian species diversity will enhance the quantification and analysis of global patterns of diversity and distribution, as well as provide a more appropriate framework for understanding the evolutionary history of birds.

Space transfer concepts and analysis for exploration missions

NASA Technical Reports Server (NTRS)

1990-01-01

The progress and results are summarized for mission/system requirements database; mission analysis; GN and C (Guidance, Navigation, and Control), aeroheating, Mars landing; radiation protection; aerobrake mass analysis; Shuttle-Z, TMIS (Trans-Mars Injection Stage); Long Duration Habitat Trade Study; evolutionary lunar and Mars options; NTR (Nuclear Thermal Rocket); NEP (Nuclear Electric Propulsion) update; SEP (Solar Electric Propulsion) update; orbital and space-based requirements; technology; piloted rover; programmatic task; and evolutionary and innovative architecture.

Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity.

PubMed

Müller, Romy; Roberts, Charlotte A; Brown, Terence A

2014-04-22

The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second-nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth-nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis.

Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome

PubMed Central

2011-01-01

Background The carnivorous plant Utricularia gibba (bladderwort) is remarkable in having a minute genome, which at ca. 80 megabases is approximately half that of Arabidopsis. Bladderworts show an incredible diversity of forms surrounding a defined theme: tiny, bladder-like suction traps on terrestrial, epiphytic, or aquatic plants with a diversity of unusual vegetative forms. Utricularia plants, which are rootless, are also anomalous in physiological features (respiration and carbon distribution), and highly enhanced molecular evolutionary rates in chloroplast, mitochondrial and nuclear ribosomal sequences. Despite great interest in the genus, no genomic resources exist for Utricularia, and the substitution rate increase has received limited study. Results Here we describe the sequencing and analysis of the Utricularia gibba transcriptome. Three different organs were surveyed, the traps, the vegetative shoot bodies, and the inflorescence stems. We also examined the bladderwort transcriptome under diverse stress conditions. We detail aspects of functional classification, tissue similarity, nitrogen and phosphorus metabolism, respiration, DNA repair, and detoxification of reactive oxygen species (ROS). Long contigs of plastid and mitochondrial genomes, as well as sequences for 100 individual nuclear genes, were compared with those of other plants to better establish information on molecular evolutionary rates. Conclusion The Utricularia transcriptome provides a detailed genomic window into processes occurring in a carnivorous plant. It contains a deep representation of the complex metabolic pathways that characterize a putative minimal plant genome, permitting its use as a source of genomic information to explore the structural, functional, and evolutionary diversity of the genus. Vegetative shoots and traps are the most similar organs by functional classification of their transcriptome, the traps expressing hydrolytic enzymes for prey digestion that were previously thought to be encoded by bacteria. Supporting physiological data, global gene expression analysis shows that traps significantly over-express genes involved in respiration and that phosphate uptake might occur mainly in traps, whereas nitrogen uptake could in part take place in vegetative parts. Expression of DNA repair and ROS detoxification enzymes may be indicative of a response to increased respiration. Finally, evidence from the bladderwort transcriptome, direct measurement of ROS in situ, and cross-species comparisons of organellar genomes and multiple nuclear genes supports the hypothesis that increased nucleotide substitution rates throughout the plant may be due to the mutagenic action of amplified ROS production. PMID:21639913

What have humans done for evolutionary biology? Contributions from genes to populations.

PubMed

Briga, Michael; Griffin, Robert M; Berger, Vérane; Pettay, Jenni E; Lummaa, Virpi

2017-11-15

Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future. © 2017 The Author(s).

What have humans done for evolutionary biology? Contributions from genes to populations

PubMed Central

Briga, Michael; Griffin, Robert M.; Berger, Vérane; Pettay, Jenni E.

2017-01-01

Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future. PMID:29118130

Evolutionary dynamics with fluctuating population sizes and strong mutualism.

PubMed

Chotibut, Thiparat; Nelson, David R

2015-08-01

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

Evolutionary dynamics with fluctuating population sizes and strong mutualism

NASA Astrophysics Data System (ADS)

Chotibut, Thiparat; Nelson, David R.

2015-08-01

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

Evolutionary engineering of industrial microorganisms-strategies and applications.

PubMed

Zhu, Zhengming; Zhang, Juan; Ji, Xiaomei; Fang, Zhen; Wu, Zhimeng; Chen, Jian; Du, Guocheng

2018-06-01

Microbial cells have been widely used in the industry to obtain various biochemical products, and evolutionary engineering is a common method in biological research to improve their traits, such as high environmental tolerance and improvement of product yield. To obtain better integrate functions of microbial cells, evolutionary engineering combined with other biotechnologies have attracted more attention in recent years. Classical laboratory evolution has been proven effective to letting more beneficial mutations occur in different genes but also has some inherent limitations such as a long evolutionary period and uncontrolled mutation frequencies. However, recent studies showed that some new strategies may gradually overcome these limitations. In this review, we summarize the evolutionary strategies commonly used in industrial microorganisms and discuss the combination of evolutionary engineering with other biotechnologies such as systems biology and inverse metabolic engineering. Finally, we prospect the importance and application prospect of evolutionary engineering as a powerful tool especially in optimization of industrial microbial cell factories.

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.

The Evolutionary Tempo of Sex Chromosome Degradation in Carica papaya.

PubMed

Wu, Meng; Moore, Richard C

2015-06-01

Genes on non-recombining heterogametic sex chromosomes may degrade over time through the irreversible accumulation of deleterious mutations. In papaya, the non-recombining male-specific region of the Y (MSY) consists of two evolutionary strata corresponding to chromosomal inversions occurring approximately 7.0 and 1.9 MYA. The step-wise recombination suppression between the papaya X and Y allows for a temporal examination of the degeneration progress of the young Y chromosome. Comparative evolutionary analyses of 55 X/Y gene pairs showed that Y-linked genes have more unfavorable substitutions than X-linked genes. However, this asymmetric evolutionary pattern is confined to the oldest stratum, and is only observed when recently evolved pseudogenes are included in the analysis, indicating a slow degeneration tempo of the papaya Y chromosome. Population genetic analyses of coding sequence variation of six Y-linked focal loci in the oldest evolutionary stratum detected an excess of nonsynonymous polymorphism and reduced codon bias relative to autosomal loci. However, this pattern was also observed for corresponding X-linked loci. Both the MSY and its corresponding X-specific region are pericentromeric where recombination has been shown to be greatly reduced. Like the MSY region, overall selective efficacy on the X-specific region may be reduced due to the interference of selective forces between highly linked loci, or the Hill-Robertson effect, that is accentuated in regions of low or suppressed recombination. Thus, a pattern of gene decay on the X-specific region may be explained by relaxed purifying selection and widespread genetic hitchhiking due to its pericentromeric location.

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

Aggregation Pheromone System: A Real-parameter Optimization Algorithm using Aggregation Pheromones as the Base Metaphor

NASA Astrophysics Data System (ADS)

Tsutsui, Shigeyosi

This paper proposes an aggregation pheromone system (APS) for solving real-parameter optimization problems using the collective behavior of individuals which communicate using aggregation pheromones. APS was tested on several test functions used in evolutionary computation. The results showed APS could solve real-parameter optimization problems fairly well. The sensitivity analysis of control parameters of APS is also studied.

Genome-wide analysis of the Glycerol-3-Phosphate Acyltransferase (GPAT) gene family reveals the evolution and diversification of plant GPATs

PubMed Central

Waschburger, Edgar; Kulcheski, Franceli Rodrigues; Veto, Nicole Moreira; Margis, Rogerio; Margis-Pinheiro, Marcia; Turchetto-Zolet, Andreia Carina

2018-01-01

Abstract sn-Glycerol-3-phosphate 1-O-acyltransferase (GPAT) is an important enzyme that catalyzes the transfer of an acyl group from acyl-CoA or acyl-ACP to the sn-1 or sn-2 position of sn-glycerol-3-phosphate (G3P) to generate lysophosphatidic acids (LPAs). The functional studies of GPAT in plants demonstrated its importance in controlling storage and membrane lipid. Identifying genes encoding GPAT in a variety of plant species is crucial to understand their involvement in different metabolic pathways and physiological functions. Here, we performed genome-wide and evolutionary analyses of GPATs in plants. GPAT genes were identified in all algae and plants studied. The phylogenetic analysis showed that these genes group into three main clades. While clades I (GPAT9) and II (soluble GPAT) include GPATs from algae and plants, clade III (GPAT1-8) includes GPATs specific from plants that are involved in the biosynthesis of cutin or suberin. Gene organization and the expression pattern of GPATs in plants corroborate with clade formation in the phylogeny, suggesting that the evolutionary patterns is reflected in their functionality. Overall, our results provide important insights into the evolution of the plant GPATs and allowed us to explore the evolutionary mechanism underlying the functional diversification among these genes. PMID:29583156

Dynamic evolution and biogenesis of small RNAs during sex reversal.

PubMed

Liu, Jie; Luo, Majing; Sheng, Yue; Hong, Qiang; Cheng, Hanhua; Zhou, Rongjia

2015-05-06

Understanding origin, evolution and functions of small RNA (sRNA) genes has been a great challenge in the past decade. Molecular mechanisms underlying sexual reversal in vertebrates, particularly sRNAs involved in this process, are largely unknown. By deep-sequencing of small RNA transcriptomes in combination with genomic analysis, we identified a large amount of piRNAs and miRNAs including over 1,000 novel miRNAs, which were differentially expressed during gonad reversal from ovary to testis via ovotesis. Biogenesis and expressions of miRNAs were dynamically changed during the reversal. Notably, phylogenetic analysis revealed dynamic expansions of miRNAs in vertebrates and an evolutionary trajectory of conserved miR-17-92 cluster in the Eukarya. We showed that the miR-17-92 cluster in vertebrates was generated through multiple duplications from ancestor miR-92 in invertebrates Tetranychus urticae and Daphnia pulex from the Chelicerata around 580 Mya. Moreover, we identified the sexual regulator Dmrt1 as a direct target of the members miR-19a and -19b in the cluster. These data suggested dynamic biogenesis and expressions of small RNAs during sex reversal and revealed multiple expansions and evolutionary trajectory of miRNAs from invertebrates to vertebrates, which implicate small RNAs in sexual reversal and provide new insight into evolutionary and molecular mechanisms underlying sexual reversal.

The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers[W][OPEN

PubMed Central

Cheng, Shifeng; van den Bergh, Erik; Zeng, Peng; Zhong, Xiao; Xu, Jiajia; Liu, Xin; Hofberger, Johannes; de Bruijn, Suzanne; Bhide, Amey S.; Kuelahoglu, Canan; Bian, Chao; Chen, Jing; Fan, Guangyi; Kaufmann, Kerstin; Hall, Jocelyn C.; Becker, Annette; Bräutigam, Andrea; Weber, Andreas P.M.; Shi, Chengcheng; Zheng, Zhijun; Li, Wujiao; Lv, Mingju; Tao, Yimin; Wang, Junyi; Zou, Hongfeng; Quan, Zhiwu; Hibberd, Julian M.; Zhang, Gengyun; Zhu, Xin-Guang; Xu, Xun; Schranz, M. Eric

2013-01-01

The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-α) that is independent of the Brassicaceae-specific duplication (At-α) and nested Brassica (Br-α) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes. PMID:23983221

Evolutionary Patterns among Living and Fossil Kogiid Sperm Whales: Evidence from the Neogene of Central America

PubMed Central

Velez-Juarbe, Jorge; Wood, Aaron R.; De Gracia, Carlos; Hendy, Austin J. W.

2015-01-01

Kogiids are known by two living species, the pygmy and dwarf sperm whale (Kogia breviceps and K. sima). Both are relatively rare, and as their names suggest, they are closely related to the sperm whale, all being characterized by the presence of a spermaceti organ. However, this organ is much reduced in kogiids and may have become functionally different. Here we describe a fossil kogiid from the late Miocene of Panama and we explore the evolutionary history of the group with special attention to this evolutionary reduction. The fossil consists of cranial material from the late Tortonian (~7.5 Ma) Piña facies of the Chagres Formation in Panama. Detailed comparison with other fossil and extant kogiids and the results of a phylogenetic analysis place the Panamanian kogiid, herein named Nanokogia isthmia gen. et sp. nov., as a taxon most closely related to Praekogia cedrosensis from the Messinian (~6 Ma) of Baja California and to Kogia spp. Furthermore our results show that reduction of the spermaceti organ has occurred iteratively in kogiids, once in Thalassocetus antwerpiensis in the early-middle Miocene, and more recently in Kogia spp. Additionally, we estimate the divergence between extant species of Kogia at around the late Pliocene, later than previously predicted by molecular estimates. Finally, comparison of Nanokogia with the coeval Scaphokogia cochlearis from Peru shows that these two species display a greater morphological disparity between them than that observed between the extant members of the group. We hypothesize that this reflects differences in feeding ecologies of the two species, with Nanokogia being more similar to extant Kogia. Nanokogia shows that kogiids have been part of the Neotropical marine mammal communities at least since the late Miocene, and gives us insight into the evolutionary history and origins of one of the rarest groups of living whales. PMID:25923213

The puzzle of partial migration: Adaptive dynamics and evolutionary game theory perspectives.

PubMed

De Leenheer, Patrick; Mohapatra, Anushaya; Ohms, Haley A; Lytle, David A; Cushing, J M

2017-01-07

We consider the phenomenon of partial migration which is exhibited by populations in which some individuals migrate between habitats during their lifetime, but others do not. First, using an adaptive dynamics approach, we show that partial migration can be explained on the basis of negative density dependence in the per capita fertilities alone, provided that this density dependence is attenuated for increasing abundances of the subtypes that make up the population. We present an exact formula for the optimal proportion of migrants which is expressed in terms of the vital rates of migrant and non-migrant subtypes only. We show that this allocation strategy is both an evolutionary stable strategy (ESS) as well as a convergence stable strategy (CSS). To establish the former, we generalize the classical notion of an ESS because it is based on invasion exponents obtained from linearization arguments, which fail to capture the stabilizing effects of the nonlinear density dependence. These results clarify precisely when the notion of a "weak ESS", as proposed in Lundberg (2013) for a related model, is a genuine ESS. Secondly, we use an evolutionary game theory approach, and confirm, once again, that partial migration can be attributed to negative density dependence alone. In this context, the result holds even when density dependence is not attenuated. In this case, the optimal allocation strategy towards migrants is the same as the ESS stemming from the analysis based on the adaptive dynamics. The key feature of the population models considered here is that they are monotone dynamical systems, which enables a rather comprehensive mathematical analysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolutionary analysis of groundwater flow: Application of multivariate statistical analysis to hydrochemical data in the Densu Basin, Ghana

NASA Astrophysics Data System (ADS)

Yidana, Sandow Mark; Bawoyobie, Patrick; Sakyi, Patrick; Fynn, Obed Fiifi

2018-02-01

An evolutionary trend has been postulated through the analysis of hydrochemical data of a crystalline rock aquifer system in the Densu Basin, Southern Ghana. Hydrochemcial data from 63 groundwater samples, taken from two main groundwater outlets (Boreholes and hand dug wells) were used to postulate an evolutionary theory for the basin. Sequential factor and hierarchical cluster analysis were used to disintegrate the data into three factors and five clusters (spatial associations). These were used to characterize the controls on groundwater hydrochemistry and its evolution in the terrain. The dissolution of soluble salts and cation exchange processes are the dominant processes controlling groundwater hydrochemistry in the terrain. The trend of evolution of this set of processes follows the pattern of groundwater flow predicted by a calibrated transient groundwater model in the area. The data suggest that anthropogenic activities represent the second most important process in the hydrochemistry. Silicate mineral weathering is the third most important set of processes. Groundwater associations resulting from Q-mode hierarchical cluster analysis indicate an evolutionary pattern consistent with the general groundwater flow pattern in the basin. These key findings are at variance with results of previous investigations and indicate that when carefully done, groundwater hydrochemical data can be very useful for conceptualizing groundwater flow in basins.

Evolutionary genetics of maternal effects

PubMed Central

Wolf, Jason B.; Wade, Michael J.

2016-01-01

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

Self-care Concept Analysis in Cancer Patients: An Evolutionary Concept Analysis.

PubMed

Hasanpour-Dehkordi, Ali

2016-01-01

Self-care is a frequently used concept in both the theory and the clinical practice of nursing and is considered an element of nursing theory by Orem. The aim of this paper is to identify the core attributes of the self-care concept in cancer patients. We used Rodgers' evolutionary method of concept analysis. The articles published in English language from 1980 to 2015 on nursing and non-nursing disciplines were analyzed. Finally, 85 articles, an MSc thesis, and a PhD thesis were selected, examined, and analyzed in-depth. Two experts checked the process of analysis and monitored and reviewed the articles. The analysis showed that self-care concept is determined by four attributes of education, interaction, self-control, and self-reliance. Three types of antecedents in the present study were client-related (self-efficacy, self-esteem), system-related (adequate sources, social networks, and cultural factors), and healthcare professionals-related (participation). The self-care concept has considerably evolved among patients with chronic diseases, particularly cancer, over the past 35 years, and nurses have managed to enhance their knowledge about self-care remarkably for the clients so that the nurses in healthcare teams have become highly efficient and able to assume the responsibility for self-care teams.

Self-care Concept Analysis in Cancer Patients: An Evolutionary Concept Analysis

PubMed Central

Hasanpour-Dehkordi, Ali

2016-01-01

Background: Self-care is a frequently used concept in both the theory and the clinical practice of nursing and is considered an element of nursing theory by Orem. The aim of this paper is to identify the core attributes of the self-care concept in cancer patients. Materials and Methods: We used Rodgers’ evolutionary method of concept analysis. The articles published in English language from 1980 to 2015 on nursing and non-nursing disciplines were analyzed. Finally, 85 articles, an MSc thesis, and a PhD thesis were selected, examined, and analyzed in-depth. Two experts checked the process of analysis and monitored and reviewed the articles. Results: The analysis showed that self-care concept is determined by four attributes of education, interaction, self-control, and self-reliance. Three types of antecedents in the present study were client-related (self-efficacy, self-esteem), system-related (adequate sources, social networks, and cultural factors), and healthcare professionals-related (participation). Conclusion: The self-care concept has considerably evolved among patients with chronic diseases, particularly cancer, over the past 35 years, and nurses have managed to enhance their knowledge about self-care remarkably for the clients so that the nurses in healthcare teams have become highly efficient and able to assume the responsibility for self-care teams. PMID:27803559

Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

PubMed Central

Prangishvili, David

2016-01-01

ABSTRACT Archaea and particularly hyperthermophilic crenarchaea are hosts to many unusual viruses with diverse virion shapes and distinct gene compositions. As is typical of viruses in general, there are no universal genes in the archaeal virosphere. Therefore, to obtain a comprehensive picture of the evolutionary relationships between viruses, network analysis methods are more productive than traditional phylogenetic approaches. Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses. We constructed a bipartite network of archaeal viruses that includes two classes of nodes, the genomes and gene families that connect them. Dissection of this network using formal community detection methods reveals strong modularity, with 10 distinct modules and 3 putative supermodules. However, compared to similar previously analyzed networks of eukaryotic and bacterial viruses, the archaeal virus network is sparsely connected. With the exception of the tailed viruses related to bacteriophages of the order Caudovirales and the families Turriviridae and Sphaerolipoviridae that are linked to a distinct supermodule of eukaryotic and bacterial viruses, there are few connector genes shared by different archaeal virus modules. In contrast, most of these modules include, in addition to viruses, capsidless mobile elements, emphasizing tight evolutionary connections between the two types of entities in archaea. The relative contributions of distinct evolutionary origins, in particular from nonviral elements, and insufficient sampling to the sparsity of the archaeal virus network remain to be determined by further exploration of the archaeal virosphere. IMPORTANCE Viruses infecting archaea are among the most mysterious denizens of the virosphere. Many of these viruses display no genetic or even morphological relationship to viruses of bacteria and eukaryotes, raising questions regarding their origins and position in the global virosphere. Analysis of 5,740 protein sequences from 116 genomes allowed dissection of the archaeal virus network and showed that most groups of archaeal viruses are evolutionarily connected to capsidless mobile genetic elements, including various plasmids and transposons. This finding could reflect actual independent origins of the distinct groups of archaeal viruses from different nonviral elements, providing important insights into the emergence and evolution of the archaeal virome. PMID:27681128

The Comet Cometh: Evolving Developmental Systems.

PubMed

Jaeger, Johannes; Laubichler, Manfred; Callebaut, Werner

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

The role of sexual and natural selection in shaping patterns of sexual dichromatism in the largest family of songbirds (Aves: Thraupidae).

PubMed

Shultz, Allison J; Burns, Kevin J

2017-04-01

Males and females can be under different evolutionary pressures if sexual and natural selection is differentially operating in each sex. As a result, many species have evolved sexual dichromatism, or differences in coloration between sexes. Although sexual dichromatism is often used as an index of the magnitude of sexual selection, sexual dichromatism is a composite trait. Here, we examine the evolution of sexual dichromatism in one of the largest and most ecologically diverse families of birds, the tanagers, using the avian visual perspective and a species-level phylogeny. Our results demonstrate that the evolutionary decreases of sexual dichromatism are more often associated with larger and more frequent changes in male plumage coloration, and evolutionary increases are not more often associated with larger changes in either sex. Furthermore, we show that the crown and ventral plumage regions are correlated with sexual dichromatism in males, and that only male plumage complexity is positively correlated with sexual dichromatism. Finally, we demonstrate that light environment is important in shaping both plumage brilliance and complexity. By conducting a multilevel analysis of plumage evolution in males and females, we show that sexual dichromatism evolves via a mosaic of sexual and natural selection in both sexes. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Loss of Genetic Diversity Means Loss of Geological Information: The Endangered Japanese Crayfish Exhibits Remarkable Historical Footprints

PubMed Central

Koizumi, Itsuro; Usio, Nisikawa; Kawai, Tadashi; Azuma, Noriko; Masuda, Ryuichi

2012-01-01

Intra-specific genetic diversity is important not only because it influences population persistence and evolutionary potential, but also because it contains past geological, climatic and environmental information. In this paper, we show unusually clear genetic structure of the endangered Japanese crayfish that, as a sedentary species, provides many insights into lesser-known past environments in northern Japan. Over the native range, most populations consisted of unique 16S mtDNA haplotypes, resulting in significant genetic divergence (overall F ST = 0.96). Owing to the simple and clear structure, a new graphic approach unraveled a detailed evolutionary history; regional crayfish populations were comprised of two distinct lineages that had experienced contrasting demographic processes (i.e. rapid expansion vs. slow stepwise range expansion) following differential drainage topologies and past climate events. Nuclear DNA sequences also showed deep separation between the lineages. Current ocean barriers to dispersal did not significantly affect the genetic structure of the freshwater crayfish, indicating the formation of relatively recent land bridges. This study provides one of the best examples of how phylogeographic analysis can unravel a detailed evolutionary history of a species and how this history contributes to the understanding of the past environment in the region. Ongoing local extinctions of the crayfish lead not only to loss of biodiversity but also to the loss of a significant information regarding past geological and climatic events. PMID:22470505

A multivariate analysis of genetic variation in the advertisement call of the gray treefrog, Hyla versicolor.

PubMed

Welch, Allison M; Smith, Michael J; Gerhardt, H Carl

2014-06-01

Genetic variation in sexual displays is crucial for an evolutionary response to sexual selection, but can be eroded by strong selection. Identifying the magnitude and sources of additive genetic variance underlying sexually selected traits is thus an important issue in evolutionary biology. We conducted a quantitative genetics experiment with gray treefrogs (Hyla versicolor) to investigate genetic variances and covariances among features of the male advertisement call. Two energetically expensive traits showed significant genetic variation: call duration, expressed as number of pulses per call, and call rate, represented by its inverse, call period. These two properties also showed significant genetic covariance, consistent with an energetic constraint to call production. Combining the genetic variance-covariance matrix with previous estimates of directional sexual selection imposed by female preferences predicts a limited increase in call duration but no change in call rate despite significant selection on both traits. In addition to constraints imposed by the genetic covariance structure, an evolutionary response to sexual selection may also be limited by high energetic costs of long-duration calls and by preferences that act most strongly against very short-duration calls. Meanwhile, the persistence of these preferences could be explained by costs of mating with males with especially unattractive calls. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Convergent evolution at the pathway level: predictable regulatory changes during flower color transitions.

PubMed

Larter, Maximilian; Dunbar-Wallis, Amy; Berardi, Andrea E; Smith, Stacey D

2018-06-07

The predictability of evolution, or whether lineages repeatedly follow the same evolutionary trajectories during phenotypic convergence remains an open question of evolutionary biology. In this study, we investigate evolutionary convergence at the biochemical pathway level and test the predictability of evolution using floral anthocyanin pigmentation, a trait with a well-understood genetic and regulatory basis. We reconstructed the evolution of floral anthocyanin content across 28 species of the Andean clade Iochrominae (Solanaceae) and investigated how shifts in pigmentation are related to changes in expression of 7 key anthocyanin pathway genes. We used phylogenetic multivariate analysis of gene expression to test for phenotypic and developmental convergence at a macroevolutionary scale. Our results show that the four independent losses of the ancestral pigment delphinidin involved convergent losses of expression of the three late pathway genes (F3'5'h, Dfr and Ans). Transitions between pigment types affecting floral hue (e.g. blue to red) involve changes to the expression of branching genes F3'h and F3'5'h, while the expression levels of early steps of the pathway are strongly conserved in all species. These patterns support the idea that the macroevolution of floral pigmentation follows predictable evolutionary trajectories to reach convergent phenotype space, repeatedly involving regulatory changes. This is likely driven by constraints at the pathway level, such as pleiotropy and regulatory structure.

DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood.

PubMed

Kim, Tane; Hao, Weilong

2014-09-27

The study of discrete characters is crucial for the understanding of evolutionary processes. Even though great advances have been made in the analysis of nucleotide sequences, computer programs for non-DNA discrete characters are often dedicated to specific analyses and lack flexibility. Discrete characters often have different transition rate matrices, variable rates among sites and sometimes contain unobservable states. To obtain the ability to accurately estimate a variety of discrete characters, programs with sophisticated methodologies and flexible settings are desired. DiscML performs maximum likelihood estimation for evolutionary rates of discrete characters on a provided phylogeny with the options that correct for unobservable data, rate variations, and unknown prior root probabilities from the empirical data. It gives users options to customize the instantaneous transition rate matrices, or to choose pre-determined matrices from models such as birth-and-death (BD), birth-death-and-innovation (BDI), equal rates (ER), symmetric (SYM), general time-reversible (GTR) and all rates different (ARD). Moreover, we show application examples of DiscML on gene family data and on intron presence/absence data. DiscML was developed as a unified R program for estimating evolutionary rates of discrete characters with no restriction on the number of character states, and with flexibility to use different transition models. DiscML is ideal for the analyses of binary (1s/0s) patterns, multi-gene families, and multistate discrete morphological characteristics.

Sexual selection on female ornaments in the sex-role-reversed Gulf pipefish (Syngnathus scovelli).

PubMed

Flanagan, S P; Johnson, J B; Rose, E; Jones, A G

2014-11-01

Understanding how selection acts on traits individually and in combination is an important step in deciphering the mechanisms driving evolutionary change, but for most species, and especially those in which sexual selection acts more strongly on females than on males, we have no estimates of selection coefficients pertaining to the multivariate sexually selected phenotype. Here, we use a laboratory-based mesocosm experiment to quantify pre- and post-mating selection on female secondary sexual traits in the Gulf pipefish (Syngnathus scovelli), a sexually dimorphic, sex-role-reversed species in which ornamented females compete for access to choosy males. We calculate selection differentials and gradients on female traits, including ornament area, ornament number and body size for three episodes of selection related to female reproductive success (number of mates, number of eggs transferred and number of surviving embryos). Selection is strong on both ornament area and ornament size, and the majority of selection occurs during the premating episode of selection. Interestingly, selection on female body size, which has been detected in previous studies of Gulf pipefish, appears to be indirect, as evidenced by a multivariate analysis of selection gradients. Our results show that sexual selection favours either many bands or larger bands in female Gulf pipefish. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Differential evolution of members of the rhomboid gene family with conservative and divergent patterns.

PubMed

Li, Qi; Zhang, Ning; Zhang, Liangsheng; Ma, Hong

2015-04-01

Rhomboid proteins are intramembrane serine proteases that are involved in a plethora of biological functions, but the evolutionary history of the rhomboid gene family is not clear. We performed a comprehensive molecular evolutionary analysis of the rhomboid gene family and also investigated the organization and sequence features of plant rhomboids in different subfamilies. Our results showed that eukaryotic rhomboids could be divided into five subfamilies (RhoA-RhoD and PARL). Most orthology groups appeared to be conserved only as single or low-copy genes in all lineages in RhoB-RhoD and PARL, whereas RhoA genes underwent several duplication events, resulting in multiple gene copies. These duplication events were due to whole genome duplications in plants and animals and the duplicates might have experienced functional divergence. We also identified a novel group of plant rhomboid (RhoB1) that might have lost their enzymatic activity; their existence suggests that they might have evolved new mechanisms. Plant and animal rhomboids have similar evolutionary patterns. In addition, there are mutations affecting key active sites in RBL8, RBL9 and one of the Brassicaceae PARL duplicates. This study delineates a possible evolutionary scheme for intramembrane proteins and illustrates distinct fates and a mechanism of evolution of gene duplicates. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium

PubMed Central

Willems, Rob J. L.; Top, Janetta; van Schaik, Willem; Leavis, Helen; Bonten, Marc; Sirén, Jukka; Hanage, William P.; Corander, Jukka

2012-01-01

ABSTRACT Enterococcus faecium has recently emerged as an important multiresistant nosocomial pathogen. Defining population structure in this species is required to provide insight into the existence, distribution, and dynamics of specific multiresistant or pathogenic lineages in particular environments, like the hospital. Here, we probe the population structure of E. faecium using Bayesian-based population genetic modeling implemented in Bayesian Analysis of Population Structure (BAPS) software. The analysis involved 1,720 isolates belonging to 519 sequence types (STs) (491 for E. faecium and 28 for Enterococcus faecalis). E. faecium isolates grouped into 13 BAPS (sub)groups, but the large majority (80%) of nosocomial isolates clustered in two subgroups (2-1 and 3-3). Phylogenetic and eBURST analysis of BAPS groups 2 and 3 confirmed the existence of three separate hospital lineages (17, 18, and 78), highlighting different evolutionary trajectories for BAPS 2-1 (lineage 78) and 3-3 (lineage 17 and lineage 18) isolates. Phylogenomic analysis of 29 E. faecium isolates showed agreement between BAPS assignment of STs and their relative positions in the phylogenetic tree. Odds ratio calculation confirmed the significant association between hospital isolates with BAPS 3-3 and lineages 17, 18, and 78. Admixture analysis showed a scarce number of recombination events between the different BAPS groups. For the E. faecium hospital population, we propose an evolutionary model in which strains with a high propensity to colonize and infect hospitalized patients arise through horizontal gene transfer. Once adapted to the distinct hospital niche, this subpopulation becomes isolated, and recombination with other populations declines. PMID:22807567

Comprehensive evolutionary analysis of the Anthroherpon radiation (Coleoptera, Leiodidae, Leptodirini).

PubMed

Njunjić, Iva; Perrard, Adrien; Hendriks, Kasper; Schilthuizen, Menno; Perreau, Michel; Merckx, Vincent; Baylac, Michel; Deharveng, Louis

2018-01-01

The genus Anthroherpon Reitter, 1889 exhibits the most pronounced troglomorphic characters among Coleoptera, and represents one of the most spectacular radiations of subterranean beetles. However, radiation, diversification, and biogeography of this genus have never been studied in a phylogenetic context. This study provides a comprehensive evolutionary analysis of the Anthroherpon radiation, using a dated molecular phylogeny as a framework for understanding Anthroherpon diversification, reconstructing the ancestral range, and exploring troglomorphic diversity. Based on 16 species and 22 subspecies, i.e. the majority of Anthroherpon diversity, we reconstructed the phylogeny using Bayesian analysis of six loci, both mitochondrial and nuclear, comprising a total of 4143 nucleotides. In parallel, a morphometric analysis was carried out with 79 landmarks on the body that were subjected to geometric morphometrics. We optimized morphometric features to phylogeny, in order to recognize the way troglomorphy was expressed in different clades of the tree, and did character evolution analyses. Finally, we reconstructed the ancestral range of the genus using BioGeoBEARS. Besides further elucidating the suprageneric classification of the East-Mediterranean Leptodirini, our main findings also show that Anthroherpon dates back to the Early Miocene (ca. 22 MYA) and that the genus diversified entirely underground. Biogeographic reconstruction of the ancestral range shows the origin of the genus in the area comprising three high mountains in western Montenegro, which is in the accordance with the available data on the paleogeography of the Balkan Peninsula. Character evolution analysis indicates that troglomorphic morphometric traits in Anthroherpon mostly evolve neutrally but may diverge adaptively under syntopic competition.

An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries

PubMed Central

Habermann, Bianca; Bebin, Anne-Gaelle; Herklotz, Stephan; Volkmer, Michael; Eckelt, Kay; Pehlke, Kerstin; Epperlein, Hans Henning; Schackert, Hans Konrad; Wiebe, Glenis; Tanaka, Elly M

2004-01-01

Background The ambystomatid salamander, Ambystoma mexicanum (axolotl), is an important model organism in evolutionary and regeneration research but relatively little sequence information has so far been available. This is a major limitation for molecular studies on caudate development, regeneration and evolution. To address this lack of sequence information we have generated an expressed sequence tag (EST) database for A. mexicanum. Results Two cDNA libraries, one made from stage 18-22 embryos and the other from day-6 regenerating tail blastemas, generated 17,352 sequences. From the sequenced ESTs, 6,377 contigs were assembled that probably represent 25% of the expressed genes in this organism. Sequence comparison revealed significant homology to entries in the NCBI non-redundant database. Further examination of this gene set revealed the presence of genes involved in important cell and developmental processes, including cell proliferation, cell differentiation and cell-cell communication. On the basis of these data, we have performed phylogenetic analysis of key cell-cycle regulators. Interestingly, while cell-cycle proteins such as the cyclin B family display expected evolutionary relationships, the cyclin-dependent kinase inhibitor 1 gene family shows an unusual evolutionary behavior among the amphibians. Conclusions Our analysis reveals the importance of a comprehensive sequence set from a representative of the Caudata and illustrates that the EST sequence database is a rich source of molecular, developmental and regeneration studies. To aid in data mining, the ESTs have been organized into an easily searchable database that is freely available online. PMID:15345051

Analysis of phylogeny and codon usage bias and relationship of GC content, amino acid composition with expression of the structural nif genes.

PubMed

Mondal, Sunil Kanti; Kundu, Sudip; Das, Rabindranath; Roy, Sujit

2016-08-01

Bacteria and archaea have evolved with the ability to fix atmospheric dinitrogen in the form of ammonia, catalyzed by the nitrogenase enzyme complex which comprises three structural genes nifK, nifD and nifH. The nifK and nifD encodes for the beta and alpha subunits, respectively, of component 1, while nifH encodes for component 2 of nitrogenase. Phylogeny based on nifDHK have indicated that Cyanobacteria is closer to Proteobacteria alpha and gamma but not supported by the tree based on 16SrRNA. The evolutionary ancestor for the different trees was also different. The GC1 and GC2% analysis showed more consistency than GC3% which appeared to below for Firmicutes, Cyanobacteria and Euarchaeota while highest in Proteobacteria beta and clearly showed the proportional effect on the codon usage with a few exceptions. Few genes from Firmicutes, Euryarchaeota, Proteobacteria alpha and delta were found under mutational pressure. These nif genes with low and high GC3% from different classes of organisms showed similar expected number of codons. Distribution of the genes and codons, based on codon usage demonstrated opposite pattern for different orientation of mirror plane when compared with each other. Overall our results provide a comprehensive analysis on the evolutionary relationship of the three structural nif genes, nifK, nifD and nifH, respectively, in the context of codon usage bias, GC content relationship and amino acid composition of the encoded proteins and exploration of crucial statistical method for the analysis of positive data with non-constant variance to identify the shape factors of codon adaptation index.

Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon.

PubMed

Chen, Lihong; Hu, Wei; Tan, Shenglong; Wang, Min; Ma, Zhanbing; Zhou, Shiyi; Deng, Xiaomin; Zhang, Yang; Huang, Chao; Yang, Guangxiao; He, Guangyuan

2012-01-01

MAPK cascades are universal signal transduction modules and play important roles in plant growth, development and in response to a variety of biotic and abiotic stresses. Although MAPKs and MAPKKs have been systematically investigated in several plant species including Arabidopsis, rice and poplar, no systematic analysis has been conducted in the emerging monocot model plant Brachypodium distachyon. In the present study, a total of 16 MAPK genes and 12 MAPKK genes were identified from B. distachyon. An analysis of the genomic evolution showed that both tandem and segment duplications contributed significantly to the expansion of MAPK and MAPKK families. Evolutionary relationships within subfamilies were supported by exon-intron organizations and the architectures of conserved protein motifs. Synteny analysis between B. distachyon and the other two plant species of rice and Arabidopsis showed that only one homolog of B. distachyon MAPKs was found in the corresponding syntenic blocks of Arabidopsis, while 13 homologs of B. distachyon MAPKs and MAPKKs were found in that of rice, which was consistent with the speciation process of the three species. In addition, several interactive protein pairs between the two families in B. distachyon were found through yeast two hybrid assay, whereas their orthologs of a pair in Arabidopsis and other plant species were not found to interact with each other. Finally, expression studies of closely related family members among B. distachyon, Arabidopsis and rice showed that even recently duplicated representatives may fulfill different functions and be involved in different signal pathways. Taken together, our data would provide a foundation for evolutionary and functional characterization of MAPK and MAPKK gene families in B. distachyon and other plant species to unravel their biological roles.

Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants.

PubMed

Mohanta, Tapan Kumar; Arora, Pankaj Kumar; Mohanta, Nibedita; Parida, Pratap; Bae, Hanhong

2015-02-06

Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses. The MAPKs are constitute the most downstream module of the three tier MAPK cascade and are phosphorylated by upstream MAP kinase kinases (MAPKK), which are in turn are phosphorylated by MAP kinase kinase kinase (MAPKKK). The MAPKs play pivotal roles in regulation of many cytoplasmic and nuclear substrates, thus regulating several biological processes. A total of 589 MAPKs genes were identified from the genome wide analysis of 40 species. The sequence analysis has revealed the presence of several N- and C-terminal conserved domains. The MAPKs were previously believed to be characterized by the presence of TEY/TDY activation loop motifs. The present study showed that, in addition to presence of activation loop TEY/TDY motifs, MAPKs are also contain MEY, TEM, TQM, TRM, TVY, TSY, TEC and TQY activation loop motifs. Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with Arabidopsis or Oryza MAPKs. We conducted global analysis of the MAPK gene family of plants from lower eukaryotes to higher eukaryotes and analyzed their genomic and evolutionary aspects. Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs. Advance study of newly identified activation loop motifs can provide further information regarding the downstream signaling cascade activated in response to a wide array of stress conditions, as well as plant growth and development.

Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications.

PubMed

Yu, Jingyin; Tehrim, Sadia; Wang, Linhai; Dossa, Komivi; Zhang, Xiurong; Ke, Tao; Liao, Boshou

2017-09-18

The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional divergence of P450s in Brassica after splitting from a common ancestor with Arabidopsis thaliana. Using Hidden Markov Model search and manual curation, we detected that Brassica species have nearly 1.4-fold as many P450 members as A. thaliana. Most P450s in A. thaliana and Brassica species were located on pseudo-chromosomes. The inferred phylogeny indicated that all P450s were clustered into two different subgroups. Analysis of WGD event revealed that different P450 gene families had appeared after evolutionary events of species. For the TD event analyses, the P450s from TD events in Brassica species can be divided into ancient and recent parts. Our comparison of influence of WGD and TD events on the P450 gene superfamily between A. thaliana and Brassica species indicated that the family-specific evolution in the Brassica lineage can be attributed to both WGD and TD, whereas WGD was recognized as the major mechanism for the recent evolution of the P450 super gene family. Expression analysis of P450s from A. thaliana and Brassica species indicated that WGD-type P450s showed the same expression pattern but completely different expression with TD-type P450s across different tissues in Brassica species. Selection force analysis suggested that P450 orthologous gene pairs between A. thaliana and Brassica species underwent negative selection, but no significant differences were found between P450 orthologous gene pairs in A. thaliana-B. rapa and A. thaliana-B. oleracea lineages, as well as in different subgenomes in B. rapa or B. oleracea compared with A. thaliana. This study is the first to investigate the effects of WGD and TD on the evolutionary history and functional divergence of P450 gene families in A. thaliana and Brassica species. This study provides a biology model to study the mechanism of gene family formation, particularly in the context of the evolutionary history of angiosperms, and offers novel insights for the study of angiosperm genomes.

Identification of evolutionary hotspots based on genetic data from multiple terrestrial and aquatic taxa and gap analysis of hotspots in protected lands encompassed by the South Atlantic Landscape Conservation Cooperative.

USGS Publications Warehouse

Robinson, J.; Snider, M.; Duke, J.; Moyer, G.R.

2014-01-01

 The southeastern United States is a recognized hotspot of biodiversity for a variety of aquatic taxa, including fish, amphibians, and mollusks. Unfortunately, the great diversity of the area is accompanied by a large proportion of species at risk of extinction . Gap analysis was employed to assess the representation of evolutionary hotspots in protected lands w h ere an evolutionary hotspot was defined as an area with high evolutionary potential and measured by atypical patterns of genetic divergence, genetic diversity, and to a lesser extent genetic similarity across multiple terrestrial or aquatic taxa. A survey of the primary literature produced 16 terrestrial and 14 aquatic genetic datasets for estimation of genetic divergence and diversity. Relative genetic diversity and divergence values for each terrestrial and aquatic dataset were used for interpolation of multispecies genetic surfaces and subsequent visualization using ArcGIS. The multispecies surfaces interpolated from relative divergences and diversity data identified numerous evolutionary hotspots for both terrestrial and aquatic taxa , many of which were afforded some current protection. For instance, 14% of the cells identified as hotspots of aquatic diversity were encompassed by currently protected areas. Additionally, 25% of the highest 1% of terrestrial diversity cells were afforded some level of protection. In contrast, areas of high and low divergence among species, and areas of high variance in diversity were poorly represented in the protected lands. Of particular interest were two areas that were consistently identified by several different measures as important from a conservation perspective. These included an area encompassing the panhandle of Florida and southern Georgia near the Apalachicola National Forest (displaying varying levels of genetic divergence and greater than average levels of genetic diversity) and a large portion of the coastal regions of North and South Carolina (displaying low genetic divergence and greater than average levels of genetic diversity) . Our results show the utility o f genetic data sets for identifying cross - species patterns of genetic  diversity and divergence (i.e., evolutionary hotspots) in aquatic and terrestrial environments for use in conservation design and delivery across the southeastern United States. 

Evo-devo of human adolescence: beyond disease models of early puberty

PubMed Central

2013-01-01

Despite substantial heritability in pubertal development, much variation remains to be explained, leaving room for the influence of environmental factors to adjust its phenotypic trajectory in the service of fitness goals. Utilizing evolutionary development biology (evo-devo), we examine adolescence as an evolutionary life-history stage in its developmental context. We show that the transition from the preceding stage of juvenility entails adaptive plasticity in response to energy resources, other environmental cues, social needs of adolescence and maturation toward youth and adulthood. Using the evolutionary theory of socialization, we show that familial psychosocial stress fosters a fast life history and reproductive strategy rather than early maturation being just a risk factor for aggression and delinquency. Here we explore implications of an evolutionary-developmental-endocrinological-anthropological framework for theory building, while illuminating new directions for research. PMID:23627891

The Simulation and Analysis of an Evolutionary Model of Deoxyribonucleic Acid (DNA).

DTIC Science & Technology

1983-09-01

current interest in evolutionary biology . This section identifies the organization of the remainder of the paper. The second chapter reports the...the field of evolutionary biology . 77 APPENDIX 78 APPENDIX A PROGRAM SOURCE LISTING -79 PROGRAM SOURCE LISTING 00005 PROGRAM (COMPUTERANDOM MUTATIONS...34Some Theoretical Aspects of the Problem of Life Origin," Journal 2f Theoreical Biology : 13-23, 1975. 27. Chirpich, Thomas P. "Rates of Protein

Evolutionary space platform concept study. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1982-01-01

The Evolutionary Space Platform Concept Study encompassed a 10 month effort to define, evaluate and compare approaches and concepts for evolving unmanned and manned capability platforms beyond the current Space Platform concepts to an evolutionary goal of establishing a permanent manned presence in space. Areas addressed included: special emphasis trade studies on the current unmanned concept, assessment of manned platform concepts, and utility analysis of a manned platform for defense related missions.

Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies

PubMed Central

Majeský, Ľuboš; Schwarzacher, Trude; Gornall, Richard; Heslop-Harrison, Pat

2017-01-01

Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems. PMID:28182646

Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies.

PubMed

M Salih, Rubar Hussein; Majeský, Ľuboš; Schwarzacher, Trude; Gornall, Richard; Heslop-Harrison, Pat

2017-01-01

Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems.

Mean-field approximations of fixation time distributions of evolutionary game dynamics on graphs

NASA Astrophysics Data System (ADS)

Ying, Li-Min; Zhou, Jie; Tang, Ming; Guan, Shu-Guang; Zou, Yong

2018-02-01

The mean fixation time is often not accurate for describing the timescales of fixation probabilities of evolutionary games taking place on complex networks. We simulate the game dynamics on top of complex network topologies and approximate the fixation time distributions using a mean-field approach. We assume that there are two absorbing states. Numerically, we show that the mean fixation time is sufficient in characterizing the evolutionary timescales when network structures are close to the well-mixing condition. In contrast, the mean fixation time shows large inaccuracies when networks become sparse. The approximation accuracy is determined by the network structure, and hence by the suitability of the mean-field approach. The numerical results show good agreement with the theoretical predictions.

Genomics and evolutionary aspect of calcium signaling event in calmodulin and calmodulin-like proteins in plants.

PubMed

Mohanta, Tapan Kumar; Kumar, Pradeep; Bae, Hanhong

2017-02-03

Ca 2+ ion is a versatile second messenger that operate in a wide ranges of cellular processes that impact nearly every aspect of life. Ca 2+ regulates gene expression and biotic and abiotic stress responses in organisms ranging from unicellular algae to multi-cellular higher plants through the cascades of calcium signaling processes. In this study, we deciphered the genomics and evolutionary aspects of calcium signaling event of calmodulin (CaM) and calmodulin like- (CML) proteins. We studied the CaM and CML gene family of 41 different species across the plant lineages. Genomic analysis showed that plant encodes more calmodulin like-protein than calmodulins. Further analyses showed, the majority of CMLs were intronless, while CaMs were intron rich. Multiple sequence alignment showed, the EF-hand domain of CaM contains four conserved D-x-D motifs, one in each EF-hand while CMLs contain only one D-x-D-x-D motif in the fourth EF-hand. Phylogenetic analysis revealed that, the CMLs were evolved earlier than CaM and later diversified. Gene expression analysis demonstrated that different CaM and CMLs genes were express differentially in different tissues in a spatio-temporal manner. In this study we provided in detailed genome-wide identifications and characterization of CaM and CML protein family, phylogenetic relationships, and domain structure. Expression study of CaM and CML genes were conducted in Glycine max and Phaseolus vulgaris. Our study provides a strong foundation for future functional research in CaM and CML gene family in plant kingdom.

EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity

PubMed Central

Nahum, Laila A; Reynolds, Matthew T; Wang, Zhengyuan O; Faith, Jeremiah J; Jonna, Rahul; Jiang, Zhi J; Meyer, Thomas J; Pollock, David D

2006-01-01

Background Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; ) to begin to address this. Description EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs. Conclusion EGenBio was designed to serve as a platform for tools and resources to ease combined analysis in evolution, genomics, and biodiversity. PMID:17118150

Random drift versus selection in academic vocabulary: an evolutionary analysis of published keywords.

PubMed

Bentley, R Alexander

2008-08-27

The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example.

Random Drift versus Selection in Academic Vocabulary: An Evolutionary Analysis of Published Keywords

PubMed Central

Bentley, R. Alexander

2008-01-01

The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example. PMID:18728786

Phylogenetics.

PubMed

Sleator, Roy D

2011-04-01

The recent rapid expansion in the DNA and protein databases, arising from large-scale genomic and metagenomic sequence projects, has forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet's inhabitants. Advances in phylogenetic analysis have greatly transformed our view of the landscape of evolutionary biology, transcending the view of the tree of life that has shaped evolutionary theory since Darwinian times. Indeed, modern phylogenetic analysis no longer focuses on the restricted Darwinian-Mendelian model of vertical gene transfer, but must also consider the significant degree of lateral gene transfer, which connects and shapes almost all living things. Herein, I review the major tree-building methods, their strengths, weaknesses and future prospects.

NexGen PVAs: Incorporating Eco-Evolutionary Processes into Population Viability Models

EPA Science Inventory

We examine how the integration of evolutionary and ecological processes in population dynamics – an emerging framework in ecology – could be incorporated into population viability analysis (PVA). Driven by parallel, complementary advances in population genomics and computational ...

A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus.

PubMed

Lyu, Xueliang; Shen, Cuicui; Xie, Jiatao; Fu, Yanping; Jiang, Daohong; Hu, Zijin; Tang, Lihua; Tang, Liguang; Ding, Feng; Li, Kunfei; Wu, Song; Hu, Yanping; Luo, Lilian; Li, Yuanhao; Wang, Qihua; Li, Guoqing; Cheng, Jiasen

2015-08-11

Carbon fixation pathway of plants (CFPP) in photosynthesis converts solar energy to biomass, bio-products and biofuel. Intriguingly, a large number of heterotrophic fungi also possess enzymes functionally associated with CFPP, raising the questions about their roles in fungal development and in evolution. Here, we report on the presence of 17 CFPP associated enzymes (ten in Calvin-Benson-Basham reductive pentose phosphate pathway and seven in C4-dicarboxylic acid cycle) in the genome of Sclerotinia sclerotiorum, a heterotrophic phytopathogenic fungus, and only two unique enzymes: ribulose-1, 5-bisphosphate carboxylase-oxygenase (Rubisco) and phosphoribulokinase (PRK) were absent. This data suggested an incomplete CFPP-like pathway (CLP) in fungi. Functional profile analysis demonstrated that the activity of the incomplete CLP was dramatically regulated during different developmental stages of S. sclerotiorum. Subsequent experiments confirmed that many of them were essential to the virulence and/or sclerotial formation. Most of the CLP associated genes are conserved in fungi. Phylogenetic analysis showed that many of them have undergone gene duplication, gene acquisition or loss and functional diversification in evolutionary history. These findings showed an evolutionary links in the carbon fixation processes of autotrophs and heterotrophs and implicated the functions of related genes were in course of continuous change in different organisms in evolution.

Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform1[OPEN

PubMed Central

Sun, Pengchuan; Li, Yuxian; Liu, Yinzhe; Yu, Jigao; Ma, Xuelian; Sun, Sangrong; Yang, Nanshan; Xia, Ruiyan; Lei, Tianyu; Liu, Xiaojian; Jiao, Beibei; Xing, Yue; Ge, Weina; Wang, Li; Song, Xiaoming; Yuan, Min; Guo, Di; Zhang, Lan; Zhang, Jiaqi; Chen, Wei; Pan, Yuxin; Liu, Tao; Jin, Ling; Sun, Jinshuai; Yu, Jiaxiang; Duan, Xueqian; Shen, Shaoqi; Qin, Jun; Zhang, Meng-chen; Paterson, Andrew H.

2017-01-01

Mainly due to their economic importance, genomes of 10 legumes, including soybean (Glycine max), wild peanut (Arachis duranensis and Arachis ipaensis), and barrel medic (Medicago truncatula), have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape (Vitis vinifera) and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by widespread gene losses after the polyploidizations. Notably, high similarity in gene retention between recently duplicated chromosomes in soybean supported the likely autopolyploidy nature of its tetraploid ancestor. Moreover, although most gene losses were nearly random, largely but not fully described by geometric distribution, we showed that polyploidization contributed divergently to the copy number variation of important gene families. Besides, we showed significantly divergent evolutionary levels among legumes and, by performing synonymous nucleotide substitutions at synonymous sites correction, redated major evolutionary events during their expansion. This effort laid a solid foundation for further genomics exploration in the legume research community and beyond. We describe only a tiny fraction of legume comparative genomics analysis that we performed; more information was stored in the newly constructed Legume Comparative Genomics Research Platform (www.legumegrp.org). PMID:28325848

Archaea: The First Domain of Diversified Life

PubMed Central

Caetano-Anollés, Gustavo; Nasir, Arshan; Zhou, Kaiyue; Caetano-Anollés, Derek; Mittenthal, Jay E.; Sun, Feng-Jie; Kim, Kyung Mo

2014-01-01

The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea. PMID:24987307

Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region

PubMed Central

Dolz, Roser; Valle, Rosa; Perera, Carmen L.; Bertran, Kateri; Frías, Maria T.; Majó, Natàlia; Ganges, Llilianne; Pérez, Lester J.

2013-01-01

Background Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains. Methodology/Principal Findings Sequences of the hyper-variable region of the VP2 (HVR-VP2) gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank database; Cuban sequences were obtained in the current work. All sequences were analysed by Bayesian phylogeographic analysis, implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST), Bayesian Tip-association Significance testing (BaTS) and Spatial Phylogenetic Reconstruction of Evolutionary Dynamics (SPREAD) software packages. Selection pressure on the HVR-VP2 was also assessed. The phylogeographic association-trait analysis showed that viruses sampled from individual countries tend to cluster together, suggesting a geographic pattern for IBDV strains. Spatial analysis from this study revealed that strains carrying sequences that were linked to increased virulence of IBDV appeared in Iran in 1981 and spread to Western Europe (Belgium) in 1987, Africa (Egypt) around 1990, East Asia (China and Japan) in 1993, the Caribbean Region (Cuba) by 1995 and South America (Brazil) around 2000. Selection pressure analysis showed that several codons in the HVR-VP2 region were under purifying selection. Conclusions/Significance To our knowledge, this work is the first study applying the Bayesian phylogeographic reconstruction approach to analyse the emergence and spread of vvIBDV strains worldwide. PMID:23805195

Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region.

PubMed

Alfonso-Morales, Abdulahi; Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L; Bertran, Kateri; Frías, Maria T; Majó, Natàlia; Ganges, Llilianne; Pérez, Lester J

2013-01-01

Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains. Sequences of the hyper-variable region of the VP2 (HVR-VP2) gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank database; Cuban sequences were obtained in the current work. All sequences were analysed by Bayesian phylogeographic analysis, implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST), Bayesian Tip-association Significance testing (BaTS) and Spatial Phylogenetic Reconstruction of Evolutionary Dynamics (SPREAD) software packages. Selection pressure on the HVR-VP2 was also assessed. The phylogeographic association-trait analysis showed that viruses sampled from individual countries tend to cluster together, suggesting a geographic pattern for IBDV strains. Spatial analysis from this study revealed that strains carrying sequences that were linked to increased virulence of IBDV appeared in Iran in 1981 and spread to Western Europe (Belgium) in 1987, Africa (Egypt) around 1990, East Asia (China and Japan) in 1993, the Caribbean Region (Cuba) by 1995 and South America (Brazil) around 2000. Selection pressure analysis showed that several codons in the HVR-VP2 region were under purifying selection. To our knowledge, this work is the first study applying the Bayesian phylogeographic reconstruction approach to analyse the emergence and spread of vvIBDV strains worldwide.

Evolutionary process of deep-sea bathymodiolus mussels.

PubMed

Miyazaki, Jun-Ichi; de Oliveira Martins, Leonardo; Fujita, Yuko; Matsumoto, Hiroto; Fujiwara, Yoshihiro

2010-04-27

Since the discovery of deep-sea chemosynthesis-based communities, much work has been done to clarify their organismal and environmental aspects. However, major topics remain to be resolved, including when and how organisms invade and adapt to deep-sea environments; whether strategies for invasion and adaptation are shared by different taxa or unique to each taxon; how organisms extend their distribution and diversity; and how they become isolated to speciate in continuous waters. Deep-sea mussels are one of the dominant organisms in chemosynthesis-based communities, thus investigations of their origin and evolution contribute to resolving questions about life in those communities. We investigated worldwide phylogenetic relationships of deep-sea Bathymodiolus mussels and their mytilid relatives by analyzing nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 4 (ND4) genes. Phylogenetic analysis of the concatenated sequence data showed that mussels of the subfamily Bathymodiolinae from vents and seeps were divided into four groups, and that mussels of the subfamily Modiolinae from sunken wood and whale carcasses assumed the outgroup position and shallow-water modioline mussels were positioned more distantly to the bathymodioline mussels. We provisionally hypothesized the evolutionary history of Bathymodilolus mussels by estimating evolutionary time under a relaxed molecular clock model. Diversification of bathymodioline mussels was initiated in the early Miocene, and subsequently diversification of the groups occurred in the early to middle Miocene. The phylogenetic relationships support the "Evolutionary stepping stone hypothesis," in which mytilid ancestors exploited sunken wood and whale carcasses in their progressive adaptation to deep-sea environments. This hypothesis is also supported by the evolutionary transition of symbiosis in that nutritional adaptation to the deep sea proceeded from extracellular to intracellular symbiotic states in whale carcasses. The estimated evolutionary time suggests that the mytilid ancestors were able to exploit whales during adaptation to the deep sea.

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.

An Orthogonal Evolutionary Algorithm With Learning Automata for Multiobjective Optimization.

PubMed

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

2016-12-01

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

Why flying dogs are rare: A general theory of luck in evolutionary transitions.

PubMed

Fleming, Leonore; Brandon, Robert

2015-02-01

There is a worry that the 'major transitions in evolution' represent an arbitrary group of events. This worry is warranted, and we show why. We argue that the transition to a new level of hierarchy necessarily involves a nonselectionist chance process. Thus any unified theory of evolutionary transitions must be more like a general theory of fortuitous luck, rather than a rigid formulation of expected events. We provide a systematic account of evolutionary transitions based on a second-order regularity of chance events, as stipulated by the ZFEL (Zero Force Evolutionary Law). And in doing so, we make evolutionary transitions explainable and predictable, and so not entirely contingent after all. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mean-Potential Law in Evolutionary Games

NASA Astrophysics Data System (ADS)

Nałecz-Jawecki, Paweł; Miekisz, Jacek

2018-01-01

The Letter presents a novel way to connect random walks, stochastic differential equations, and evolutionary game theory. We introduce a new concept of a potential function for discrete-space stochastic systems. It is based on a correspondence between one-dimensional stochastic differential equations and random walks, which may be exact not only in the continuous limit but also in finite-state spaces. Our method is useful for computation of fixation probabilities in discrete stochastic dynamical systems with two absorbing states. We apply it to evolutionary games, formulating two simple and intuitive criteria for evolutionary stability of pure Nash equilibria in finite populations. In particular, we show that the 1 /3 law of evolutionary games, introduced by Nowak et al. [Nature, 2004], follows from a more general mean-potential law.

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

PubMed Central

Vanneste, Kevin; Baele, Guy; Maere, Steven; Van de Peer, Yves

2014-01-01

Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous–Paleogene (K–Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K–Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids. PMID:24835588

Effects of Mitochondrial DNA Rate Variation on Reconstruction of Pleistocene Demographic History in a Social Avian Species, Pomatostomus superciliosus

PubMed Central

Norman, Janette A.; Blackmore, Caroline J.; Rourke, Meaghan; Christidis, Les

2014-01-01

Mitochondrial sequence data is often used to reconstruct the demographic history of Pleistocene populations in an effort to understand how species have responded to past climate change events. However, departures from neutral equilibrium conditions can confound evolutionary inference in species with structured populations or those that have experienced periods of population expansion or decline. Selection can affect patterns of mitochondrial DNA variation and variable mutation rates among mitochondrial genes can compromise inferences drawn from single markers. We investigated the contribution of these factors to patterns of mitochondrial variation and estimates of time to most recent common ancestor (TMRCA) for two clades in a co-operatively breeding avian species, the white-browed babbler Pomatostomus superciliosus. Both the protein-coding ND3 gene and hypervariable domain I control region sequences showed departures from neutral expectations within the superciliosus clade, and a two-fold difference in TMRCA estimates. Bayesian phylogenetic analysis provided evidence of departure from a strict clock model of molecular evolution in domain I, leading to an over-estimation of TMRCA for the superciliosus clade at this marker. Our results suggest mitochondrial studies that attempt to reconstruct Pleistocene demographic histories should rigorously evaluate data for departures from neutral equilibrium expectations, including variation in evolutionary rates across multiple markers. Failure to do so can lead to serious errors in the estimation of evolutionary parameters and subsequent demographic inferences concerning the role of climate as a driver of evolutionary change. These effects may be especially pronounced in species with complex social structures occupying heterogeneous environments. We propose that environmentally driven differences in social structure may explain observed differences in evolutionary rate of domain I sequences, resulting from longer than expected retention times for matriarchal lineages in the superciliosus clade. PMID:25181547

The Evolutionary History of Protein Domains Viewed by Species Phylogeny

PubMed Central

Yang, Song; Bourne, Philip E.

2009-01-01

Background Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest. Methodology/Principal Findings A methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed. Conclusions/Significance We show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species. PMID:20041107

Evolutionary inevitability of sexual antagonism.

PubMed

Connallon, Tim; Clark, Andrew G

2014-02-07

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

Reconstructing evolutionary trees in parallel for massive sequences.

PubMed

Zou, Quan; Wan, Shixiang; Zeng, Xiangxiang; Ma, Zhanshan Sam

2017-12-14

Building the evolutionary trees for massive unaligned DNA sequences is challenging and crucial. However, reconstructing evolutionary tree for ultra-large sequences is hard. Massive multiple sequence alignment is also challenging and time/space consuming. Hadoop and Spark are developed recently, which bring spring light for the classical computational biology problems. In this paper, we tried to solve the multiple sequence alignment and evolutionary reconstruction in parallel. HPTree, which is developed in this paper, can deal with big DNA sequence files quickly. It works well on the >1GB files, and gets better performance than other evolutionary reconstruction tools. Users could use HPTree for reonstructing evolutioanry trees on the computer clusters or cloud platform (eg. Amazon Cloud). HPTree could help on population evolution research and metagenomics analysis. In this paper, we employ the Hadoop and Spark platform and design an evolutionary tree reconstruction software tool for unaligned massive DNA sequences. Clustering and multiple sequence alignment are done in parallel. Neighbour-joining model was employed for the evolutionary tree building. We opened our software together with source codes via http://lab.malab.cn/soft/HPtree/ .

Evolutionary adaptations: theoretical and practical implications for visual ergonomics.

PubMed

Fostervold, Knut Inge; Watten, Reidulf G; Volden, Frode

2014-01-01

The literature discussing visual ergonomics often mention that human vision is adapted to light emitted by the sun. However, theoretical and practical implications of this viewpoint is seldom discussed or taken into account. The paper discusses some of the main theoretical implications of an evolutionary approach to visual ergonomics. Based on interactional theory and ideas from ecological psychology an evolutionary stress model is proposed as a theoretical framework for future research in ergonomics and human factors. The model stresses the importance of developing work environments that fits with our evolutionary adaptations. In accordance with evolutionary psychology, the environment of evolutionary adaptedness (EEA) and evolutionarily-novel environments (EN) are used as key concepts. Using work with visual display units (VDU) as an example, the paper discusses how this knowledge can be utilized in an ergonomic analysis of risk factors in the work environment. The paper emphasises the importance of incorporating evolutionary theory in the field of ergonomics. Further, the paper encourages scientific practices that further our understanding of any phenomena beyond the borders of traditional proximal explanations.

Neuronal boost to evolutionary dynamics.

PubMed

de Vladar, Harold P; Szathmáry, Eörs

2015-12-06

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

Eco-evolutionary dynamics in a coevolving host-virus system.

PubMed

Frickel, Jens; Sieber, Michael; Becks, Lutz

2016-04-01

Eco-evolutionary dynamics have been shown to be important for understanding population and community stability and their adaptive potential. However, coevolution in the framework of eco-evolutionary theory has not been addressed directly. Combining experiments with an algal host and its viral parasite, and mathematical model analyses we show eco-evolutionary dynamics in antagonistic coevolving populations. The interaction between antagonists initially resulted in arms race dynamics (ARD) with selective sweeps, causing oscillating host-virus population dynamics. However, ARD ended and populations stabilised after the evolution of a general resistant host, whereas a trade-off between host resistance and growth then maintained host diversity over time (trade-off driven dynamics). Most importantly, our study shows that the interaction between ecology and evolution had important consequences for the predictability of the mode and tempo of adaptive change and for the stability and adaptive potential of populations. © 2016 John Wiley & Sons Ltd/CNRS.

Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution

PubMed Central

Mannakee, Brian K.; Gutenkunst, Ryan N.

2016-01-01

The long-held principle that functionally important proteins evolve slowly has recently been challenged by studies in mice and yeast showing that the severity of a protein knockout only weakly predicts that protein’s rate of evolution. However, the relevance of these studies to evolutionary changes within proteins is unknown, because amino acid substitutions, unlike knockouts, often only slightly perturb protein activity. To quantify the phenotypic effect of small biochemical perturbations, we developed an approach to use computational systems biology models to measure the influence of individual reaction rate constants on network dynamics. We show that this dynamical influence is predictive of protein domain evolutionary rate within networks in vertebrates and yeast, even after controlling for expression level and breadth, network topology, and knockout effect. Thus, our results not only demonstrate the importance of protein domain function in determining evolutionary rate, but also the power of systems biology modeling to uncover unanticipated evolutionary forces. PMID:27380265

Learning dynamics explains human behaviour in prisoner's dilemma on networks.

PubMed

Cimini, Giulio; Sánchez, Angel

2014-05-06

Cooperative behaviour lies at the very basis of human societies, yet its evolutionary origin remains a key unsolved puzzle. Whereas reciprocity or conditional cooperation is one of the most prominent mechanisms proposed to explain the emergence of cooperation in social dilemmas, recent experimental findings on networked Prisoner's Dilemma games suggest that conditional cooperation also depends on the previous action of the player-namely on the 'mood' in which the player is currently in. Roughly, a majority of people behave as conditional cooperators if they cooperated in the past, whereas they ignore the context and free ride with high probability if they did not. However, the ultimate origin of this behaviour represents a conundrum itself. Here, we aim specifically to provide an evolutionary explanation of moody conditional cooperation (MCC). To this end, we perform an extensive analysis of different evolutionary dynamics for players' behavioural traits-ranging from standard processes used in game theory based on pay-off comparison to others that include non-economic or social factors. Our results show that only a dynamic built upon reinforcement learning is able to give rise to evolutionarily stable MCC, and at the end to reproduce the human behaviours observed in the experiments.

An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism.

PubMed

Mélade, Julien; Wieseke, Nicolas; Ramasindrazana, Beza; Flores, Olivier; Lagadec, Erwan; Gomard, Yann; Goodman, Steven M; Dellagi, Koussay; Pascalis, Hervé

2016-04-12

An eco-epidemiological investigation was carried out on Madagascar bat communities to better understand the evolutionary mechanisms and environmental factors that affect virus transmission among bat species in closely related members of the genus Morbillivirus, currently referred to as Unclassified Morbilli-related paramyxoviruses (UMRVs). A total of 947 bats were investigated originating from 52 capture sites (22 caves, 18 buildings, and 12 outdoor sites) distributed over different bioclimatic zones of the island. Using RT-PCR targeting the L-polymerase gene of the Paramyxoviridae family, we found that 10.5% of sampled bats were infected, representing six out of seven families and 15 out of 31 species analyzed. Univariate analysis indicates that both abiotic and biotic factors may promote viral infection. Using generalized linear modeling of UMRV infection overlaid on biotic and abiotic variables, we demonstrate that sympatric occurrence of bats is a major factor for virus transmission. Phylogenetic analyses revealed that all paramyxoviruses infecting Malagasy bats are UMRVs and showed little host specificity. Analyses using the maximum parsimony reconciliation tool CoRe-PA, indicate that host-switching, rather than co-speciation, is the dominant macro-evolutionary mechanism of UMRVs among Malagasy bats.

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

PubMed Central

2017-01-01

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

On the Evolution of the Cardiac Pacemaker

PubMed Central

Burkhard, Silja; van Eif, Vincent; Garric, Laurence; Christoffels, Vincent M.; Bakkers, Jeroen

2017-01-01

The rhythmic contraction of the heart is initiated and controlled by an intrinsic pacemaker system. Cardiac contractions commence at very early embryonic stages and coordination remains crucial for survival. The underlying molecular mechanisms of pacemaker cell development and function are still not fully understood. Heart form and function show high evolutionary conservation. Even in simple contractile cardiac tubes in primitive invertebrates, cardiac function is controlled by intrinsic, autonomous pacemaker cells. Understanding the evolutionary origin and development of cardiac pacemaker cells will help us outline the important pathways and factors involved. Key patterning factors, such as the homeodomain transcription factors Nkx2.5 and Shox2, and the LIM-homeodomain transcription factor Islet-1, components of the T-box (Tbx), and bone morphogenic protein (Bmp) families are well conserved. Here we compare the dominant pacemaking systems in various organisms with respect to the underlying molecular regulation. Comparative analysis of the pathways involved in patterning the pacemaker domain in an evolutionary context might help us outline a common fundamental pacemaker cell gene programme. Special focus is given to pacemaker development in zebrafish, an extensively used model for vertebrate development. Finally, we conclude with a summary of highly conserved key factors in pacemaker cell development and function. PMID:29367536

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

PubMed

Diniz-Filho, José Alexandre Felizola; Raia, Pasquale

2017-06-28

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

Genetic Architecture of Hybrid Male Sterility in Drosophila: Analysis of Intraspecies Variation for Interspecies Isolation

PubMed Central

Reed, Laura K.; LaFlamme, Brooke A.; Markow, Therese A.

2008-01-01

Background The genetic basis of postzygotic isolation is a central puzzle in evolutionary biology. Evolutionary forces causing hybrid sterility or inviability act on the responsible genes while they still are polymorphic, thus we have to study these traits as they arise, before isolation is complete. Methodology/Principal Findings Isofemale strains of D. mojavensis vary significantly in their production of sterile F1 sons when females are crossed to D. arizonae males. We took advantage of the intraspecific polymorphism, in a novel design, to perform quantitative trait locus (QTL) mapping analyses directly on F1 hybrid male sterility itself. We found that the genetic architecture of the polymorphism for hybrid male sterility (HMS) in the F1 is complex, involving multiple QTL, epistasis, and cytoplasmic effects. Conclusions/Significance The role of extensive intraspecific polymorphism, multiple QTL, and epistatic interactions in HMS in this young species pair shows that HMS is arising as a complex trait in this system. Directional selection alone would be unlikely to maintain polymorphism at multiple loci, thus we hypothesize that directional selection is unlikely to be the only evolutionary force influencing postzygotic isolation. PMID:18728782

Maintaining replication origins in the face of genomic change.

PubMed

Di Rienzi, Sara C; Lindstrom, Kimberly C; Mann, Tobias; Noble, William S; Raghuraman, M K; Brewer, Bonita J

2012-10-01

Origins of replication present a paradox to evolutionary biologists. As a collection, they are absolutely essential genomic features, but individually are highly redundant and nonessential. It is therefore difficult to predict to what extent and in what regard origins are conserved over evolutionary time. Here, through a comparative genomic analysis of replication origins and chromosomal replication patterns in the budding yeasts Saccharomyces cerevisiae and Lachancea waltii, we assess to what extent replication origins survived genomic change produced from 150 million years of evolution. We find that L. waltii origins exhibit a core consensus sequence and nucleosome occupancy pattern highly similar to those of S. cerevisiae origins. We further observe that the overall progression of chromosomal replication is similar between L. waltii and S. cerevisiae. Nevertheless, few origins show evidence of being conserved in location between the two species. Among the conserved origins are those surrounding centromeres and adjacent to histone genes, suggesting that proximity to an origin may be important for their regulation. We conclude that, over evolutionary time, origins maintain sequence, structure, and regulation, but are continually being created and destroyed, with the result that their locations are generally not conserved.

Maintaining replication origins in the face of genomic change

PubMed Central

Di Rienzi, Sara C.; Lindstrom, Kimberly C.; Mann, Tobias; Noble, William S.; Raghuraman, M.K.; Brewer, Bonita J.

2012-01-01

Origins of replication present a paradox to evolutionary biologists. As a collection, they are absolutely essential genomic features, but individually are highly redundant and nonessential. It is therefore difficult to predict to what extent and in what regard origins are conserved over evolutionary time. Here, through a comparative genomic analysis of replication origins and chromosomal replication patterns in the budding yeasts Saccharomyces cerevisiae and Lachancea waltii, we assess to what extent replication origins survived genomic change produced from 150 million years of evolution. We find that L. waltii origins exhibit a core consensus sequence and nucleosome occupancy pattern highly similar to those of S. cerevisiae origins. We further observe that the overall progression of chromosomal replication is similar between L. waltii and S. cerevisiae. Nevertheless, few origins show evidence of being conserved in location between the two species. Among the conserved origins are those surrounding centromeres and adjacent to histone genes, suggesting that proximity to an origin may be important for their regulation. We conclude that, over evolutionary time, origins maintain sequence, structure, and regulation, but are continually being created and destroyed, with the result that their locations are generally not conserved. PMID:22665441

A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases.

PubMed

Cummins, Carla A; McInerney, James O

2011-12-01

Current phylogenetic methods attempt to account for evolutionary rate variation across characters in a matrix. This is generally achieved by the use of sophisticated evolutionary models, combined with dense sampling of large numbers of characters. However, systematic biases and superimposed substitutions make this task very difficult. Model adequacy can sometimes be achieved at the cost of adding large numbers of free parameters, with each parameter being optimized according to some criterion, resulting in increased computation times and large variances in the model estimates. In this study, we develop a simple approach that estimates the relative evolutionary rate of each homologous character. The method that we describe uses the similarity between characters as a proxy for evolutionary rate. In this article, we work on the premise that if the character-state distribution of a homologous character is similar to many other characters, then this character is likely to be relatively slowly evolving. If the character-state distribution of a homologous character is not similar to many or any of the rest of the characters in a data set, then it is likely to be the result of rapid evolution. We show that in some test cases, at least, the premise can hold and the inferences are robust. Importantly, the method does not use a "starting tree" to make the inference and therefore is tree independent. We demonstrate that this approach can work as well as a maximum likelihood (ML) approach, though the ML method needs to have a known phylogeny, or at least a very good estimate of that phylogeny. We then demonstrate some uses for this method of analysis, including the improvement in phylogeny reconstruction for both deep-level and recent relationships and overcoming systematic biases such as base composition bias. Furthermore, we compare this approach to two well-established methods for reweighting or removing characters. These other methods are tree-based and we show that they can be systematically biased. We feel this method can be useful for phylogeny reconstruction, understanding evolutionary rate variation, and for understanding selection variation on different characters.

The Inevitability of Ethnocentrism Revisited: Ethnocentrism Diminishes As Mobility Increases.

PubMed

De, Soham; Gelfand, Michele J; Nau, Dana; Roos, Patrick

2015-12-08

Nearly all major conflicts across the globe, both current and historical, are characterized by individuals defining themselves and others by group membership. This existence of group-biased behavior (in-group favoring and out-group hostile) has been well established empirically, and has been shown to be an inevitable outcome in many evolutionary studies. Thus it is puzzling that statistics show violence and out-group conflict declining dramatically over the past few centuries of human civilization. Using evolutionary game-theoretic models, we solve this puzzle by showing for the first time that out-group hostility is dramatically reduced by mobility. Technological and societal advances over the past centuries have greatly increased the degree to which humans change physical locations, and our results show that in highly mobile societies, one's choice of action is more likely to depend on what individual one is interacting with, rather than the group to which the individual belongs. Our empirical analysis of archival data verifies that contexts with high residential mobility indeed have less out-group hostility than those with low mobility. This work suggests that, in fact, group-biased behavior that discriminates against out-groups is not inevitable after all.

The Inevitability of Ethnocentrism Revisited: Ethnocentrism Diminishes As Mobility Increases

PubMed Central

De, Soham; Gelfand, Michele J.; Nau, Dana; Roos, Patrick

2015-01-01

Nearly all major conflicts across the globe, both current and historical, are characterized by individuals defining themselves and others by group membership. This existence of group-biased behavior (in-group favoring and out-group hostile) has been well established empirically, and has been shown to be an inevitable outcome in many evolutionary studies. Thus it is puzzling that statistics show violence and out-group conflict declining dramatically over the past few centuries of human civilization. Using evolutionary game-theoretic models, we solve this puzzle by showing for the first time that out-group hostility is dramatically reduced by mobility. Technological and societal advances over the past centuries have greatly increased the degree to which humans change physical locations, and our results show that in highly mobile societies, one’s choice of action is more likely to depend on what individual one is interacting with, rather than the group to which the individual belongs. Our empirical analysis of archival data verifies that contexts with high residential mobility indeed have less out-group hostility than those with low mobility. This work suggests that, in fact, group-biased behavior that discriminates against out-groups is not inevitable after all. PMID:26644192

Comparative genomic analysis of SET domain family reveals the origin, expansion, and putative function of the arthropod-specific SmydA genes as histone modifiers in insects.

PubMed

Jiang, Feng; Liu, Qing; Wang, Yanli; Zhang, Jie; Wang, Huimin; Song, Tianqi; Yang, Meiling; Wang, Xianhui; Kang, Le

2017-06-01

The SET domain is an evolutionarily conserved motif present in histone lysine methyltransferases, which are important in the regulation of chromatin and gene expression in animals. In this study, we searched for SET domain-containing genes (SET genes) in all of the 147 arthropod genomes sequenced at the time of carrying out this experiment to understand the evolutionary history by which SET domains have evolved in insects. Phylogenetic and ancestral state reconstruction analysis revealed an arthropod-specific SET gene family, named SmydA, that is ancestral to arthropod animals and specifically diversified during insect evolution. Considering that pseudogenization is the most probable fate of the new emerging gene copies, we provided experimental and evolutionary evidence to demonstrate their essential functions. Fluorescence in situ hybridization analysis and in vitro methyltransferase activity assays showed that the SmydA-2 gene was transcriptionally active and retained the original histone methylation activity. Expression knockdown by RNA interference significantly increased mortality, implying that the SmydA genes may be essential for insect survival. We further showed predominantly strong purifying selection on the SmydA gene family and a potential association between the regulation of gene expression and insect phenotypic plasticity by transcriptome analysis. Overall, these data suggest that the SmydA gene family retains essential functions that may possibly define novel regulatory pathways in insects. This work provides insights into the roles of lineage-specific domain duplication in insect evolution. © The Authors 2017. Published by Oxford University Press.

Comparative genomic analysis of SET domain family reveals the origin, expansion, and putative function of the arthropod-specific SmydA genes as histone modifiers in insects

PubMed Central

Jiang, Feng; Liu, Qing; Wang, Yanli; Zhang, Jie; Wang, Huimin; Song, Tianqi; Yang, Meiling

2017-01-01

Abstract The SET domain is an evolutionarily conserved motif present in histone lysine methyltransferases, which are important in the regulation of chromatin and gene expression in animals. In this study, we searched for SET domain–containing genes (SET genes) in all of the 147 arthropod genomes sequenced at the time of carrying out this experiment to understand the evolutionary history by which SET domains have evolved in insects. Phylogenetic and ancestral state reconstruction analysis revealed an arthropod-specific SET gene family, named SmydA, that is ancestral to arthropod animals and specifically diversified during insect evolution. Considering that pseudogenization is the most probable fate of the new emerging gene copies, we provided experimental and evolutionary evidence to demonstrate their essential functions. Fluorescence in situ hybridization analysis and in vitro methyltransferase activity assays showed that the SmydA-2 gene was transcriptionally active and retained the original histone methylation activity. Expression knockdown by RNA interference significantly increased mortality, implying that the SmydA genes may be essential for insect survival. We further showed predominantly strong purifying selection on the SmydA gene family and a potential association between the regulation of gene expression and insect phenotypic plasticity by transcriptome analysis. Overall, these data suggest that the SmydA gene family retains essential functions that may possibly define novel regulatory pathways in insects. This work provides insights into the roles of lineage-specific domain duplication in insect evolution. PMID:28444351

Evolutionary biology: microsporidia sex--a missing link to fungi.

PubMed

Dyer, Paul S

2008-11-11

The evolutionary origins of the microsporidia, a group of intracellular eukaryotic pathogens, have been unclear. Genome analysis of a sex locus and other gene clusters has now revealed conserved synteny with zygomycete fungi, indicating that microsporidia are true fungi descended from a zygomycete ancestor.

Despotism, democracy, and the evolutionary dynamics of leadership and followership.

PubMed

Van Vugt, Mark

2009-01-01

Responds to comments made by George B. Graen and Stephen J. Guastello on the current author's article Leadership, followership, and evolution: Some lessons from the past by Van Vugt, Hogan, and Kaiser. In the original article my co-authors and I proposed a new way of thinking about leadership, informed by evolutionary (neo-Darwinian) theory. In the first commentary, Graen noted that we ignored a number of recently developed psychological theories of leadership that take into account the leader-follower relationship, most notably LMX theory. LMX theory asserts that leadership effectiveness and team performance are affected by the quality of working relationships between superior and subordinates. Because the original article primarily dealt with questions about the origins of leadership--the phylogenetic and evolutionary causes--we had to be concise in our review of proximate psychological theories of leadership. In the second commentary, Guastello concurred with the importance of an evolutionary game analysis for studying leadership but disagreed with certain details of our analysis. (PsycINFO Database Record (c) 2009 APA, all rights reserved).

Monophyletic origin of domestic bactrian camel (Camelus bactrianus) and its evolutionary relationship with the extant wild camel (Camelus bactrianus ferus)

PubMed Central

Ji, R; Cui, P; Ding, F; Geng, J; Gao, H; Zhang, H; Yu, J; Hu, S; Meng, H

2009-01-01

The evolutionary relationship between the domestic bactrian camel and the extant wild two-humped camel and the factual origin of the domestic bactrian camel remain elusive. We determined the sequence of mitochondrial cytb gene from 21 camel samples, including 18 domestic camels (three Camelus bactrianus xinjiang, three Camelus bactrianus sunite, three Camelus bactrianus alashan, three Camelus bactrianus red, three Camelus bactrianus brown and three Camelus bactrianus normal) and three wild camels (Camelus bactrianus ferus). Our phylogenetic analyses revealed that the extant wild two-humped camel may not share a common ancestor with the domestic bactrian camel and they are not the same subspecies at least in their maternal origins. Molecular clock analysis based on complete mitochondrial genome sequences indicated that the sub-speciation of the two lineages had begun in the early Pleistocene, about 0.7 million years ago. According to the archaeological dating of the earliest known two-humped camel domestication (5000–6000 years ago), we could conclude that the extant wild camel is a separate lineage but not the direct progenitor of the domestic bactrian camel. Further phylogenetic analysis suggested that the bactrian camel appeared monophyletic in evolutionary origin and that the domestic bactrian camel could originate from a single wild population. The data presented here show how conservation strategies should be implemented to protect the critically endangered wild camel, as it is the last extant form of the wild tribe Camelina. PMID:19292708

Comparative genomics of the bacterial genus Streptococcus illuminates evolutionary implications of species groups.

PubMed

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun

2014-01-01

Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into "species groups". However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups.

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.

Comparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups

PubMed Central

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun

2014-01-01

Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into “species groups”. However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups. PMID:24977706

Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

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

Nakhleh, Luay

I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbialmore » genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.« less

Evolutionary dynamics of taxonomic structure

PubMed Central

Foote, Michael

2012-01-01

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

The complete genome sequence and genetic analysis of ΦCA82 a novel uncultured microphage from the turkey gastrointestinal system

PubMed Central

2011-01-01

The genomic DNA sequence of a novel enteric uncultured microphage, ΦCA82 from a turkey gastrointestinal system was determined utilizing metagenomics techniques. The entire circular, single-stranded nucleotide sequence of the genome was 5,514 nucleotides. The ΦCA82 genome is quite different from other microviruses as indicated by comparisons of nucleotide similarity, predicted protein similarity, and functional classifications. Only three genes showed significant similarity to microviral proteins as determined by local alignments using BLAST analysis. ORF1 encoded a predicted phage F capsid protein that was phylogenetically most similar to the Microviridae ΦMH2K member's major coat protein. The ΦCA82 genome also encoded a predicted minor capsid protein (ORF2) and putative replication initiation protein (ORF3) most similar to the microviral bacteriophage SpV4. The distant evolutionary relationship of ΦCA82 suggests that the divergence of this novel turkey microvirus from other microviruses may reflect unique evolutionary pressures encountered within the turkey gastrointestinal system. PMID:21714899

SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees.

PubMed

DeBlasio, Dan F; Wisecaver, Jennifer H

2016-01-01

We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.

Alignment-Independent Comparisons of Human Gastrointestinal Tract Microbial Communities in a Multidimensional 16S rRNA Gene Evolutionary Space▿

PubMed Central

Rudi, Knut; Zimonja, Monika; Kvenshagen, Bente; Rugtveit, Jarle; Midtvedt, Tore; Eggesbø, Merete

2007-01-01

We present a novel approach for comparing 16S rRNA gene clone libraries that is independent of both DNA sequence alignment and definition of bacterial phylogroups. These steps are the major bottlenecks in current microbial comparative analyses. We used direct comparisons of taxon density distributions in an absolute evolutionary coordinate space. The coordinate space was generated by using alignment-independent bilinear multivariate modeling. Statistical analyses for clone library comparisons were based on multivariate analysis of variance, partial least-squares regression, and permutations. Clone libraries from both adult and infant gastrointestinal tract microbial communities were used as biological models. We reanalyzed a library consisting of 11,831 clones covering complete colons from three healthy adults in addition to a smaller 390-clone library from infant feces. We show that it is possible to extract detailed information about microbial community structures using our alignment-independent method. Our density distribution analysis is also very efficient with respect to computer operation time, meeting the future requirements of large-scale screenings to understand the diversity and dynamics of microbial communities. PMID:17337554

Immune defence, parasite evasion strategies and their relevance for ‘macroscopic phenomena’ such as virulence

PubMed Central

Schmid-Hempel, Paul

2008-01-01

The discussion of host–parasite interactions, and of parasite virulence more specifically, has so far, with a few exceptions, not focused much attention on the accumulating evidence that immune evasion by parasites is not only almost universal but also often linked to pathogenesis, i.e. the appearance of virulence. Now, the immune evasion hypothesis offers a deeper insight into the evolution of virulence than previous hypotheses. Sensitivity analysis for parasite fitness and life-history theory shows promise to generate a more general evolutionary theory of virulence by including a major element, immune evasion to prevent parasite clearance from the host. Also, the study of dose–response relationships and multiple infections should be particularly illuminating to understand the evolution of virulence. Taking into account immune evasion brings immunological processes to the core of understanding the evolution of parasite virulence and for a range of related issues such as dose, host specificity or immunopathology. The aim of this review is to highlight the mechanism underlying immune evasion and to discuss possible consequences for the evolutionary ecology analysis of host–parasite interactions. PMID:18930879

Islamic Medicine and Evolutionary Medicine: A Comparative Analysis

PubMed Central

Saniotis, Arthur

2012-01-01

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

Islamic medicine and evolutionary medicine: a comparative analysis.

PubMed

Saniotis, Arthur

2012-01-01

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

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.

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.

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

PubMed Central

Williams, Tom A.; Embley, T. Martin; Heinz, Eva

2011-01-01

Mimivirus is a nucleocytoplasmic large DNA virus (NCLDV) with a genome size (1.2 Mb) and coding capacity ( 1000 genes) comparable to that of some cellular organisms. Unlike other viruses, Mimivirus and its NCLDV relatives encode homologs of broadly conserved informational genes found in Bacteria, Archaea, and Eukaryotes, raising the possibility that they could be placed on the tree of life. A recent phylogenetic analysis of these genes showed the NCLDVs emerging as a monophyletic group branching between Eukaryotes and Archaea. These trees were interpreted as evidence for an independent “fourth domain” of life that may have contributed DNA processing genes to the ancestral eukaryote. However, the analysis of ancient evolutionary events is challenging, and tree reconstruction is susceptible to bias resulting from non-phylogenetic signals in the data. These include compositional heterogeneity and homoplasy, which can lead to the spurious grouping of compositionally-similar or fast-evolving sequences. Here, we show that these informational gene alignments contain both significant compositional heterogeneity and homoplasy, which were not adequately modelled in the original analysis. When we use more realistic evolutionary models that better fit the data, the resulting trees are unable to reject a simple null hypothesis in which these informational genes, like many other NCLDV genes, were acquired by horizontal transfer from eukaryotic hosts. Our results suggest that a fourth domain is not required to explain the available sequence data. PMID:21698163

Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors.

PubMed

Furlong, Michael; Seong, Jae Young

2017-01-01

Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples.

Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors

PubMed Central

Furlong, Michael; Seong, Jae Young

2017-01-01

Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples. PMID:28035082

Phylomemetics—Evolutionary Analysis beyond the Gene

PubMed Central

Howe, Christopher J.; Windram, Heather F.

2011-01-01

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

Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India.

PubMed

Lewnard, Joseph A; Townsend, Jeffrey P

2016-12-20

Immune heterogeneity in wild host populations indicates that disease-mediated selection is common in nature. However, the underlying dynamic feedbacks involving the ecology of disease transmission, evolutionary processes, and their interaction with environmental drivers have proven challenging to characterize. Plague presents an optimal system for interrogating such couplings: Yersinia pestis transmission exerts intense selective pressure driving the local persistence of disease resistance among its wildlife hosts in endemic areas. Investigations undertaken in colonial India after the introduction of plague in 1896 suggest that, only a decade after plague arrived, a heritable, plague-resistant phenotype had become prevalent among commensal rats of cities undergoing severe plague epidemics. To understand the possible evolutionary basis of these observations, we developed a mathematical model coupling environmentally forced plague dynamics with evolutionary selection of rats, capitalizing on extensive archival data from Indian Plague Commission investigations. Incorporating increased plague resistance among rats as a consequence of intense natural selection permits the model to reproduce observed changes in seasonal epidemic patterns in several cities and capture experimentally observed associations between climate and flea population dynamics in India. Our model results substantiate Victorian era claims of host evolution based on experimental observations of plague resistance and reveal the buffering effect of such evolution against environmental drivers of transmission. Our analysis shows that historical datasets can yield powerful insights into the transmission dynamics of reemerging disease agents with which we have limited contemporary experience to guide quantitative modeling and inference.

Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India

PubMed Central

Lewnard, Joseph A.

2016-01-01

Immune heterogeneity in wild host populations indicates that disease-mediated selection is common in nature. However, the underlying dynamic feedbacks involving the ecology of disease transmission, evolutionary processes, and their interaction with environmental drivers have proven challenging to characterize. Plague presents an optimal system for interrogating such couplings: Yersinia pestis transmission exerts intense selective pressure driving the local persistence of disease resistance among its wildlife hosts in endemic areas. Investigations undertaken in colonial India after the introduction of plague in 1896 suggest that, only a decade after plague arrived, a heritable, plague-resistant phenotype had become prevalent among commensal rats of cities undergoing severe plague epidemics. To understand the possible evolutionary basis of these observations, we developed a mathematical model coupling environmentally forced plague dynamics with evolutionary selection of rats, capitalizing on extensive archival data from Indian Plague Commission investigations. Incorporating increased plague resistance among rats as a consequence of intense natural selection permits the model to reproduce observed changes in seasonal epidemic patterns in several cities and capture experimentally observed associations between climate and flea population dynamics in India. Our model results substantiate Victorian era claims of host evolution based on experimental observations of plague resistance and reveal the buffering effect of such evolution against environmental drivers of transmission. Our analysis shows that historical datasets can yield powerful insights into the transmission dynamics of reemerging disease agents with which we have limited contemporary experience to guide quantitative modeling and inference. PMID:27791071

Evolutionary analysis and lateral gene transfer of two-component regulatory systems associated with heavy-metal tolerance in bacteria.

PubMed

Bouzat, Juan L; Hoostal, Matthew J

2013-05-01

Microorganisms have adapted intricate signal transduction mechanisms to coordinate tolerance to toxic levels of metals, including two-component regulatory systems (TCRS). In particular, both cop and czc operons are regulated by TCRS; the cop operon plays a key role in bacterial tolerance to copper, whereas the czc operon is involved in the efflux of cadmium, zinc, and cobalt from the cell. Although the molecular physiology of heavy metal tolerance genes has been extensively studied, their evolutionary relationships are not well-understood. Phylogenetic relationships among heavy-metal efflux proteins and their corresponding two-component regulatory proteins revealed orthologous and paralogous relationships from species divergences and ancient gene duplications. The presence of heavy metal tolerance genes on bacterial plasmids suggests these genes may be prone to spread through horizontal gene transfer. Phylogenetic inferences revealed nine potential examples of lateral gene transfer associated with metal efflux proteins and two examples for regulatory proteins. Notably, four of the examples suggest lateral transfer across major evolutionary domains. In most cases, differences in GC content in metal tolerance genes and their corresponding host genomes confirmed lateral gene transfer events. Three-dimensional protein structures predicted for the response regulators encoded by cop and czc operons showed a high degree of structural similarity with other known proteins involved in TCRS signal transduction, which suggests common evolutionary origins of functional phenotypes and similar mechanisms of action for these response regulators.

Evolutionary Pattern of the FAE1 Gene in Brassicaceae and Its Correlation with the Erucic Acid Trait

PubMed Central

Li, Mimi; Peng, Bin; Guo, Haisong; Yan, Qinqin; Hang, Yueyu

2013-01-01

The fatty acid elongase 1 (FAE1) gene catalyzes the initial condensation step in the elongation pathway of VLCFA (very long chain fatty acid) biosynthesis and is thus a key gene in erucic acid biosynthesis. Based on a worldwide collection of 62 accessions representing 14 tribes, 31 genera, 51 species, 4 subspecies and 7 varieties, we conducted a phylogenetic reconstruction and correlation analysis between genetic variations in the FAE1 gene and the erucic acid trait, attempting to gain insight into the evolutionary patterns and the correlations between genetic variations in FAE1 and trait variations. The five clear, deeply diverged clades detected in the phylogenetic reconstruction are largely congruent with a previous multiple gene-derived phylogeny. The Ka/Ks ratio (<1) and overall low level of nucleotide diversity in the FAE1 gene suggest that purifying selection is the major evolutionary force acting on this gene. Sequence variations in FAE1 show a strong correlation with the content of erucic acid in seeds, suggesting a causal link between the two. Furthermore, we detected 16 mutations that were fixed between the low and high phenotypes of the FAE1 gene, which constitute candidate active sites in this gene for altering the content of erucic acid in seeds. Our findings begin to shed light on the evolutionary pattern of this important gene and represent the first step in elucidating how the sequence variations impact the production of erucic acid in plants. PMID:24358289

Identification of (R)-selective ω-aminotransferases by exploring evolutionary sequence space.

PubMed

Kim, Eun-Mi; Park, Joon Ho; Kim, Byung-Gee; Seo, Joo-Hyun

2018-03-01

Several (R)-selective ω-aminotransferases (R-ωATs) have been reported. The existence of additional R-ωATs having different sequence characteristics from previous ones is highly expected. In addition, it is generally accepted that R-ωATs are variants of aminotransferase group III. Based on these backgrounds, sequences in RefSeq database were scored using family profiles of branched-chain amino acid aminotransferase (BCAT) and d-alanine aminotransferase (DAT) to predict and identify putative R-ωATs. Sequences with two profile analysis scores were plotted on two-dimensional score space. Candidates with relatively similar scores in both BCAT and DAT profiles (i.e., profile analysis score using BCAT profile was similar to profile analysis score using DAT profile) were selected. Experimental results for selected candidates showed that putative R-ωATs from Saccharopolyspora erythraea (R-ωAT_Sery), Bacillus cellulosilyticus (R-ωAT_Bcel), and Bacillus thuringiensis (R-ωAT_Bthu) had R-ωAT activity. Additional experiments revealed that R-ωAT_Sery also possessed DAT activity while R-ωAT_Bcel and R-ωAT_Bthu had BCAT activity. Selecting putative R-ωATs from regions with similar profile analysis scores identified potential R-ωATs. Therefore, R-ωATs could be efficiently identified by using simple family profile analysis and exploring evolutionary sequence space. Copyright © 2017 Elsevier Inc. All rights reserved.

Mean-Potential Law in Evolutionary Games.

PubMed

Nałęcz-Jawecki, Paweł; Miękisz, Jacek

2018-01-12

The Letter presents a novel way to connect random walks, stochastic differential equations, and evolutionary game theory. We introduce a new concept of a potential function for discrete-space stochastic systems. It is based on a correspondence between one-dimensional stochastic differential equations and random walks, which may be exact not only in the continuous limit but also in finite-state spaces. Our method is useful for computation of fixation probabilities in discrete stochastic dynamical systems with two absorbing states. We apply it to evolutionary games, formulating two simple and intuitive criteria for evolutionary stability of pure Nash equilibria in finite populations. In particular, we show that the 1/3 law of evolutionary games, introduced by Nowak et al. [Nature, 2004], follows from a more general mean-potential law.

An invasive plant alters pollinator-mediated phenotypic selection on a native congener.

PubMed

Beans, Carolyn M; Roach, Deborah A

2015-01-01

• Recent studies suggest that invasive plants compete reproductively with native plants by reducing the quantity or quality of pollinator visits. Although these studies have revealed ecological consequences of pollinator-mediated competition between invasive and native plants, the evolutionary outcomes of these interactions remain largely unexplored.• We studied the ecological and evolutionary impact of pollinator-mediated competition with an invasive jewelweed, Impatiens glandulifera, on a co-occurring native congener, I. capensis. Using a pollinator choice experiment, a hand pollination experiment, and a selection analysis, we addressed the following questions: (1) Do native pollinators show preference for the invasive or native jewelweed, and do they move between the two species? (2) Does invasive jewelweed pollen inhibit seed production in the native plant? (3) Does the invasive jewelweed alter phenotypic selection on the native plant's floral traits?• The pollinator choice experiment showed that pollinators strongly preferred the invasive jewelweed. The hand pollination experiment demonstrated that invasive pollen inhibited seed production in the native plant. The selection analysis showed that the presence of the invasive jewelweed altered phenotypic selection on corolla height in the native plant.• Invasive plants have the potential to alter phenotypic selection on floral traits in native plant populations. If native plants can evolve in response to this altered selection pressure, the evolution of floral traits may play an important role in permitting long-term coexistence of native and invasive plants. © 2015 Botanical Society of America, Inc.

A comparative genome analysis of PME and PMEI families reveals the evolution of pectin metabolism in plant cell walls.

PubMed

Wang, Maojun; Yuan, Daojun; Gao, Wenhui; Li, Yang; Tan, Jiafu; Zhang, Xianlong

2013-01-01

Pectins are fundamental polysaccharides in the plant primary cell wall. Pectins are synthesized and secreted to cell walls as highly methyl-esterified polymers and then demethyl-esterified by pectin methylesterases (PMEs), which are spatially regulated by pectin methylesterase inhibitors (PMEIs). Although PME and PMEI genes are pivotal in plant cell wall formation, few studies have focused on the evolutionary patterns of the PME and PMEI gene families. In this study, the gene origin, evolution, and expression diversity of these two families were systematically analyzed using 11 representative species, including algae, bryophytes, lycophytes and flowering land plants. The results show that 1) for the two subfamilies (PME and proPME) of PME, the origin of the PME subfamily is consistent with the appearance of pectins in early charophyte cell walls, 2) Whole genome duplication (WGD) and tandem duplication contribute to the expansion of proPME and PMEI families in land plants, 3) Evidence of selection pressure shows that the proPME and PMEI families have rapidly evolved, particularly the PMEI family in vascular plants, and 4) Comparative expression profile analysis of the two families indicates that the eudicot Arabidopsis and monocot rice have different expression patterns. In addition, the gene structure and sequence analyses show that the origin of the PMEI domain may be derived from the neofunctionalization of the pro domain after WGD. This study will advance the evolutionary understanding of the PME and PMEI families and plant cell wall development.

Environmental quality and evolutionary potential: lessons from wild populations

PubMed Central

Charmantier, Anne; Garant, Dany

2005-01-01

An essential requirement to determine a population's potential for evolutionary change is to quantify the amount of genetic variability expressed for traits under selection. Early investigations in laboratory conditions showed that the magnitude of the genetic and environmental components of phenotypic variation can change with environmental conditions. However, there is no consensus as to how the expression of genetic variation is sensitive to different environmental conditions. Recently, the study of quantitative genetics in the wild has been revitalized by new pedigree analyses based on restricted maximum likelihood, resulting in a number of studies investigating these questions in wild populations. Experimental manipulation of environmental quality in the wild, as well as the use of naturally occurring favourable or stressful environments, has broadened the treatment of different taxa and traits. Here, we conduct a meta-analysis on recent studies comparing heritability in favourable versus unfavourable conditions in non-domestic and non-laboratory animals. The results provide evidence for increased heritability in more favourable conditions, significantly so for morphometric traits but not for traits more closely related to fitness. We discuss how these results are explained by underlying changes in variance components, and how they represent a major step in our understanding of evolutionary processes in wild populations. We also show how these trends contrast with the prevailing view resulting mainly from laboratory experiments on Drosophila. Finally, we underline the importance of taking into account the environmental variation in models predicting quantitative trait evolution. PMID:16011915

Evolutionary image simplification for lung nodule classification with convolutional neural networks.

PubMed

Lückehe, Daniel; von Voigt, Gabriele

2018-05-29

Understanding decisions of deep learning techniques is important. Especially in the medical field, the reasons for a decision in a classification task are as crucial as the pure classification results. In this article, we propose a new approach to compute relevant parts of a medical image. Knowing the relevant parts makes it easier to understand decisions. In our approach, a convolutional neural network is employed to learn structures of images of lung nodules. Then, an evolutionary algorithm is applied to compute a simplified version of an unknown image based on the learned structures by the convolutional neural network. In the simplified version, irrelevant parts are removed from the original image. In the results, we show simplified images which allow the observer to focus on the relevant parts. In these images, more than 50% of the pixels are simplified. The simplified pixels do not change the meaning of the images based on the learned structures by the convolutional neural network. An experimental analysis shows the potential of the approach. Besides the examples of simplified images, we analyze the run time development. Simplified images make it easier to focus on relevant parts and to find reasons for a decision. The combination of an evolutionary algorithm employing a learned convolutional neural network is well suited for the simplification task. From a research perspective, it is interesting which areas of the images are simplified and which parts are taken as relevant.

Evolutionary genomics of dog domestication.

PubMed

Wayne, Robert K; vonHoldt, Bridgett M

2012-02-01

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

Population Genomics and the Statistical Values of Race: An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research

PubMed Central

Maglo, Koffi N.; Mersha, Tesfaye B.; Martin, Lisa J.

2016-01-01

The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to “frictional” effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the “cluster” and “cline” constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin's argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces, and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors, and evolutionary forces affecting disease causation and treatment response. PMID:26925096

Peculiar Evolutionary History of miR390-Guided TAS3-Like Genes in Land Plants

PubMed Central

Krasnikova, Maria S.; Goryunov, Denis V.; Troitsky, Alexey V.; Solovyev, Andrey G.; Ozerova, Lydmila V.; Morozov, Sergey Y.

2013-01-01

PCR-based approach was used as a phylogenetic profiling tool to probe genomic DNA samples from representatives of evolutionary distant moss taxa, namely, classes Bryopsida, Tetraphidopsida, Polytrichopsida, Andreaeopsida, and Sphagnopsida. We found relatives of all Physcomitrella patens miR390 and TAS3-like loci in these plant taxa excluding Sphagnopsida. Importantly, cloning and sequencing of Marchantia polymorpha genomic DNA showed miR390 and TAS3-like sequences which were also found among genomic reads of M. polymorpha at NCBI database. Our data suggest that the ancient plant miR390-dependent TAS molecular machinery firstly evolved to target AP2-like mRNAs in Marchantiophyta and only then both ARF- and AP2-specific mRNAs in mosses. The presented analysis shows that moss TAS3 families may undergone losses of tasiAP2 sites during evolution toward ferns and seed plants. These data confirm that miR390-guided genes coding for ARF- and AP2-specific ta-siRNAs have been gradually changed during land plant evolution. PMID:24302881

Implementation and comparative analysis of the optimisations produced by evolutionary algorithms for the parameter extraction of PSP MOSFET model

NASA Astrophysics Data System (ADS)

Hadia, Sarman K.; Thakker, R. A.; Bhatt, Kirit R.

2016-05-01

The study proposes an application of evolutionary algorithms, specifically an artificial bee colony (ABC), variant ABC and particle swarm optimisation (PSO), to extract the parameters of metal oxide semiconductor field effect transistor (MOSFET) model. These algorithms are applied for the MOSFET parameter extraction problem using a Pennsylvania surface potential model. MOSFET parameter extraction procedures involve reducing the error between measured and modelled data. This study shows that ABC algorithm optimises the parameter values based on intelligent activities of honey bee swarms. Some modifications have also been applied to the basic ABC algorithm. Particle swarm optimisation is a population-based stochastic optimisation method that is based on bird flocking activities. The performances of these algorithms are compared with respect to the quality of the solutions. The simulation results of this study show that the PSO algorithm performs better than the variant ABC and basic ABC algorithm for the parameter extraction of the MOSFET model; also the implementation of the ABC algorithm is shown to be simpler than that of the PSO algorithm.

Evolutionary history and spatiotemporal dynamics of dengue virus type 1 in Asia.

PubMed

Sun, Yan; Meng, Shengli

2013-06-01

Previous studies showed that DENV-1 transmitted from monkeys to humans approximately 125 years ago. However, there is no comprehensive analysis about phylogeography and population dynamics of Asian DENV-1. Here, we adopt a Bayesian phylogeographic approach to investigate the evolutionary history and phylogeography of Asian DENV-1 using envelope (E) protein gene sequences of 450 viruses isolated from 1954 to 2010 throughout 18 Asian countries and regions. Bayesian phylogeographic analyses indicate that the high rates of viral migration possibly follows long-distance travel for humans in Southeast Asia. Our study highlights that Southeast Asian countries have acted as the main viral sources of the dengue epidemics in East Asia. The results reveal that the time to the most recent common ancestor (TMRCA) of Asian DENV-1 is 1906 (95% HPD, years 1897-1915). We show that the spatial dissemination of virus is the major source of DENV-1 outbreaks in the different localities and leads to subsequent establishment and expansion of the virus in these areas. Copyright © 2013 Elsevier B.V. All rights reserved.

Genetic variability in captive populations of the stingless bee Tetragonisca angustula.

PubMed

Santiago, Leandro R; Francisco, Flávio O; Jaffé, Rodolfo; Arias, Maria C

2016-08-01

Low genetic variability has normally been considered a consequence of animal husbandry and a major contributing factor to declining bee populations. Here, we performed a molecular analysis of captive and wild populations of the stingless bee Tetragonisca angustula, one of the most commonly kept species across South America. Microsatellite analyses showed similar genetic variability between wild and captive populations However, captive populations showed lower mitochondrial genetic variability. Male-mediated gene flow, transport and division of nests are suggested as the most probable explanations for the observed patterns of genetic structure. We conclude that increasing the number of colonies kept through nest divisions does not negatively affect nuclear genetic variability, which seems to be maintained by small-scale male dispersal and human-mediated nest transport. However, the transport of nests from distant localities should be practiced with caution given the high genetic differentiation observed between samples from western and eastern areas. The high genetic structure verified is the result of a long-term evolutionary process, and bees from distant localities may represent unique evolutionary lineages.

Evolutionary Multiobjective Design Targeting a Field Programmable Transistor Array

NASA Technical Reports Server (NTRS)

Aguirre, Arturo Hernandez; Zebulum, Ricardo S.; Coello, Carlos Coello

2004-01-01

This paper introduces the ISPAES algorithm for circuit design targeting a Field Programmable Transistor Array (FPTA). The use of evolutionary algorithms is common in circuit design problems, where a single fitness function drives the evolution process. Frequently, the design problem is subject to several goals or operating constraints, thus, designing a suitable fitness function catching all requirements becomes an issue. Such a problem is amenable for multi-objective optimization, however, evolutionary algorithms lack an inherent mechanism for constraint handling. This paper introduces ISPAES, an evolutionary optimization algorithm enhanced with a constraint handling technique. Several design problems targeting a FPTA show the potential of our approach.

Evolutionary dynamics and the phase structure of the minority game

NASA Astrophysics Data System (ADS)

Yuan, Baosheng; Chen, Kan

2004-06-01

We show that a simple evolutionary scheme, when applied to the minority game (MG), changes the phase structure of the game. In this scheme each agent evolves individually whenever his wealth reaches the specified bankruptcy level, in contrast to the evolutionary schemes used in the previous works. We show that evolution greatly suppresses herding behavior, and it leads to better overall performance of the agents. Similar to the standard nonevolutionary MG, the dependence of the standard deviation σ on the number of agents N and the memory length m can be characterized by a universal curve. We suggest a crowd-anticrowd theory for understanding the effect of evolution in the MG.

Joint evolution of specialization and dispersal in structured metapopulations.

PubMed

Nurmi, Tuomas; Parvinen, Kalle

2011-04-21

We study the joint evolution of dispersal and specialization concerning resource usage in a mechanistically underpinned structured discrete-time metapopulation model. We show that dispersal significantly affects the evolution of specialization and that specialization is a key factor that determines the possibility of evolutionary branching in dispersal propensity. Allowing both dispersal propensity and specialization to evolve as a consequence of natural selection is necessary in order to understand the evolutionary dynamics. The joint evolution of dispersal and specialization forms a natural evolutionary path leading to the coexistence of generalists and specialists. We show that in this process, the number of different patch types and the resource distribution are essential. Copyright © 2011 Elsevier Ltd. All rights reserved.

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

PubMed

Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

2014-12-10

Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

Water pollutant fingerprinting tracks recent industrial transfer from coastal to inland China: A case study

PubMed Central

Zheng, Weiwei; Wang, Xia; Tian, Dajun; Jiang, Songhui; Andersen, Melvin E.; He, Genhsjeng; Crabbe, M. James C.; Zheng, Yuxin; Zhong, Yang; Qu, Weidong

2013-01-01

In recent years, China’s developed regions have transferred industries to undeveloped regions. Large numbers of unlicensed or unregistered enterprises are widespread in these undeveloped regions and they are subject to minimal regulation. Current methods for tracing industrial transfers in these areas, based on enterprise registration information or economic surveys, do not work. We have developed an analytical framework combining water fingerprinting and evolutionary analysis to trace the pollution transfer features between water sources. We collected samples in Eastern China (industrial export) and Central China (industrial acceptance) separately from two water systems. Based on the water pollutant fingerprints and evolutionary trees, we traced the pollution transfer associated with industrial transfer between the two areas. The results are consistent with four episodes of industrial transfers over the past decade. Our results also show likely types of the transferred industries - electronics, plastics, and biomedicines - that contribute to the water pollution transfer. PMID:23301152

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage.

PubMed

Merker, Matthias; Blin, Camille; Mona, Stefano; Duforet-Frebourg, Nicolas; Lecher, Sophie; Willery, Eve; Blum, Michael G B; Rüsch-Gerdes, Sabine; Mokrousov, Igor; Aleksic, Eman; Allix-Béguec, Caroline; Antierens, Annick; Augustynowicz-Kopeć, Ewa; Ballif, Marie; Barletta, Francesca; Beck, Hans Peter; Barry, Clifton E; Bonnet, Maryline; Borroni, Emanuele; Campos-Herrero, Isolina; Cirillo, Daniela; Cox, Helen; Crowe, Suzanne; Crudu, Valeriu; Diel, Roland; Drobniewski, Francis; Fauville-Dufaux, Maryse; Gagneux, Sébastien; Ghebremichael, Solomon; Hanekom, Madeleine; Hoffner, Sven; Jiao, Wei-wei; Kalon, Stobdan; Kohl, Thomas A; Kontsevaya, Irina; Lillebæk, Troels; Maeda, Shinji; Nikolayevskyy, Vladyslav; Rasmussen, Michael; Rastogi, Nalin; Samper, Sofia; Sanchez-Padilla, Elisabeth; Savic, Branislava; Shamputa, Isdore Chola; Shen, Adong; Sng, Li-Hwei; Stakenas, Petras; Toit, Kadri; Varaine, Francis; Vukovic, Dragana; Wahl, Céline; Warren, Robin; Supply, Philip; Niemann, Stefan; Wirth, Thierry

2015-03-01

Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.

Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management

PubMed Central

Thomas, William J; Gordon, Michael I; Stevens, Danielle M; Creason, Allison L; Belcher, Michael S; Serdani, Maryna; Wiseman, Michele S; Grünwald, Niklaus J; Putnam, Melodie L

2017-01-01

Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses. PMID:29231813

Water pollutant fingerprinting tracks recent industrial transfer from coastal to inland China: A case study

NASA Astrophysics Data System (ADS)

Zheng, Weiwei; Wang, Xia; Tian, Dajun; Jiang, Songhui; Andersen, Melvin E.; He, Genhsjeng; Crabbe, M. James C.; Zheng, Yuxin; Zhong, Yang; Qu, Weidong

2013-01-01

In recent years, China's developed regions have transferred industries to undeveloped regions. Large numbers of unlicensed or unregistered enterprises are widespread in these undeveloped regions and they are subject to minimal regulation. Current methods for tracing industrial transfers in these areas, based on enterprise registration information or economic surveys, do not work. We have developed an analytical framework combining water fingerprinting and evolutionary analysis to trace the pollution transfer features between water sources. We collected samples in Eastern China (industrial export) and Central China (industrial acceptance) separately from two water systems. Based on the water pollutant fingerprints and evolutionary trees, we traced the pollution transfer associated with industrial transfer between the two areas. The results are consistent with four episodes of industrial transfers over the past decade. Our results also show likely types of the transferred industries - electronics, plastics, and biomedicines - that contribute to the water pollution transfer.

Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management.

PubMed

Savory, Elizabeth A; Fuller, Skylar L; Weisberg, Alexandra J; Thomas, William J; Gordon, Michael I; Stevens, Danielle M; Creason, Allison L; Belcher, Michael S; Serdani, Maryna; Wiseman, Michele S; Grünwald, Niklaus J; Putnam, Melodie L; Chang, Jeff H

2017-12-12

Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus , and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses.

Molluscan engrailed expression, serial organization, and shell evolution

NASA Technical Reports Server (NTRS)

Jacobs, D. K.; Wray, C. G.; Wedeen, C. J.; Kostriken, R.; DeSalle, R.; Staton, J. L.; Gates, R. D.; Lindberg, D. R.

2000-01-01

Whether the serial features found in some molluscs are ancestral or derived is considered controversial. Here, in situ hybridization and antibody studies show iterated engrailed-gene expression in transverse rows of ectodermal cells bounding plate field development and spicule formation in the chiton, Lepidochitona cavema, as well as in cells surrounding the valves and in the early development of the shell hinge in the clam, Transennella tantilla. Ectodermal expression of engrailed is associated with skeletogenesis across a range of bilaterian phyla, suggesting a single evolutionary origin of invertebrate skeletons. The shared ancestry of bilaterian-invertebrate skeletons may help explain the sudden appearance of shelly fossils in the Cambrian. Our interpretation departs from the consideration of canonical metameres or segments as units of evolutionary analysis. In this interpretation, the shared ancestry of engrailed-gene function in the terminal/posterior addition of serially repeated elements during development explains the iterative expression of engrailed genes in a range of metazoan body plans.

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.

Genomic analysis of local variation and recent evolution in Plasmodium vivax

PubMed Central

Pearson, Richard D; Miotto, Olivo; Almagro-Garcia, Jacob; Amaratunga, Chanaki; Suon, Seila; Mao, Sivanna; Noviyanti, Rintis; Trimarsanto, Hidayat; Marfurt, Jutta; Anstey, Nicholas M; William, Timothy; Boni, Maciej F; Dolecek, Christiane; Hien, Tinh Tran; White, Nicholas J; Michon, Pascal; Siba, Peter; Tavul, Livingstone; Harrison, Gabrielle; Barry, Alyssa; Mueller, Ivo; Ferreira, Marcelo U; Karunaweera, Nadira; Randrianarivelojosia, Milijaona; Gao, Qi; Hubbart, Christina; Hart, Lee; Jeffery, Ben; Drury, Eleanor; Mead, Daniel; Kekre, Mihir; Campino, Susana; Manske, Magnus; Cornelius, Victoria J; MacInnis, Bronwyn; Rockett, Kirk A; Miles, Alistair; Rayner, Julian C; Fairhurst, Rick M; Nosten, Francois; Price, Ric N; Kwiatkowski, Dominic P

2016-01-01

The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for malaria elimination. To characterise the genetic diversity of this parasite within individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region, and analysed data on >300,000 SNPs and 9 regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at novel loci, and these varied markedly between geographical locations. These findings reveal a dynamic landscape of local evolutionary adaptation in P. vivax populations, and provide a foundation for genomic surveillance to guide effective strategies for control and elimination. PMID:27348299

Dental evidence on the hominin dispersals during the Pleistocene

PubMed Central

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

2007-01-01

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

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

PubMed Central

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

2008-01-01

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

Initial implementation of a comparative data analysis ontology.

PubMed

Prosdocimi, Francisco; Chisham, Brandon; Pontelli, Enrico; Thompson, Julie D; Stoltzfus, Arlin

2009-07-03

Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species) are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: "Operational Taxonomic Units" (OTUs), representing the entities to be compared; "character-state data" representing the observations compared among OTUs; "phylogenetic tree", representing the historical path of evolution among the entities; and "transitions", the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL), we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO). CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc.) that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research.

A Strategic Approach to Joint Officer Management: Analysis and Modeling Results

DTIC Science & Technology

2009-01-01

rules. 5 Johnson and Wichern, 2002, p. 643. 6 Sullivan and Perry, 2004, p. 370. 7 Francesco Mola and Raffaele Miele, “Evolutionary Algorithms for...in Military Affairs, Newport, R.I.: Center for Naval Warfare Studies, 2003. Mola , Francesco, and Raffaele Miele, “Evolutionary Algorithms for

Telling Tales at Work: An Evolutionary Explanation

ERIC Educational Resources Information Center

Yang, Chulguen

2013-01-01

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

Testing Evolutionary Hypotheses in the Classroom with MacClade Software.

ERIC Educational Resources Information Center

Codella, Sylvio G.

2002-01-01

Introduces MacClade which is a Macintosh-based software package that uses the techniques of cladistic analysis to explore evolutionary patterns. Describes a novel and effective exercise that allows undergraduate biology majors to test a hypothesis about behavioral evolution in insects. (Contains 13 references.) (Author/YDS)

Phylogenetics and evolutionary morphology of the Neotropical true bug genus Epipolops (Hemiptera: Heteroptera: Geocoridae)

USDA-ARS?s Scientific Manuscript database

Species of Epipolops Herrich-Schaeffer (Hemiptera: Geocoridae), comprising the largest genus of Pamphantinae, are among the most bizarre true bugs because of their striking morphology. To elucidate evolutionary morphology in Epipolops, a phylogenetic analysis was performed using 17 species and 36 ad...

Analysis of evolutionary patterns of genes in campylobacter jejuni and C. coli

USDA-ARS?s Scientific Manuscript database

Background: In order to investigate the population genetics structure of thermophilic Campylobacter spp., we extracted a set of 1029 core gene families (CGF) from 25 sequenced genomes of C. jejuni, C. coli and C. lari. Based on these CGFs we employed different approaches to reveal the evolutionary ...

On the Evolutionary Bases of Consumer Reinforcement

ERIC Educational Resources Information Center

Nicholson, Michael; Xiao, Sarah Hong

2010-01-01

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

Evolutionary relationship and structural characterization of the EPF/EPFL gene family.

PubMed

Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu

2013-01-01

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

Evolutionary Relationship and Structural Characterization of the EPF/EPFL Gene Family

PubMed Central

Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu

2013-01-01

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes. PMID:23755192

Eco-evolutionary effects on population recovery following catastrophic disturbance

PubMed Central

Weese, Dylan J; Schwartz, Amy K; Bentzen, Paul; Hendry, Andrew P; Kinnison, Michael T

2011-01-01

Fine-scale genetic diversity and contemporary evolution can theoretically influence ecological dynamics in the wild. Such eco-evolutionary effects might be particularly relevant to the persistence of populations facing acute or chronic environmental change. However, experimental data on wild populations is currently lacking to support this notion. One way that ongoing evolution might influence the dynamics of threatened populations is through the role that selection plays in mediating the ‘rescue effect’, the ability of migrants to contribute to the recovery of populations facing local disturbance and decline. Here, we combine experiments with natural catastrophic events to show that ongoing evolution is a major determinant of migrant contributions to population recovery in Trinidadian guppies (Poecilia reticulata). These eco-evolutionary limits on migrant contributions appear to be mediated by the reinforcing effects of natural and sexual selection against migrants, despite the close geographic proximity of migrant sources. These findings show that ongoing adaptive evolution can be a double-edged sword for population persistence, maintaining local fitness at a cost to demographic risk. Our study further serves as a potent reminder that significant evolutionary and eco-evolutionary dynamics might be at play even where the phenotypic status quo is largely maintained generation to generation. PMID:25567978

Is mammalian chromosomal evolution driven by regions of genome fragility?

PubMed Central

Ruiz-Herrera, Aurora; Castresana, Jose; Robinson, Terence J

2006-01-01

Background A fundamental question in comparative genomics concerns the identification of mechanisms that underpin chromosomal change. In an attempt to shed light on the dynamics of mammalian genome evolution, we analyzed the distribution of syntenic blocks, evolutionary breakpoint regions, and evolutionary breakpoints taken from public databases available for seven eutherian species (mouse, rat, cattle, dog, pig, cat, and horse) and the chicken, and examined these for correspondence with human fragile sites and tandem repeats. Results Our results confirm previous investigations that showed the presence of chromosomal regions in the human genome that have been repeatedly used as illustrated by a high breakpoint accumulation in certain chromosomes and chromosomal bands. We show, however, that there is a striking correspondence between fragile site location, the positions of evolutionary breakpoints, and the distribution of tandem repeats throughout the human genome, which similarly reflect a non-uniform pattern of occurrence. Conclusion These observations provide further evidence that certain chromosomal regions in the human genome have been repeatedly used in the evolutionary process. As a consequence, the genome is a composite of fragile regions prone to reorganization that have been conserved in different lineages, and genomic tracts that do not exhibit the same levels of evolutionary plasticity. PMID:17156441

Gradual and contingent evolutionary emergence of leaf mimicry in butterfly wing patterns.

PubMed

Suzuki, Takao K; Tomita, Shuichiro; Sezutsu, Hideki

2014-11-25

Special resemblance of animals to natural objects such as leaves provides a representative example of evolutionary adaptation. The existence of such sophisticated features challenges our understanding of how complex adaptive phenotypes evolved. Leaf mimicry typically consists of several pattern elements, the spatial arrangement of which generates the leaf venation-like appearance. However, the process by which leaf patterns evolved remains unclear. In this study we show the evolutionary origin and process for the leaf pattern in Kallima (Nymphalidae) butterflies. Using comparative morphological analyses, we reveal that the wing patterns of Kallima and 45 closely related species share the same ground plan, suggesting that the pattern elements of leaf mimicry have been inherited across species with lineage-specific changes of their character states. On the basis of these analyses, phylogenetic comparative methods estimated past states of the pattern elements and enabled reconstruction of the wing patterns of the most recent common ancestor. This analysis shows that the leaf pattern has evolved through several intermediate patterns. Further, we use Bayesian statistical methods to estimate the temporal order of character-state changes in the pattern elements by which leaf mimesis evolved, and show that the pattern elements changed their spatial arrangement (e.g., from a curved line to a straight line) in a stepwise manner and finally establish a close resemblance to a leaf venation-like appearance. Our study provides the first evidence for stepwise and contingent evolution of leaf mimicry.　 Leaf mimicry patterns evolved in a gradual, rather than a sudden, manner from a non-mimetic ancestor. Through a lineage of Kallima butterflies, the leaf patterns evolutionarily originated through temporal accumulation of orchestrated changes in multiple pattern elements.

Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements.

PubMed

Iranzo, Jaime; Koonin, Eugene V; Prangishvili, David; Krupovic, Mart

2016-12-15

Archaea and particularly hyperthermophilic crenarchaea are hosts to many unusual viruses with diverse virion shapes and distinct gene compositions. As is typical of viruses in general, there are no universal genes in the archaeal virosphere. Therefore, to obtain a comprehensive picture of the evolutionary relationships between viruses, network analysis methods are more productive than traditional phylogenetic approaches. Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses. We constructed a bipartite network of archaeal viruses that includes two classes of nodes, the genomes and gene families that connect them. Dissection of this network using formal community detection methods reveals strong modularity, with 10 distinct modules and 3 putative supermodules. However, compared to similar previously analyzed networks of eukaryotic and bacterial viruses, the archaeal virus network is sparsely connected. With the exception of the tailed viruses related to bacteriophages of the order Caudovirales and the families Turriviridae and Sphaerolipoviridae that are linked to a distinct supermodule of eukaryotic and bacterial viruses, there are few connector genes shared by different archaeal virus modules. In contrast, most of these modules include, in addition to viruses, capsidless mobile elements, emphasizing tight evolutionary connections between the two types of entities in archaea. The relative contributions of distinct evolutionary origins, in particular from nonviral elements, and insufficient sampling to the sparsity of the archaeal virus network remain to be determined by further exploration of the archaeal virosphere. Viruses infecting archaea are among the most mysterious denizens of the virosphere. Many of these viruses display no genetic or even morphological relationship to viruses of bacteria and eukaryotes, raising questions regarding their origins and position in the global virosphere. Analysis of 5,740 protein sequences from 116 genomes allowed dissection of the archaeal virus network and showed that most groups of archaeal viruses are evolutionarily connected to capsidless mobile genetic elements, including various plasmids and transposons. This finding could reflect actual independent origins of the distinct groups of archaeal viruses from different nonviral elements, providing important insights into the emergence and evolution of the archaeal virome. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Investigating evolutionary constraints on the detection of threatening stimuli in preschool children.

PubMed

Zsido, Andras N; Deak, Anita; Losonci, Adrienn; Stecina, Diana; Arato, Akos; Bernath, Laszlo

2018-04-01

Numerous objects and animals could be threatening, and thus, children learn to avoid them early. Spiders and syringes are among the most common targets of fears and phobias of the modern word. However, they are of different origins: while the former is evolutionary relevant, the latter is not. We sought to investigate the underlying mechanisms that make the quick detection of such stimuli possible and enable the impulse to avoid them in the future. The respective categories of threatening and non-threatening targets were similar in shape, while low-level visual features were controlled. Our results showed that children found threatening cues faster, irrespective of the evolutionary age of the cues. However, they detected non-threatening evolutionary targets faster than non-evolutionary ones. We suggest that the underlying mechanism may be different: general feature detection can account for finding evolutionary threatening cues quickly, while specific features detection is more appropriate for modern threatening stimuli. Copyright © 2018 Elsevier B.V. All rights reserved.

Modelling and strategy optimisation for a kind of networked evolutionary games with memories under the bankruptcy mechanism

NASA Astrophysics Data System (ADS)

Fu, Shihua; Li, Haitao; Zhao, Guodong

2018-05-01

This paper investigates the evolutionary dynamic and strategy optimisation for a kind of networked evolutionary games whose strategy updating rules incorporate 'bankruptcy' mechanism, and the situation that each player's bankruptcy is due to the previous continuous low profits gaining from the game is considered. First, by using semi-tensor product of matrices method, the evolutionary dynamic of this kind of games is expressed as a higher order logical dynamic system and then converted into its algebraic form, based on which, the evolutionary dynamic of the given games can be discussed. Second, the strategy optimisation problem is investigated, and some free-type control sequences are designed to maximise the total payoff of the whole game. Finally, an illustrative example is given to show that our new results are very effective.

Neuronal boost to evolutionary dynamics

PubMed Central

de Vladar, Harold P.; Szathmáry, Eörs

2015-01-01

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

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

Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

PubMed Central

Tamura, Koichiro; Tao, Qiqing; Kumar, Sudhir

2018-01-01

Abstract RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and empirical molecular sequence data sets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of data sets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between evolutionary lineages and their respective descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits. PMID:29893954

A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate.

PubMed

Bataillon, Thomas; Galtier, Nicolas; Bernard, Aurelien; Cryer, Nicolai; Faivre, Nicolas; Santoni, Sylvain; Severac, Dany; Mikkelsen, Teis N; Larsen, Klaus S; Beier, Claus; Sørensen, Jesper G; Holmstrup, Martin; Ehlers, Bodil K

2016-07-01

Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short-time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response. © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal.

PubMed

Turajlic, Samra; Xu, Hang; Litchfield, Kevin; Rowan, Andrew; Horswell, Stuart; Chambers, Tim; O'Brien, Tim; Lopez, Jose I; Watkins, Thomas B K; Nicol, David; Stares, Mark; Challacombe, Ben; Hazell, Steve; Chandra, Ashish; Mitchell, Thomas J; Au, Lewis; Eichler-Jonsson, Claudia; Jabbar, Faiz; Soultati, Aspasia; Chowdhury, Simon; Rudman, Sarah; Lynch, Joanna; Fernando, Archana; Stamp, Gordon; Nye, Emma; Stewart, Aengus; Xing, Wei; Smith, Jonathan C; Escudero, Mickael; Huffman, Adam; Matthews, Nik; Elgar, Greg; Phillimore, Ben; Costa, Marta; Begum, Sharmin; Ward, Sophia; Salm, Max; Boeing, Stefan; Fisher, Rosalie; Spain, Lavinia; Navas, Carolina; Grönroos, Eva; Hobor, Sebastijan; Sharma, Sarkhara; Aurangzeb, Ismaeel; Lall, Sharanpreet; Polson, Alexander; Varia, Mary; Horsfield, Catherine; Fotiadis, Nicos; Pickering, Lisa; Schwarz, Roland F; Silva, Bruno; Herrero, Javier; Luscombe, Nick M; Jamal-Hanjani, Mariam; Rosenthal, Rachel; Birkbak, Nicolai J; Wilson, Gareth A; Pipek, Orsolya; Ribli, Dezso; Krzystanek, Marcin; Csabai, Istvan; Szallasi, Zoltan; Gore, Martin; McGranahan, Nicholas; Van Loo, Peter; Campbell, Peter; Larkin, James; Swanton, Charles

2018-04-19

The evolutionary features of clear-cell renal cell carcinoma (ccRCC) have not been systematically studied to date. We analyzed 1,206 primary tumor regions from 101 patients recruited into the multi-center prospective study, TRACERx Renal. We observe up to 30 driver events per tumor and show that subclonal diversification is associated with known prognostic parameters. By resolving the patterns of driver event ordering, co-occurrence, and mutual exclusivity at clone level, we show the deterministic nature of clonal evolution. ccRCC can be grouped into seven evolutionary subtypes, ranging from tumors characterized by early fixation of multiple mutational and copy number drivers and rapid metastases to highly branched tumors with >10 subclonal drivers and extensive parallel evolution associated with attenuated progression. We identify genetic diversity and chromosomal complexity as determinants of patient outcome. Our insights reconcile the variable clinical behavior of ccRCC and suggest evolutionary potential as a biomarker for both intervention and surveillance. Copyright © 2018 Francis Crick Institute. Published by Elsevier Inc. All rights reserved.

[TRANSFORMATIONS OF LIFE CYCLES IN THE EVOLUTIONARY HISTORY OF TRYPANOSOMATIDS. MACROTRANSFORMATIONS].

PubMed

Frolov, A O; Malysheva, M N; Kostygov, A Yu

2015-01-01

The review concerns analysis of life cycle macrotransformations in the evolutionary history of trypanosomatids. The term "macrotransformations" stands for evolutionary processes leading to the establishment of heteroxenous and secondary homoxenous life cycles within Trypanosomatidae. There were three direct macrotransformations in the evolution of the group resulting in the rise of heteroxenous genera Leishmania, Trypanosoma and Phytomonas, and one case of reverse macrotransformation in trypanosomes of T. (b.) brucei group. The issues of the origin, diversity and phylogeny of taxa whose emergence resulted from macrotransformations of life cycles of homoxenous trypanosomatids.

Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform.

PubMed

Wang, Jinpeng; Sun, Pengchuan; Li, Yuxian; Liu, Yinzhe; Yu, Jigao; Ma, Xuelian; Sun, Sangrong; Yang, Nanshan; Xia, Ruiyan; Lei, Tianyu; Liu, Xiaojian; Jiao, Beibei; Xing, Yue; Ge, Weina; Wang, Li; Wang, Zhenyi; Song, Xiaoming; Yuan, Min; Guo, Di; Zhang, Lan; Zhang, Jiaqi; Jin, Dianchuan; Chen, Wei; Pan, Yuxin; Liu, Tao; Jin, Ling; Sun, Jinshuai; Yu, Jiaxiang; Cheng, Rui; Duan, Xueqian; Shen, Shaoqi; Qin, Jun; Zhang, Meng-Chen; Paterson, Andrew H; Wang, Xiyin

2017-05-01

Mainly due to their economic importance, genomes of 10 legumes, including soybean ( Glycine max ), wild peanut ( Arachis duranensis and Arachis ipaensis ), and barrel medic ( Medicago truncatula ), have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape ( Vitis vinifera ) and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by widespread gene losses after the polyploidizations. Notably, high similarity in gene retention between recently duplicated chromosomes in soybean supported the likely autopolyploidy nature of its tetraploid ancestor. Moreover, although most gene losses were nearly random, largely but not fully described by geometric distribution, we showed that polyploidization contributed divergently to the copy number variation of important gene families. Besides, we showed significantly divergent evolutionary levels among legumes and, by performing synonymous nucleotide substitutions at synonymous sites correction, redated major evolutionary events during their expansion. This effort laid a solid foundation for further genomics exploration in the legume research community and beyond. We describe only a tiny fraction of legume comparative genomics analysis that we performed; more information was stored in the newly constructed Legume Comparative Genomics Research Platform (www.legumegrp.org). © 2017 American Society of Plant Biologists. All Rights Reserved.

Evolution of the BBAA Component of Bread Wheat during Its History at the Allohexaploid Level[C][W][OPEN

PubMed Central

Zhang, Huakun; Zhu, Bo; Qi, Bao; Gou, Xiaowan; Dong, Yuzhu; Xu, Chunming; Zhang, Bangjiao; Huang, Wei; Liu, Chang; Wang, Xutong; Yang, Chunwu; Zhou, Hao; Kashkush, Khalil; Feldman, Moshe; Wendel, Jonathan F.; Liu, Bao

2014-01-01

Subgenome integrity in bread wheat (Triticum aestivum; BBAADD) makes possible the extraction of its BBAA component to restitute a novel plant type. The availability of such a ploidy-reversed wheat (extracted tetraploid wheat [ETW]) provides a unique opportunity to address whether and to what extent the BBAA component of bread wheat has been modified in phenotype, karyotype, and gene expression during its evolutionary history at the allohexaploid level. We report here that ETW was anomalous in multiple phenotypic traits but maintained a stable karyotype. Microarray-based transcriptome profiling identified a large number of differentially expressed genes between ETW and natural tetraploid wheat (Triticum turgidum), and the ETW-downregulated genes were enriched for distinct Gene Ontology categories. Quantitative RT-PCR analysis showed that gene expression differences between ETW and a set of diverse durum wheat (T. turgidum subsp durum) cultivars were distinct from those characterizing tetraploid cultivars per se. Pyrosequencing revealed that the expression alterations may occur to either only one or both of the B and A homoeolog transcripts in ETW. A majority of the genes showed additive expression in a resynthesized allohexaploid wheat. Analysis of a synthetic allohexaploid wheat and diverse bread wheat cultivars revealed the rapid occurrence of expression changes to the BBAA subgenomes subsequent to allohexaploidization and their evolutionary persistence. PMID:24989045

Retention and Molecular Evolution of Lipoxygenase Genes in Modern Rosid Plants

PubMed Central

Chen, Zhu; Chen, Danmei; Chu, Wenyuan; Zhu, Dongyue; Yan, Hanwei; Xiang, Yan

2016-01-01

Whole-genome duplication events have occurred more than once in the genomes of some rosids and played a significant role over evolutionary time. Lipoxygenases (LOXs) are involved in many developmental and resistance processes in plants. Our study concerns the subject of the LOX gene family; we tracked the evolutionary process of ancestral LOX genes in four modern rosids. Here we show that some members of the LOX gene family in the Arabidopsis genome are likely to be lost during evolution, leading to a smaller size than that in Populus, Vitis, and Carica. Strong purifying selection acted as a critical role in almost all of the paralogous and orthologous genes. The structure of LOX genes in Carica and Populus are relatively stable, whereas Vitis and Arabidopsis have a difference. By searching conserved motifs of LOX genes, we found that each sub-family shared similar components. Research on intraspecies gene collinearity show that recent duplication holds an important position in Populus and Arabidopsis. Gene collinearity analysis within and between these four rosid plants revealed that all LOX genes in each modern rosid were the offspring from different ancestral genes. This study traces the evolution of LOX genes which have been differentially retained and expanded in rosid plants. Our results presented here may aid in the selection of special genes retained in the rosid plants for further analysis of biological function. PMID:27746812

Structure-based Markov random field model for representing evolutionary constraints on functional sites.

PubMed

Jeong, Chan-Seok; Kim, Dongsup

2016-02-24

Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure. In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time. The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.

PubMed

Wolf, Yuri I; Makarova, Kira S; Yutin, Natalya; Koonin, Eugene V

2012-12-14

Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major 'highways' of horizontal gene transfer. The updated collection of arCOGs is expected to become a key resource for comparative genomics, evolutionary reconstruction and functional annotation of new archaeal genomes. Given that, in spite of the major increase in the number of genomes, the conserved core of archaeal genes appears to be stabilizing, the major evolutionary trends revealed here have a chance to stand the test of time. This article was reviewed by (for complete reviews see the Reviewers' Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG).

Modelling the influence of parental effects on gene-network evolution.

PubMed

Odorico, Andreas; Rünneburger, Estelle; Le Rouzic, Arnaud

2018-05-01

Understanding the importance of nongenetic heredity in the evolutionary process is a major topic in modern evolutionary biology. We modified a classical gene-network model by allowing parental transmission of gene expression and studied its evolutionary properties through individual-based simulations. We identified ontogenetic time (i.e. the time gene networks have to stabilize before being submitted to natural selection) as a crucial factor in determining the evolutionary impact of this phenotypic inheritance. Indeed, fast-developing organisms display enhanced adaptation and greater robustness to mutations when evolving in presence of nongenetic inheritance (NGI). In contrast, in our model, long development reduces the influence of the inherited state of the gene network. NGI thus had a negligible effect on the evolution of gene networks when the speed at which transcription levels reach equilibrium is not constrained. Nevertheless, simulations show that intergenerational transmission of the gene-network state negatively affects the evolution of robustness to environmental disturbances for either fast- or slow-developing organisms. Therefore, these results suggest that the evolutionary consequences of NGI might not be sought only in the way species respond to selection, but also on the evolution of emergent properties (such as environmental and genetic canalization) in complex genetic architectures. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

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.

A framework for the establishment of a cnidarian gene regulatory network for "endomesoderm" specification: the inputs of ß-catenin/TCF signaling.

PubMed

Röttinger, Eric; Dahlin, Paul; Martindale, Mark Q

2012-01-01

Understanding the functional relationship between intracellular factors and extracellular signals is required for reconstructing gene regulatory networks (GRN) involved in complex biological processes. One of the best-studied bilaterian GRNs describes endomesoderm specification and predicts that both mesoderm and endoderm arose from a common GRN early in animal evolution. Compelling molecular, genomic, developmental, and evolutionary evidence supports the hypothesis that the bifunctional gastrodermis of the cnidarian-bilaterian ancestor is derived from the same evolutionary precursor of both endodermal and mesodermal germ layers in all other triploblastic bilaterian animals. We have begun to establish the framework of a provisional cnidarian "endomesodermal" gene regulatory network in the sea anemone, Nematostella vectensis, by using a genome-wide microarray analysis on embryos in which the canonical Wnt/ß-catenin pathway was ectopically targeted for activation by two distinct pharmaceutical agents (lithium chloride and 1-azakenpaullone) to identify potential targets of endomesoderm specification. We characterized 51 endomesodermally expressed transcription factors and signaling molecule genes (including 18 newly identified) with fine-scale temporal (qPCR) and spatial (in situ) analysis to define distinct co-expression domains within the animal plate of the embryo and clustered genes based on their earliest zygotic expression. Finally, we determined the input of the canonical Wnt/ß-catenin pathway into the cnidarian endomesodermal GRN using morpholino and mRNA overexpression experiments to show that NvTcf/canonical Wnt signaling is required to pattern both the future endomesodermal and ectodermal domains prior to gastrulation, and that both BMP and FGF (but not Notch) pathways play important roles in germ layer specification in this animal. We show both evolutionary conserved as well as profound differences in endomesodermal GRN structure compared to bilaterians that may provide fundamental insight into how GRN subcircuits have been adopted, rewired, or co-opted in various animal lineages that give rise to specialized endomesodermal cell types.

Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica.

PubMed

Yang, J; Liu, G; Zhao, N; Chen, S; Liu, D; Ma, W; Hu, Z; Zhang, M

2016-05-01

The genus Brassica has many species that are important for oil, vegetable and other food products. Three mitochondrial genome types (mitotype) originated from its common ancestor. In this paper, a B. nigra mitochondrial main circle genome with 232,407 bp was generated through de novo assembly. Synteny analysis showed that the mitochondrial genomes of B. rapa and B. oleracea had a better syntenic relationship than B. nigra. Principal components analysis and development of a phylogenetic tree indicated maternal ancestors of three allotetraploid species in Us triangle of Brassica. Diversified mitotypes were found in allotetraploid B. napus, in which napus-type B. napus was derived from B. oleracea, while polima-type B. napus was inherited from B. rapa. In addition, the mitochondrial genome of napus-type B. napus was closer to botrytis-type than capitata-type B. oleracea. The sub-stoichiometric shifting of several mitochondrial genes suggested that mitochondrial genome rearrangement underwent evolutionary selection during domestication and/or plant breeding. Our findings clarify the role of diploid species in the maternal origin of allotetraploid species in Brassica and suggest the possibility of breeding selection of the mitochondrial genome. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions.

PubMed

Liu, Maoyan; Liu, Xiangning; Li, Xun; Zhang, Deyong; Dai, Liangyin; Tang, Qianjun

2016-03-01

The genome sequence of pepper vein yellows virus (PeVYV) (PeVYV-HN, accession number KP326573), isolated from pepper plants (Capsicum annuum L.) grown at the Hunan Vegetables Institute (Changsha, Hunan, China), was determined by deep sequencing of small RNAs. The PeVYV-HN genome consists of 6244 nucleotides, contains six open reading frames (ORFs), and is similar to that of an isolate (AB594828) from Japan. Its genomic organization is similar to that of members of the genus Polerovirus. Sequence analysis revealed that PeVYV-HN shared 92% sequence identity with the Japanese PeVYV genome at both the nucleotide and amino acid levels. Evolutionary analysis based on the coat protein (CP), movement protein (MP), and RNA-dependent RNA polymerase (RdRP) showed that PeVYV could be divided into two major lineages corresponding to their geographical origins. The Asian isolates have a higher population expansion frequency than the African isolates. Negative selection and genetic drift (founder effect) were found to be the potential drivers of the molecular evolution of PeVYV. Moreover, recombination was not the distinct cause of PeVYV evolution. This is the first report of a complete genomic sequence of PeVYV in China.

Phenotype–genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence

PubMed Central

Kashuk, Carl S.; Stone, Eric A.; Grice, Elizabeth A.; Portnoy, Matthew E.; Green, Eric D.; Sidow, Arend; Chakravarti, Aravinda; McCallion, Andrew S.

2005-01-01

The ability to discriminate between deleterious and neutral amino acid substitutions in the genes of patients remains a significant challenge in human genetics. The increasing availability of genomic sequence data from multiple vertebrate species allows inclusion of sequence conservation and physicochemical properties of residues to be used for functional prediction. In this study, the RET receptor tyrosine kinase serves as a model disease gene in which a broad spectrum (≥116) of disease-associated mutations has been identified among patients with Hirschsprung disease and multiple endocrine neoplasia type 2. We report the alignment of the human RET protein sequence with the orthologous sequences of 12 non-human vertebrates (eight mammalian, one avian, and three teleost species), their comparative analysis, the evolutionary topology of the RET protein, and predicted tolerance for all published missense mutations. We show that, although evolutionary conservation alone provides significant information to predict the effect of a RET mutation, a model that combines comparative sequence data with analysis of physiochemical properties in a quantitative framework provides far greater accuracy. Although the ability to discern the impact of a mutation is imperfect, our analyses permit substantial discrimination between predicted functional classes of RET mutations and disease severity even for a multigenic disease such as Hirschsprung disease. PMID:15956201

The evolution of coloniality in birds in relation to food, habitat, predation, and life-history traits: a comparative analysis.

PubMed

Rolland, C; Danchin, E; de Fraipont, M

1998-06-01

Coloniality in birds has been intensively studied under the cost and benefit approach, but no general conclusion can be given concerning its evolutionary function. Here, we report on a comparative analysis carried out on 320 species of birds using the general method of comparative analysis for discrete variables and the contrast method to analyze the evolution of coloniality. Showing a mean of 23 convergences and 10 reversals, coloniality appears to be a rather labile trait. Colonial breeding appears strongly correlated with the absence of feeding territory, the aquatic habitat, and nest exposure to predators but was not correlated with changes in life-history traits (body mass and clutch size). The correlation of coloniality with the aquatic habitat is in fact explained by a strong correlation with the marine habitat. Unexpectedly, we found that the evolution toward a marine habitat in birds was contingent on coloniality and that coloniality evolved before the passage to a marine life. These results-along with the lack of transitions from the nonmarine to marine habitat in solitary species and the precedence of the loss of feeding territoriality on the passage to a marine life-contradict most of the hypotheses classically accepted to explain coloniality and suggest that we use a different framework to study this evolutionary enigma.

Modelling Evolutionary Algorithms with Stochastic Differential Equations.

PubMed

Heredia, Jorge Pérez

2017-11-20

There has been renewed interest in modelling the behaviour of evolutionary algorithms (EAs) by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics. On the other hand, unlike ordinary differential equations (ODEs), they do not discard information about the stochasticity of the process. We show that these are especially suitable for the analysis of fixed budget scenarios and present analogues of the additive and multiplicative drift theorems from runtime analysis. In addition, we derive a new more general multiplicative drift theorem that also covers non-elitist EAs. This theorem simultaneously allows for positive and negative results, providing information on the algorithm's progress even when the problem cannot be optimised efficiently. Finally, we provide results for some well-known heuristics namely Random Walk (RW), Random Local Search (RLS), the (1+1) EA, the Metropolis Algorithm (MA), and the Strong Selection Weak Mutation (SSWM) algorithm.

Transcriptome profile and unique genetic evolution of positively selected genes in yak lungs.

PubMed

Lan, DaoLiang; Xiong, XianRong; Ji, WenHui; Li, Jian; Mipam, Tserang-Donko; Ai, Yi; Chai, ZhiXin

2018-04-01

The yak (Bos grunniens), which is a unique bovine breed that is distributed mainly in the Qinghai-Tibetan Plateau, is considered a good model for studying plateau adaptability in mammals. The lungs are important functional organs that enable animals to adapt to their external environment. However, the genetic mechanism underlying the adaptability of yak lungs to harsh plateau environments remains unknown. To explore the unique evolutionary process and genetic mechanism of yak adaptation to plateau environments, we performed transcriptome sequencing of yak and cattle (Bos taurus) lungs using RNA-Seq technology and a subsequent comparison analysis to identify the positively selected genes in the yak. After deep sequencing, a normal transcriptome profile of yak lung that containing a total of 16,815 expressed genes was obtained, and the characteristics of yak lungs transcriptome was described by functional analysis. Furthermore, Ka/Ks comparison statistics result showed that 39 strong positively selected genes are identified from yak lungs. Further GO and KEGG analysis was conducted for the functional annotation of these genes. The results of this study provide valuable data for further explorations of the unique evolutionary process of high-altitude hypoxia adaptation in yaks in the Tibetan Plateau and the genetic mechanism at the molecular level.

Compassion: An Evolutionary Analysis and Empirical Review

ERIC Educational Resources Information Center

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

2010-01-01

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

Analysis of Knowledge-Sharing Evolutionary Game in University Teacher Team

ERIC Educational Resources Information Center

Huo, Mingkui

2013-01-01

The knowledge-sharing activity is a major drive force behind the progress and innovation of university teacher team. Based on the evolutionary game theory, this article analyzes the knowledge-sharing process model of this team, studies the influencing mechanism of various factors such as knowledge aggregate gap, incentive coefficient and risk…

Genome-Wide Analysis of Evolutionary Markers of Human Influenza A(H1N1)pdm09 and A(H3N2) Viruses May Guide Selection of Vaccine Strain Candidates.

PubMed

Belanov, Sergei S; Bychkov, Dmitrii; Benner, Christian; Ripatti, Samuli; Ojala, Teija; Kankainen, Matti; Kai Lee, Hong; Wei-Tze Tang, Julian; Kainov, Denis E

2015-11-27

Here we analyzed whole-genome sequences of 3,969 influenza A(H1N1)pdm09 and 4,774 A(H3N2) strains that circulated during 2009-2015 in the world. The analysis revealed changes at 481 and 533 amino acid sites in proteins of influenza A(H1N1)pdm09 and A(H3N2) strains, respectively. Many of these changes were introduced as a result of random drift. However, there were 61 and 68 changes that were present in relatively large number of A(H1N1)pdm09 and A(H3N2) strains, respectively, that circulated during relatively long time. We named these amino acid substitutions evolutionary markers, as they seemed to contain valuable information regarding the viral evolution. Interestingly, influenza A(H1N1)pdm09 and A(H3N2) viruses acquired non-overlapping sets of evolutionary markers. We next analyzed these characteristic markers in vaccine strains recommended by the World Health Organization for the past five years. Our analysis revealed that vaccine strains carried only few evolutionary markers at antigenic sites of viral hemagglutinin (HA) and neuraminidase (NA). The absence of these markers at antigenic sites could affect the recognition of HA and NA by human antibodies generated in response to vaccinations. This could, in part, explain moderate efficacy of influenza vaccines during 2009-2014. Finally, we identified influenza A(H1N1)pdm09 and A(H3N2) strains, which contain all the evolutionary markers of influenza A strains circulated in 2015, and which could be used as vaccine candidates for the 2015/2016 season. Thus, genome-wide analysis of evolutionary markers of influenza A(H1N1)pdm09 and A(H3N2) viruses may guide selection of vaccine strain candidates. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

[Analysis of horizontal transfer gene of Bombyx mori NPV].

PubMed

Duan, Hai-Rong; Qiu, De-Bin; Gong, Cheng-Liang; Huang, Mo-Li

2011-06-01

For research on genetic characters and evolutionary origin of the genome of baculoviruses, a comprehensive homology search and phylogenetic analysis of the complete genomes of Bombyx mori NPV and Bombyx mori were used. Three horizontally transferred genes (inhibitor of apoptosis, chitinase, and UDP-glucosyltransferase) were identified, and there was evidence that all of these genes were derived from the insect host. The results of analysis showed lots of differences between the features of horizontal transferred genes and the ones of whole genomic genes, such as nucleotide composition, codon usagebias and selection pressure. These results reconfirmed that the horizontally transferred genes are exogenous. The analysis of gene function suggested that horizontally transferred genes acquired from an ancestral host insect can increase the efficiency of baculoviruses transmission.

Visualizing Phylogenetic Treespace Using Cartographic Projections

NASA Astrophysics Data System (ADS)

Sundberg, Kenneth; Clement, Mark; Snell, Quinn

Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a known NP-Hard problem. The size of the data sets which can be analyzed is limited by the exponential growth in the number of trees that must be considered as the problem size increases. A better understanding of the problem space could lead to better methods, which in turn could lead to the feasible analysis of more data sets. We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure. This structure can be used to develop search methods capable of handling much larger datasets.

Rapid molecular evolution of human bocavirus revealed by Bayesian coalescent inference.

PubMed

Zehender, Gianguglielmo; De Maddalena, Chiara; Canuti, Marta; Zappa, Alessandra; Amendola, Antonella; Lai, Alessia; Galli, Massimo; Tanzi, Elisabetta

2010-03-01

Human bocavirus (HBoV) is a linear single-stranded DNA virus belonging to the Parvoviridae family that has recently been isolated from the upper respiratory tract of children with acute respiratory infection. All of the strains observed so far segregate into two genotypes (1 and 2) with a low level of polymorphism. Given the recent description of the infection and the lack of epidemiological and molecular data, we estimated the virus's rates of molecular evolution and population dynamics. A dataset of forty-nine dated VP2 sequences, including also eight new isolates obtained from pharyngeal swabs of Italian patients with acute respiratory tract infections, was submitted to phylogenetic analysis. The model parameters, evolutionary rates and population dynamics were co-estimated using a Bayesian Markov Chain Monte Carlo approach, and site-specific positive and negative selection was also investigated. Recombination was investigated by seven different methods and one suspected recombinant strain was excluded from further analysis. The estimated mean evolutionary rate of HBoV was 8.6x10(-4)subs/site/year, and that of the 1st+2nd codon positions was more than 15 times less than that of the 3rd codon position. Viral population dynamics analysis revealed that the two known genotypes diverged recently (mean tMRCA: 24 years), and that the epidemic due to HBoV genotype 2 grew exponentially at a rate of 1.01year(-1). Selection analysis of the partial VP2 showed that 8.5% of sites were under significant negative pressure and the absence of positive selection. Our results show that, like other parvoviruses, HBoV is characterised by a rapid evolution. The low level of polymorphism is probably due to a relatively recent divergence between the circulating genotypes and strong purifying selection acting on viral antigens.

Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface

PubMed Central

2012-01-01

Background Despite computational challenges, elucidating conformations that a protein system assumes under physiologic conditions for the purpose of biological activity is a central problem in computational structural biology. While these conformations are associated with low energies in the energy surface that underlies the protein conformational space, few existing conformational search algorithms focus on explicitly sampling low-energy local minima in the protein energy surface. Methods This work proposes a novel probabilistic search framework, PLOW, that explicitly samples low-energy local minima in the protein energy surface. The framework combines algorithmic ingredients from evolutionary computation and computational structural biology to effectively explore the subspace of local minima. A greedy local search maps a conformation sampled in conformational space to a nearby local minimum. A perturbation move jumps out of a local minimum to obtain a new starting conformation for the greedy local search. The process repeats in an iterative fashion, resulting in a trajectory-based exploration of the subspace of local minima. Results and conclusions The analysis of PLOW's performance shows that, by navigating only the subspace of local minima, PLOW is able to sample conformations near a protein's native structure, either more effectively or as well as state-of-the-art methods that focus on reproducing the native structure for a protein system. Analysis of the actual subspace of local minima shows that PLOW samples this subspace more effectively that a naive sampling approach. Additional theoretical analysis reveals that the perturbation function employed by PLOW is key to its ability to sample a diverse set of low-energy conformations. This analysis also suggests directions for further research and novel applications for the proposed framework. PMID:22759582

Evolutionary dynamics of the traveler's dilemma and minimum-effort coordination games on complex networks.

PubMed

Iyer, Swami; Killingback, Timothy

2014-10-01

The traveler's dilemma game and the minimum-effort coordination game are social dilemmas that have received significant attention resulting from the fact that the predictions of classical game theory are inconsistent with the results found when the games are studied experimentally. Moreover, both the traveler's dilemma and the minimum-effort coordination games have potentially important applications in evolutionary biology. Interestingly, standard deterministic evolutionary game theory, as represented by the replicator dynamics in a well-mixed population, is also inadequate to account for the behavior observed in these games. Here we study the evolutionary dynamics of both these games in populations with interaction patterns described by a variety of complex network topologies. We investigate the evolutionary dynamics of these games through agent-based simulations on both model and empirical networks. In particular, we study the effects of network clustering and assortativity on the evolutionary dynamics of both games. In general, we show that the evolutionary behavior of the traveler's dilemma and minimum-effort coordination games on complex networks is in good agreement with that observed experimentally. Thus, formulating the traveler's dilemma and the minimum-effort coordination games on complex networks neatly resolves the paradoxical aspects of these games.

Evolutionary dynamics of the traveler's dilemma and minimum-effort coordination games on complex networks

NASA Astrophysics Data System (ADS)

Iyer, Swami; Killingback, Timothy

2014-10-01

The traveler's dilemma game and the minimum-effort coordination game are social dilemmas that have received significant attention resulting from the fact that the predictions of classical game theory are inconsistent with the results found when the games are studied experimentally. Moreover, both the traveler's dilemma and the minimum-effort coordination games have potentially important applications in evolutionary biology. Interestingly, standard deterministic evolutionary game theory, as represented by the replicator dynamics in a well-mixed population, is also inadequate to account for the behavior observed in these games. Here we study the evolutionary dynamics of both these games in populations with interaction patterns described by a variety of complex network topologies. We investigate the evolutionary dynamics of these games through agent-based simulations on both model and empirical networks. In particular, we study the effects of network clustering and assortativity on the evolutionary dynamics of both games. In general, we show that the evolutionary behavior of the traveler's dilemma and minimum-effort coordination games on complex networks is in good agreement with that observed experimentally. Thus, formulating the traveler's dilemma and the minimum-effort coordination games on complex networks neatly resolves the paradoxical aspects of these games.

Evolutionary diversification of the bean beetle genus Callosobruchus (Coleoptera: Bruchidae): traits associated with stored-product pest status.

PubMed

Tuda, M; Rönn, J; Buranapanichpan, S; Wasano, N; Arnqvist, G

2006-10-01

Despite the fact that many plant-feeding insects are pests, little effort has been made to identify key evolutionary trait transitions that allow taxa to acquire or lose pest status. A large proportion of species in the genus Callosobruchus are economically important pests of stored, dry postharvest beans of the tribe Phaseoleae. However, the evolution of this feeding habit is poorly understood. Here, we present a reconstruction of the phylogeny of the Asian and African Callosobruchus based on three mitochondrial genes, and assess which traits have been associated with the evolutionary origin or loss of ability to reproduce on dry beans. Our phylogenetic analysis showed that species group into the chinensis and the maculatus clades, which are also supported by genital morphology, and an additional paraphyletic group. Ancestral ability to use dry beans has been lost in the chinensis clade but acquired again in C. chinensis. Dry-bean use and host-plant use were both phylogenetically constrained and transitions in the two were significantly correlated. Host shifts from the subtribe Phaseolinae to Cajaninae were more common than the reverse and were more likely in species using young beans. The ability to use dry beans was more likely gained when using Phaseolinae hosts and promoted habitat shifts from tropical to temperate regions. Adaptation to arid climate was also associated with the ability to reproduce on dry beans and on Phaseolinae. Thus, our analysis suggests that physiological adaptations to an arid climate and to Phaseolinae hosts both render beetles predisposed to become pests of cultivated beans.

NSVS 7051868: A system in a key evolutionary stage. First multi-color photometric study

NASA Astrophysics Data System (ADS)

Barani, C.; Martignoni, M.; Acerbi, F.

2017-01-01

The first CCD photometric complete light curves of the eclipsing binary NSVS 7051868 were obtained during six nights in January 2016 in the B, V and Ic bands using the 0.25 m telescope of the Stazione Astronomica Betelgeuse in Magnago, Italy. These observations confirm the short period (P = 0.517 days) variation found by Shaw and collaborators in their online list (http://www.physast.uga.edu/ jss/nsvs/) of periodic variable stars found in the Northern Sky Variability Survey. The light curves were modelled using the Wilson-Devinney code and the elements obtained from this analysis are used to compute the physical parameters of the system in order to study its evolutionary status. A grid of solutions for several fixed values of mass ratio was calculated. A reasonable fit of the synthetic light curves of the data indicate that NSVS 7051868 is an A-subtype W Ursae Majoris contact binary system, with a low mass ratio of q = 0.22, a degree of contact factor f = 35.5% and inclination i = 85°. Our light curves shows a time of constant light in the secondary eclipse of approximately 0.1 in phase. The light curve solution reveals a component temperature difference of about 700 K. Both the value of the fill-out factor and the temperature difference suggests that NSVS 7051868 is a system in a key evolutionary stage of the Thermal Relaxation Oscillation theory. The distance to NSVS 7051868 was calculated as 180 pc from this analysis, taking into account interstellar extinction.

New method for predicting estrogen receptor status utilizing breast MRI texture kinetic analysis

NASA Astrophysics Data System (ADS)

Chaudhury, Baishali; Hall, Lawrence O.; Goldgof, Dmitry B.; Gatenby, Robert A.; Gillies, Robert; Drukteinis, Jennifer S.

2014-03-01

Magnetic Resonance Imaging (MRI) of breast cancer typically shows that tumors are heterogeneous with spatial variations in blood flow and cell density. Here, we examine the potential link between clinical tumor imaging and the underlying evolutionary dynamics behind heterogeneity in the cellular expression of estrogen receptors (ER) in breast cancer. We assume, in an evolutionary environment, that ER expression will only occur in the presence of significant concentrations of estrogen, which is delivered via the blood stream. Thus, we hypothesize, the expression of ER in breast cancer cells will correlate with blood flow on gadolinium enhanced breast MRI. To test this hypothesis, we performed quantitative analysis of blood flow on dynamic contrast enhanced MRI (DCE-MRI) and correlated it with the ER status of the tumor. Here we present our analytic methods, which utilize a novel algorithm to analyze 20 volumetric DCE-MRI breast cancer tumors. The algorithm generates post initial enhancement (PIE) maps from DCE-MRI and then performs texture features extraction from the PIE map, feature selection, and finally classification of tumors into ER positive and ER negative status. The combined gray level co-occurrence matrices, gray level run length matrices and local binary pattern histogram features allow quantification of breast tumor heterogeneity. The algorithm predicted ER expression with an accuracy of 85% using a Naive Bayes classifier in leave-one-out cross-validation. Hence, we conclude that our data supports the hypothesis that imaging characteristics can, through application of evolutionary principles, provide insights into the cellular and molecular properties of cancer cells.

Evolutionary genetics of plant adaptation.

PubMed

Anderson, Jill T; Willis, John H; Mitchell-Olds, Thomas

2011-07-01

Plants provide unique opportunities to study the mechanistic basis and evolutionary processes of adaptation to diverse environmental conditions. Complementary laboratory and field experiments are important for testing hypotheses reflecting long-term ecological and evolutionary history. For example, these approaches can infer whether local adaptation results from genetic tradeoffs (antagonistic pleiotropy), where native alleles are best adapted to local conditions, or if local adaptation is caused by conditional neutrality at many loci, where alleles show fitness differences in one environment, but not in a contrasting environment. Ecological genetics in natural populations of perennial or outcrossing plants can also differ substantially from model systems. In this review of the evolutionary genetics of plant adaptation, we emphasize the importance of field studies for understanding the evolutionary dynamics of model and nonmodel systems, highlight a key life history trait (flowering time) and discuss emerging conservation issues. Copyright © 2011 Elsevier Ltd. All rights reserved.

Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia.

PubMed

Wang, Jiguang; Khiabanian, Hossein; Rossi, Davide; Fabbri, Giulia; Gattei, Valter; Forconi, Francesco; Laurenti, Luca; Marasca, Roberto; Del Poeta, Giovanni; Foà, Robin; Pasqualucci, Laura; Gaidano, Gianluca; Rabadan, Raul

2014-12-11

Cancer is a clonal evolutionary process, caused by successive accumulation of genetic alterations providing milestones of tumor initiation, progression, dissemination, and/or resistance to certain therapeutic regimes. To unravel these milestones we propose a framework, tumor evolutionary directed graphs (TEDG), which is able to characterize the history of genetic alterations by integrating longitudinal and cross-sectional genomic data. We applied TEDG to a chronic lymphocytic leukemia (CLL) cohort of 70 patients spanning 12 years and show that: (a) the evolution of CLL follows a time-ordered process represented as a global flow in TEDG that proceeds from initiating events to late events; (b) there are two distinct and mutually exclusive evolutionary paths of CLL evolution; (c) higher fitness clones are present in later stages of the disease, indicating a progressive clonal replacement with more aggressive clones. Our results suggest that TEDG may constitute an effective framework to recapitulate the evolutionary history of tumors.

Universality and predictability in molecular quantitative genetics.

PubMed

Nourmohammad, Armita; Held, Torsten; Lässig, Michael

2013-12-01

Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary point of view, are important as targets of natural selection. We review recent developments in evolutionary theory and experiments that are expected to become building blocks of a quantitative genetics of molecular traits. We focus on universal evolutionary characteristics: these are largely independent of a trait's genetic basis, which is often at least partially unknown. We show that universal measurements can be used to infer selection on a quantitative trait, which determines its evolutionary mode of conservation or adaptation. Furthermore, universality is closely linked to predictability of trait evolution across lineages. We argue that universal trait statistics extends over a range of cellular scales and opens new avenues of quantitative evolutionary systems biology. Copyright © 2013. Published by Elsevier Ltd.

A Philosophical Perspective on Evolutionary Systems Biology

PubMed Central

Soyer, Orkun S.; Siegal, Mark L.

2015-01-01

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

Evolutionary disarmament in interspecific competition.

PubMed

Kisdi, E; Geritz, S A

2001-12-22

Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races.

Evolutionary disarmament in interspecific competition.

PubMed Central

Kisdi, E.; Geritz, S. A.

2001-01-01

Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races. PMID:11749715

Shaping communicative colour signals over evolutionary time

PubMed Central

Oyola Morales, José R.; Vital-García, Cuauhcihuatl; Hews, Diana K.; Martins, Emília P.

2016-01-01

Many evolutionary forces can shape the evolution of communicative signals, and the long-term impact of each force may depend on relative timing and magnitude. We use a phylogenetic analysis to infer the history of blue belly patches of Sceloporus lizards, and a detailed spectrophotometric analysis of four species to explore the specific forces shaping evolutionary change. We find that the ancestor of Sceloporus had blue patches. We then focus on four species; the first evolutionary shift (captured by comparison of S. merriami and S. siniferus) represents an ancient loss of the belly patch by S. siniferus, and the second evolutionary shift, bounded by S. undulatus and S. virgatus, represents a more recent loss of blue belly patch by S. virgatus. Conspicuousness measurements suggest that the species with the recent loss (S. virgatus) is the least conspicuous. Results for two other species (S. siniferus and S. merriami) suggest that over longer periods of evolutionary time, new signal colours have arisen which minimize absolute contrast with the habitat while maximizing conspicuousness to a lizard receiver. Specifically, males of the species representing an ancient loss of blue patch (S. siniferus) are more conspicuous than are females in the UV, whereas S. merriami males have evolved a green element that makes their belly patches highly sexually dimorphic but no more conspicuous than the white bellies of S. merriami females. Thus, our results suggest that natural selection may act more immediately to reduce conspicuousness, whereas sexual selection may have a more complex impact on communicative signals through the introduction of new colours. PMID:28018661

Shaping communicative colour signals over evolutionary time.

PubMed

Ossip-Drahos, Alison G; Oyola Morales, José R; Vital-García, Cuauhcihuatl; Zúñiga-Vega, J Jaime; Hews, Diana K; Martins, Emília P

2016-11-01

Many evolutionary forces can shape the evolution of communicative signals, and the long-term impact of each force may depend on relative timing and magnitude. We use a phylogenetic analysis to infer the history of blue belly patches of Sceloporus lizards, and a detailed spectrophotometric analysis of four species to explore the specific forces shaping evolutionary change. We find that the ancestor of Sceloporus had blue patches. We then focus on four species; the first evolutionary shift (captured by comparison of S. merriami and S. siniferus ) represents an ancient loss of the belly patch by S. siniferus , and the second evolutionary shift, bounded by S. undulatus and S. virgatus , represents a more recent loss of blue belly patch by S. virgatus . Conspicuousness measurements suggest that the species with the recent loss ( S. virgatus ) is the least conspicuous. Results for two other species ( S. siniferus and S. merriami ) suggest that over longer periods of evolutionary time, new signal colours have arisen which minimize absolute contrast with the habitat while maximizing conspicuousness to a lizard receiver. Specifically, males of the species representing an ancient loss of blue patch ( S. siniferus ) are more conspicuous than are females in the UV, whereas S. merriami males have evolved a green element that makes their belly patches highly sexually dimorphic but no more conspicuous than the white bellies of S. merriami females. Thus, our results suggest that natural selection may act more immediately to reduce conspicuousness, whereas sexual selection may have a more complex impact on communicative signals through the introduction of new colours.

Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus.

PubMed

Ruffner, Beat; Péchy-Tarr, Maria; Höfte, Monica; Bloemberg, Guido; Grunder, Jürg; Keel, Christoph; Maurhofer, Monika

2015-08-16

Root-colonizing fluorescent pseudomonads are known for their excellent abilities to protect plants against soil-borne fungal pathogens. Some of these bacteria produce an insecticidal toxin (Fit) suggesting that they may exploit insect hosts as a secondary niche. However, the ecological relevance of insect toxicity and the mechanisms driving the evolution of toxin production remain puzzling. Screening a large collection of plant-associated pseudomonads for insecticidal activity and presence of the Fit toxin revealed that Fit is highly indicative of insecticidal activity and predicts that Pseudomonas protegens and P. chlororaphis are exclusive Fit producers. A comparative evolutionary analysis of Fit toxin-producing Pseudomonas including the insect-pathogenic bacteria Photorhabdus and Xenorhadus, which produce the Fit related Mcf toxin, showed that fit genes are part of a dynamic genomic region with substantial presence/absence polymorphism and local variation in GC base composition. The patchy distribution and phylogenetic incongruence of fit genes indicate that the Fit cluster evolved via horizontal transfer, followed by functional integration of vertically transmitted genes, generating a unique Pseudomonas-specific insect toxin cluster. Our findings suggest that multiple independent evolutionary events led to formation of at least three versions of the Mcf/Fit toxin highlighting the dynamic nature of insect toxin evolution.

Evolutionary Design of Convolutional Neural Networks for Human Activity Recognition in Sensor-Rich Environments.

PubMed

Baldominos, Alejandro; Saez, Yago; Isasi, Pedro

2018-04-23

Human activity recognition is a challenging problem for context-aware systems and applications. It is gaining interest due to the ubiquity of different sensor sources, wearable smart objects, ambient sensors, etc. This task is usually approached as a supervised machine learning problem, where a label is to be predicted given some input data, such as the signals retrieved from different sensors. For tackling the human activity recognition problem in sensor network environments, in this paper we propose the use of deep learning (convolutional neural networks) to perform activity recognition using the publicly available OPPORTUNITY dataset. Instead of manually choosing a suitable topology, we will let an evolutionary algorithm design the optimal topology in order to maximize the classification F1 score. After that, we will also explore the performance of committees of the models resulting from the evolutionary process. Results analysis indicates that the proposed model was able to perform activity recognition within a heterogeneous sensor network environment, achieving very high accuracies when tested with new sensor data. Based on all conducted experiments, the proposed neuroevolutionary system has proved to be able to systematically find a classification model which is capable of outperforming previous results reported in the state-of-the-art, showing that this approach is useful and improves upon previously manually-designed architectures.

Evolutionary dynamics of Hepatitis C virus in a chronic HIV co-infected patient and its correlation with the immune status.

PubMed

Culasso, Andrés Carlos Alberto; Monzani, María Cecilia; Baré, Patricia; Campos, Rodolfo Hector

2018-05-04

The HCV evolutionary dynamics play a key role in the infection onset, maintenance of chronicity, pathogenicity, and drug resistance variants fixation, and are thought to be one of the main caveats in the development of an effective vaccine. Previous studies in HCV/HIV co-infected patients suggest that a decline in the immune status is related with increases in the HCV intra-host genetic diversity. However, these findings are based on single point sequence diversity measures or coalescence analyses in several virus-host interactions. In this work, we describe the molecular evolution of HCV-E2 region in a single HIV-co-infected patient with two clearly defined immune conditions. The phylogenetic analysis of the HCV-1a sequences from the studied patient showed that he was co-infected with three different viral lineages. These lineages were not evenly detected throughout time. The sequence diversity and coalescence analyses of these lineages suggested the action of different evolutionary patterns in different immune conditions: a slow rate, drift-like process in an immunocompromised condition (low levels of CD4+ T lymphocytes); and a fast rate, variant-switch process in an immunocompetent condition (high levels of CD4+ T lymphocytes). Copyright © 2017. Published by Elsevier B.V.

Versatility and Invariance in the Evolution of Homologous Heteromeric Interfaces

PubMed Central

Andreani, Jessica; Faure, Guilhem; Guerois, Raphaël

2012-01-01

Evolutionary pressures act on protein complex interfaces so that they preserve their complementarity. Nonetheless, the elementary interactions which compose the interface are highly versatile throughout evolution. Understanding and characterizing interface plasticity across evolution is a fundamental issue which could provide new insights into protein-protein interaction prediction. Using a database of 1,024 couples of close and remote heteromeric structural interologs, we studied protein-protein interactions from a structural and evolutionary point of view. We systematically and quantitatively analyzed the conservation of different types of interface contacts. Our study highlights astonishing plasticity regarding polar contacts at complex interfaces. It also reveals that up to a quarter of the residues switch out of the interface when comparing two homologous complexes. Despite such versatility, we identify two important interface descriptors which correlate with an increased conservation in the evolution of interfaces: apolar patches and contacts surrounding anchor residues. These observations hold true even when restricting the dataset to transiently formed complexes. We show that a combination of six features related either to sequence or to geometric properties of interfaces can be used to rank positions likely to share similar contacts between two interologs. Altogether, our analysis provides important tracks for extracting meaningful information from multiple sequence alignments of conserved binding partners and for discriminating near-native interfaces using evolutionary information. PMID:22952442

The evolutionary history of bears is characterized by gene flow across species

PubMed Central

Kumar, Vikas; Lammers, Fritjof; Bidon, Tobias; Pfenninger, Markus; Kolter, Lydia; Nilsson, Maria A.; Janke, Axel

2017-01-01

Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow. PMID:28422140

On the evolutionary status and pulsations of the recently discovered blue large-amplitude pulsators (BLAPs)

NASA Astrophysics Data System (ADS)

Romero, Alejandra D.; Córsico, A. H.; Althaus, L. G.; Pelisoli, I.; Kepler, S. O.

2018-06-01

The blue large-amplitude pulsators (BLAPs) constitute a new class of pulsating stars. They are hot stars with effective temperatures of ˜30 000 K and surface gravities of log g ˜ 4.9, that pulsate with periods in the range 20-40 min. Until now, their origin and evolutionary state, as well as the nature of their pulsations, were not been unveiled. In this paper, we propose that the BLAPs are the hot counterpart of the already known pulsating pre-extremely low mass (pre-ELM) white dwarf (WD) stars, that are He-core low-mass stars resulting from interacting binary evolution. Using fully evolutionary sequences, we show that the BLAPs are well represented by pre-ELM WD models with high effective temperature and stellar masses ˜0.34 M⊙. From the analysis of their pulsational properties, we find that the observed variabilities can be explained by high-order non-radial g-mode pulsations or, in the case of the shortest periods, also by low-order radial modes, including the fundamental radial mode. The theoretical modes with periods in the observed range are unstable due to the κ mechanism associated with the Z-bump in the opacity at log T ˜ 5.25.

Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution.

PubMed

Hopkins, Melanie J; Smith, Andrew B

2015-03-24

How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with "early bursts" of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today's oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis.

Evolutionary Design of Convolutional Neural Networks for Human Activity Recognition in Sensor-Rich Environments

PubMed Central

2018-01-01

Human activity recognition is a challenging problem for context-aware systems and applications. It is gaining interest due to the ubiquity of different sensor sources, wearable smart objects, ambient sensors, etc. This task is usually approached as a supervised machine learning problem, where a label is to be predicted given some input data, such as the signals retrieved from different sensors. For tackling the human activity recognition problem in sensor network environments, in this paper we propose the use of deep learning (convolutional neural networks) to perform activity recognition using the publicly available OPPORTUNITY dataset. Instead of manually choosing a suitable topology, we will let an evolutionary algorithm design the optimal topology in order to maximize the classification F1 score. After that, we will also explore the performance of committees of the models resulting from the evolutionary process. Results analysis indicates that the proposed model was able to perform activity recognition within a heterogeneous sensor network environment, achieving very high accuracies when tested with new sensor data. Based on all conducted experiments, the proposed neuroevolutionary system has proved to be able to systematically find a classification model which is capable of outperforming previous results reported in the state-of-the-art, showing that this approach is useful and improves upon previously manually-designed architectures. PMID:29690587

Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology.

PubMed

Ruths, Troy; Nakhleh, Luay

2013-05-07

Cis-regulatory networks (CRNs) play a central role in cellular decision making. Like every other biological system, CRNs undergo evolution, which shapes their properties by a combination of adaptive and nonadaptive evolutionary forces. Teasing apart these forces is an important step toward functional analyses of the different components of CRNs, designing regulatory perturbation experiments, and constructing synthetic networks. Although tests of neutrality and selection based on molecular sequence data exist, no such tests are currently available based on CRNs. In this work, we present a unique genotype model of CRNs that is grounded in a genomic context and demonstrate its use in identifying portions of the CRN with properties explainable by neutral evolutionary forces at the system, subsystem, and operon levels. We leverage our model against experimentally derived data from Escherichia coli. The results of this analysis show statistically significant and substantial neutral trends in properties previously identified as adaptive in origin--degree distribution, clustering coefficient, and motifs--within the E. coli CRN. Our model captures the tightly coupled genome-interactome of an organism and enables analyses of how evolutionary events acting at the genome level, such as mutation, and at the population level, such as genetic drift, give rise to neutral patterns that we can quantify in CRNs.

A Model of the Pulsating Extremely Low-mass White Dwarf Precursor WASP 0247-25B

NASA Astrophysics Data System (ADS)

Istrate, A. G.; Fontaine, G.; Heuser, C.

2017-10-01

We present an analysis of the evolutionary and pulsation properties of the extremely low-mass white dwarf precursor (B) component of the double-lined eclipsing system WASP 0247-25. Given that the fundamental parameters of that star have been obtained previously at a unique level of precision, WASP 0247-25B represents the ideal case for testing evolutionary models of this newly found category of pulsators. Taking into account the known constraints on the mass, orbital period, effective temperature, surface gravity, and atmospheric composition, we present a model that is compatible with these constraints and show pulsation modes that have periods very close to the observed values. Importantly, these modes are predicted to be excited. Although the overall consistency remains perfectible, the observable properties of WASP 0247-25B are closely reproduced. A key ingredient of our binary evolutionary models is represented by rotational mixing as the main competitor against gravitational settling. Depending on assumptions made about the values of the degree index ℓ for the observed pulsation modes, we found three possible seismic solutions. We discuss two tests, rotational splitting and multicolor photometry, that should readily identify the modes and discriminate between these solutions. However, this will require improved temporal resolution and higher S/N observations, which are currently unavailable.

Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members

PubMed Central

Yan, Xiping; Wang, Guosong; Liu, Hehe; Gan, Xiang; Zhang, Tao; Wang, Jiwen; Li, Liang

2015-01-01

Peroxisome proliferators-activated receptor (PPAR) gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors) domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors) are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3′ UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3′ UTR are essential for PPARs evolution and diversity functions acquired. PMID:25961030

Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members.

PubMed

Zhou, Tianyu; Yan, Xiping; Wang, Guosong; Liu, Hehe; Gan, Xiang; Zhang, Tao; Wang, Jiwen; Li, Liang

2015-01-01

Peroxisome proliferators-activated receptor (PPAR) gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors) domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors) are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3' UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3' UTR are essential for PPARs evolution and diversity functions acquired.

Microsporidia, amitochondrial protists, possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin.

PubMed

Peyretaillade, E; Broussolle, V; Peyret, P; Méténier, G; Gouy, M; Vivarès, C P

1998-06-01

An intronless gene encoding a protein of 592 amino acid residues with similarity to 70-kDa heat shock proteins (HSP70s) has been cloned and sequenced from the amitochondrial protist Encephalitozoon cuniculi (phylum Microsporidia). Southern blot analyses show the presence of a single gene copy located on chromosome XI. The encoded protein exhibits an N-terminal hydrophobic leader sequence and two motifs shared by proteobacterial and mitochondrially expressed HSP70 homologs. Phylogenetic analysis using maximum likelihood and evolutionary distances place the E. cuniculi sequence in the cluster of mitochondrially expressed HSP70s, with a higher evolutionary rate than those of homologous sequences. Similar results were obtained after cloning a fragment of the homologous gene in the closely related species E. hellem. The presence of a nuclear targeting signal-like sequence supports a role of the Encephalitozoon HSP70 as a molecular chaperone of nuclear proteins. No evidence for cytosolic or endoplasmic reticulum forms of HSP70 was obtained through PCR amplification. These data suggest that Encephalitozoon species have evolved from an ancestor bearing mitochondria, which is in disagreement with the postulated presymbiotic origin of Microsporidia. The specific role and intracellular localization of the mitochondrial HSP70-like protein remain to be elucidated.

Massive gene acquisitions in Mycobacterium indicus pranii provide a perspective on mycobacterial evolution

PubMed Central

Saini, Vikram; Raghuvanshi, Saurabh; Khurana, Jitendra P.; Ahmed, Niyaz; Hasnain, Seyed E.; Tyagi, Akhilesh K.; Tyagi, Anil K.

2012-01-01

Understanding the evolutionary and genomic mechanisms responsible for turning the soil-derived saprophytic mycobacteria into lethal intracellular pathogens is a critical step towards the development of strategies for the control of mycobacterial diseases. In this context, Mycobacterium indicus pranii (MIP) is of specific interest because of its unique immunological and evolutionary significance. Evolutionarily, it is the progenitor of opportunistic pathogens belonging to M. avium complex and is endowed with features that place it between saprophytic and pathogenic species. Herein, we have sequenced the complete MIP genome to understand its unique life style, basis of immunomodulation and habitat diversification in mycobacteria. As a case of massive gene acquisitions, 50.5% of MIP open reading frames (ORFs) are laterally acquired. We show, for the first time for Mycobacterium, that MIP genome has mosaic architecture. These gene acquisitions have led to the enrichment of selected gene families critical to MIP physiology. Comparative genomic analysis indicates a higher antigenic potential of MIP imparting it a unique ability for immunomodulation. Besides, it also suggests an important role of genomic fluidity in habitat diversification within mycobacteria and provides a unique view of evolutionary divergence and putative bottlenecks that might have eventually led to intracellular survival and pathogenic attributes in mycobacteria. PMID:22965120

The evolutionary history of bears is characterized by gene flow across species.

PubMed

Kumar, Vikas; Lammers, Fritjof; Bidon, Tobias; Pfenninger, Markus; Kolter, Lydia; Nilsson, Maria A; Janke, Axel

2017-04-19

Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.

Application of time series discretization using evolutionary programming for classification of precancerous cervical lesions.

PubMed

Acosta-Mesa, Héctor-Gabriel; Rechy-Ramírez, Fernando; Mezura-Montes, Efrén; Cruz-Ramírez, Nicandro; Hernández Jiménez, Rodolfo

2014-06-01

In this work, we present a novel application of time series discretization using evolutionary programming for the classification of precancerous cervical lesions. The approach optimizes the number of intervals in which the length and amplitude of the time series should be compressed, preserving the important information for classification purposes. Using evolutionary programming, the search for a good discretization scheme is guided by a cost function which considers three criteria: the entropy regarding the classification, the complexity measured as the number of different strings needed to represent the complete data set, and the compression rate assessed as the length of the discrete representation. This discretization approach is evaluated using a time series data based on temporal patterns observed during a classical test used in cervical cancer detection; the classification accuracy reached by our method is compared with the well-known times series discretization algorithm SAX and the dimensionality reduction method PCA. Statistical analysis of the classification accuracy shows that the discrete representation is as efficient as the complete raw representation for the present application, reducing the dimensionality of the time series length by 97%. This representation is also very competitive in terms of classification accuracy when compared with similar approaches. Copyright © 2014 Elsevier Inc. All rights reserved.

Characterization of the Avian Trojan Gene Family Reveals Contrasting Evolutionary Constraints

PubMed Central

Petrov, Petar; Syrjänen, Riikka; Smith, Jacqueline; Gutowska, Maria Weronika; Uchida, Tatsuya; Vainio, Olli; Burt, David W

2015-01-01

“Trojan” is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules. PMID:25803627

Characterization of the avian Trojan gene family reveals contrasting evolutionary constraints.

PubMed

Petrov, Petar; Syrjänen, Riikka; Smith, Jacqueline; Gutowska, Maria Weronika; Uchida, Tatsuya; Vainio, Olli; Burt, David W

2015-01-01

"Trojan" is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules.

Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours

PubMed Central

Wickham, Shelley; Large, Maryanne C.J; Poladian, Leon; Jermiin, Lars S

2005-01-01

Many butterfly species possess ‘structural’ colour, where colour is due to optical microstructures found in the wing scales. A number of such structures have been identified in butterfly scales, including three variations on a simple multi-layer structure. In this study, we optically characterize examples of all three types of multi-layer structure, as found in 10 species. The optical mechanism of the suppression and exaggeration of the angle-dependent optical properties (iridescence) of these structures is described. In addition, we consider the phylogeny of the butterflies, and are thus able to relate the optical properties of the structures to their evolutionary development. By applying two different types of analysis, the mechanism of adaptation is addressed. A simple parsimony analysis, in which all evolutionary changes are given an equal weighting, suggests convergent evolution of one structure. A Dollo parsimony analysis, in which the evolutionary ‘cost’ of losing a structure is less than that of gaining it, implies that ‘latent’ structures can be reused. PMID:16849221

Toward a revised evolutionary adaptationist analysis of depression: the social navigation hypothesis.

PubMed

Watson, Paul J; Andrews, Paul W

2002-10-01

Evolutionary biologists use Darwinian theory and functional design ("reverse engineering") analyses, to develop and test hypotheses about the adaptive functions of traits. Based upon a consideration of human social life and a functional design analysis of depression's core symptomatology we offer a comprehensive theory of its adaptive significance called the Social Navigation Hypothesis (SNH). The SNH attempts to account for all intensities of depression based on standard evolutionary theories of sociality, communication and psychological pain. The SNH suggests that depression evolved to perform two complimentary social problem-solving functions. First, depression induces cognitive changes that focus and enhance capacities for the accurate analysis and solution of key social problems, suggesting a social rumination function. Second, the costs associated with the anhedonia and psychomotor perturbation of depression can persuade reluctant social partners to provide help or make concessions via two possible mechanisms, namely, honest signaling and passive, unintentional fitness extortion. Thus it may also have a social motivation function.

Meta-analysis of magnitudes, differences and variation in evolutionary parameters.

PubMed

Morrissey, M B

2016-10-01

Meta-analysis is increasingly used to synthesize major patterns in the large literatures within ecology and evolution. Meta-analytic methods that do not account for the process of observing data, which we may refer to as 'informal meta-analyses', may have undesirable properties. In some cases, informal meta-analyses may produce results that are unbiased, but do not necessarily make the best possible use of available data. In other cases, unbiased statistical noise in individual reports in the literature can potentially be converted into severe systematic biases in informal meta-analyses. I first present a general description of how failure to account for noise in individual inferences should be expected to lead to biases in some kinds of meta-analysis. In particular, informal meta-analyses of quantities that reflect the dispersion of parameters in nature, for example, the mean absolute value of a quantity, are likely to be generally highly misleading. I then re-analyse three previously published informal meta-analyses, where key inferences were of aspects of the dispersion of values in nature, for example, the mean absolute value of selection gradients. Major biological conclusions in each original informal meta-analysis closely match those that could arise as artefacts due to statistical noise. I present alternative mixed-model-based analyses that are specifically tailored to each situation, but where all analyses may be implemented with widely available open-source software. In each example meta-re-analysis, major conclusions change substantially. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

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

PubMed

Kögler, Anja; Schmidt, Thomas; Wenke, Torsten

2017-11-01

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

Evolutionary dynamics on graphs: Efficient method for weak selection

NASA Astrophysics Data System (ADS)

Fu, Feng; Wang, Long; Nowak, Martin A.; Hauert, Christoph

2009-04-01

Investigating the evolutionary dynamics of game theoretical interactions in populations where individuals are arranged on a graph can be challenging in terms of computation time. Here, we propose an efficient method to study any type of game on arbitrary graph structures for weak selection. In this limit, evolutionary game dynamics represents a first-order correction to neutral evolution. Spatial correlations can be empirically determined under neutral evolution and provide the basis for formulating the game dynamics as a discrete Markov process by incorporating a detailed description of the microscopic dynamics based on the neutral correlations. This framework is then applied to one of the most intriguing questions in evolutionary biology: the evolution of cooperation. We demonstrate that the degree heterogeneity of a graph impedes cooperation and that the success of tit for tat depends not only on the number of rounds but also on the degree of the graph. Moreover, considering the mutation-selection equilibrium shows that the symmetry of the stationary distribution of states under weak selection is skewed in favor of defectors for larger selection strengths. In particular, degree heterogeneity—a prominent feature of scale-free networks—generally results in a more pronounced increase in the critical benefit-to-cost ratio required for evolution to favor cooperation as compared to regular graphs. This conclusion is corroborated by an analysis of the effects of population structures on the fixation probabilities of strategies in general 2×2 games for different types of graphs. Computer simulations confirm the predictive power of our method and illustrate the improved accuracy as compared to previous studies.

Evolutionary relationships among pollinators and repeated pollinator sharing in sexually deceptive orchids.

PubMed

Phillips, R D; Brown, G R; Dixon, K W; Hayes, C; Linde, C C; Peakall, R

2017-09-01

The mechanism of pollinator attraction is predicted to strongly influence both plant diversification and the extent of pollinator sharing between species. Sexually deceptive orchids rely on mimicry of species-specific sex pheromones to attract their insect pollinators. Given that sex pheromones tend to be conserved among related species, we predicted that in sexually deceptive orchids, (i) pollinator sharing is rare, (ii) closely related orchids use closely related pollinators and (iii) there is strong bias in the wasp lineages exploited by orchids. We focused on species that are pollinated by sexual deception of thynnine wasps in the distantly related genera Caladenia and Drakaea, including new field observations for 45 species of Caladenia. Specialization was extreme with most orchids using a single pollinator species. Unexpectedly, seven cases of pollinator sharing were found, including two between Caladenia and Drakaea, which exhibit strikingly different floral morphology. Phylogenetic analysis of pollinators using four nuclear sequence loci demonstrated that although orchids within major clades primarily use closely related pollinator species, up to 17% of orchids within these clades are pollinated by a member of a phylogenetically distant wasp genus. Further, compared to the total diversity of thynnine wasps within the study region, orchids show a strong bias towards exploiting certain genera. Although these patterns may arise through conservatism in the chemical classes used in sex pheromones, apparent switches between wasp clades suggest unexpected flexibility in floral semiochemical production. Alternatively, wasp sex pheromones within lineages may exhibit greater chemical diversity than currently appreciated. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Genes mirror geography in Daphnia magna.

PubMed

Fields, Peter D; Reisser, Céline; Dukić, Marinela; Haag, Christoph R; Ebert, Dieter

2015-09-01

Identifying the presence and magnitude of population genetic structure remains a major consideration in evolutionary biology as doing so allows one to understand the demographic history of a species as well as make predictions of how the evolutionary process will proceed. Next-generation sequencing methods allow us to reconsider previous ideas and conclusions concerning the distribution of genetic variation, and what this distribution implies about a given species evolutionary history. A previous phylogeographic study of the crustacean Daphnia magna suggested that, despite strong genetic differentiation among populations at a local scale, the species shows only moderate genetic structure across its European range, with a spatially patchy occurrence of individual lineages. We apply RAD sequencing to a sample of D. magna collected across a wide swath of the species' Eurasian range and analyse the data using principle component analysis (PCA) of genetic variation and Procrustes analytical approaches, to quantify spatial genetic structure. We find remarkable consistency between the first two PCA axes and the geographic coordinates of individual sampling points, suggesting that, on a continent-wide scale, genetic differentiation is driven to a large extent by geographic distance. The observed pattern is consistent with unimpeded (i.e. no barriers, landscape or otherwise) migration at large spatial scales, despite the fragmented and patchy nature of favourable habitats at local scales. With high-resolution genetic data similar patterns may be uncovered for other species with wide geographic distributions, allowing an increased understanding of how genetic drift and selection have shaped their evolutionary history. © 2015 John Wiley & Sons Ltd.

Dentine morphology of Atapuerca-Sima de los Huesos lower molars: Evolutionary implications through three-dimensional geometric morphometric analysis.

PubMed

Hanegraef, Hester; Martinón-Torres, María; Martínez de Pinillos, Marina; Martín-Francés, Laura; Vialet, Amélie; Arsuaga, Juan Luis; Bermúdez de Castro, José María

2018-06-01

This study aims to explore the affinities of the Sima de los Huesos (SH) population in relation to Homo neanderthalensis, Arago, and early and contemporary Homo sapiens. By characterizing SH intra-population variation, we test current models to explain the Neanderthal origins. Three-dimensional reconstructions of dentine surfaces of lower first and second molars were produced by micro-computed tomography. Landmarks and sliding semilandmarks were subjected to generalized Procrustes analysis and principal components analysis. SH is often similar in shape to Neanderthals, and both groups are generally discernible from Homo sapiens. For example, the crown height of SH and Neanderthals is lower than for modern humans. Differences in the presence of a mid-trigonid crest are also observed, with contemporary Homo sapiens usually lacking this feature. Although SH and Neanderthals show strong affinities, they can be discriminated based on certain traits. SH individuals are characterized by a lower intra-population variability, and show a derived dental reduction in lower second molars compared to Neanderthals. SH also differs in morphological features from specimens that are often classified as Homo heidelbergensis, such as a lower crown height and less pronounced mid-trigonid crest in the Arago fossils. Our results are compatible with the idea that multiple evolutionary lineages or populations coexisted in Europe during the Middle Pleistocene, with the SH paradigm phylogenetically closer to Homo neanderthalensis. Further research could support the possibility of SH as a separate taxon. Alternatively, SH could be a subspecies of Neanderthals, with the variability of this clade being remarkably higher than previously thought. © 2018 Wiley Periodicals, Inc.

Darwin's "Imaginary Illustrations": Creatively Teaching Evolutionary Concepts & the Nature of Science

ERIC Educational Resources Information Center

Love, Alan C.

2010-01-01

An overlooked feature of Darwin's work is his use of "imaginary illustrations" to show that natural selection is competent to produce adaptive, evolutionary change. When set in the context of Darwin's methodology, these thought experiments provide a novel way to teach natural selection and the nature of science.

Attachment in Middle Childhood: An Evolutionary-Developmental Perspective

ERIC Educational Resources Information Center

Del Giudice, Marco

2015-01-01

Middle childhood is a key transitional stage in the development of attachment processes and representations. Here I discuss the middle childhood transition from an evolutionary-developmental perspective and show how this approach offers fresh insight into the function and organization of attachment in this life stage. I begin by presenting an…

The Relationship between College Zoology Students' Beliefs about Evolutionary Theory and Religion.

ERIC Educational Resources Information Center

Sinclair, Anne; And Others

1997-01-01

Researchers administered surveys to college zoology students prior to, and immediately following a study of evolutionary theory, to assess their understanding and acceptance of evidence supporting the theory. Results showed students had many misconceptions about the theory. Their beliefs interfered with their ability to objectively view scientific…

From Down House Landlord to Brazilian High School Students: What Happened to Evolutionary Knowledge on the Way?

ERIC Educational Resources Information Center

Bizzo, Neilo Marco Vincenzo

1994-01-01

Reports results of interviews and tests carried out with students after they had been taught the topic of evolution. Different interpretations of Charles Darwin's theories are also analyzed. Results revealed that students show a poor understanding of evolutionary theories. (ZWH)

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…

Concept Analysis of Spirituality: An Evolutionary Approach.

PubMed

Weathers, Elizabeth; McCarthy, Geraldine; Coffey, Alice

2016-04-01

The aim of this article is to clarify the concept of spirituality for future nursing research. Previous concept analyses of spirituality have mostly reviewed the conceptual literature with little consideration of the empirical literature. The literature reviewed in prior concept analyses extends from 1972 to 2005, with no analysis conducted in the past 9 years. Rodgers' evolutionary framework was used to review both the theoretical and empirical literature pertaining to spirituality. Evolutionary concept analysis is a formal method of philosophical inquiry, in which papers are analyzed to identify attributes, antecedents, and consequences of the concept. Empirical and conceptual literature. Three defining attributes of spirituality were identified: connectedness, transcendence, and meaning in life. A conceptual definition of spirituality was proposed based on the findings. Also, four antecedents and five primary consequences of spirituality were identified. Spirituality is a complex concept. This concept analysis adds some clarification by proposing a definition of spirituality that is underpinned by both conceptual and empirical research. Furthermore, exemplars of spirituality, based on prior qualitative research, are presented to support the findings. Hence, the findings of this analysis could guide future nursing research on spirituality. © 2015 Wiley Periodicals, Inc.

The shape of pterosaur evolution: evidence from the fossil record.

PubMed

Dyke, G J; McGowan, A J; Nudds, R L; Smith, D

2009-04-01

Although pterosaurs are a well-known lineage of Mesozoic flying reptiles, their fossil record and evolutionary dynamics have never been adequately quantified. On the basis of a comprehensive data set of fossil occurrences correlated with taxon-specific limb measurements, we show that the geological ages of pterosaur specimens closely approximate hypothesized patterns of phylogenetic divergence. Although the fossil record has expanded greatly in recent years, collectorship still approximates a sigmoid curve over time as many more specimens (and thus taxa) still remain undiscovered, yet our data suggest that the pterosaur fossil record is unbiased by sites of exceptional preservation (lagerstätte). This is because as new species are discovered the number of known formations and sites yielding pterosaur fossils has also increased - this would not be expected if the bulk of the record came from just a few exceptional faunas. Pterosaur morphological diversification is, however, strongly age biased: rarefaction analysis shows that peaks of diversity occur in the Late Jurassic and Early Cretaceous correlated with periods of increased limb disparity. In this respect, pterosaurs appear unique amongst flying vertebrates in that their disparity seems to have peaked relatively late in clade history. Comparative analyses also show that there is little evidence that the evolutionary diversification of pterosaurs was in any way constrained by the appearance and radiation of birds.

A geometric morphometric analysis of hominin lower molars: Evolutionary implications and overview of postcanine dental variation.

PubMed

Gómez-Robles, Aida; Bermúdez de Castro, José María; Martinón-Torres, María; Prado-Simón, Leyre; Arsuaga, Juan Luis

2015-05-01

Lower molars have been extensively studied in the context of hominin evolution using classic and geometric morphometric analyses, 2D and 3D approaches, evaluations of the external (outer enamel surface) and internal anatomy (dentine, pulp chamber, and radicular canals), and studies of the crown and root variation. In this study, we present a 2D geometric morphometric analysis of the crown anatomy of lower first, second, and third molars of a broad sample of hominins, including Pliocene and Lower, Middle, and Upper Pleistocene species coming from Africa, Asia, and Europe. We show that shape variability increases from first to second and third molars. While first molars tend to retain a relatively stable 5-cusped conformation throughout the hominin fossil record, second and third molars show marked distal reductions in later Homo species. This trend to distal reduction is similar to that observed in previous studies of premolars and upper second and third molars, and points to a correlated reduction of distal areas across the whole postcanine dentition. Results on lower molar variation, as well as on other postcanine teeth, show certain trends in European Pleistocene populations from the Atapuerca sites. Middle Pleistocene hominins from Sima de los Huesos show Neanderthal affinities and strong dental reduction, especially in the most distal molars. The degree of dental reduction in this population is stronger than that observed in classic Neanderthals. Homo antecessor hominins from Gran Dolina-TD6 have primitive lower teeth that contrast with their more derived upper teeth. The evolutionary implications of these dental affinities are discussed in light of recent paleogenetic studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparative Sex Chromosome Genomics in Snakes: Differentiation, Evolutionary Strata, and Lack of Global Dosage Compensation

PubMed Central

Zektser, Yulia; Mahajan, Shivani; Bachtrog, Doris

2013-01-01

Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution. PMID:24015111

Parametric Sensitivity Analysis of Oscillatory Delay Systems with an Application to Gene Regulation.

PubMed

Ingalls, Brian; Mincheva, Maya; Roussel, Marc R

2017-07-01

A parametric sensitivity analysis for periodic solutions of delay-differential equations is developed. Because phase shifts cause the sensitivity coefficients of a periodic orbit to diverge, we focus on sensitivities of the extrema, from which amplitude sensitivities are computed, and of the period. Delay-differential equations are often used to model gene expression networks. In these models, the parametric sensitivities of a particular genotype define the local geometry of the evolutionary landscape. Thus, sensitivities can be used to investigate directions of gradual evolutionary change. An oscillatory protein synthesis model whose properties are modulated by RNA interference is used as an example. This model consists of a set of coupled delay-differential equations involving three delays. Sensitivity analyses are carried out at several operating points. Comments on the evolutionary implications of the results are offered.

Protein sectors: evolutionary units of three-dimensional structure

PubMed Central

Halabi, Najeeb; Rivoire, Olivier; Leibler, Stanislas; Ranganathan, Rama

2011-01-01

Proteins display a hierarchy of structural features at primary, secondary, tertiary, and higher-order levels, an organization that guides our current understanding of their biological properties and evolutionary origins. Here, we reveal a structural organization distinct from this traditional hierarchy by statistical analysis of correlated evolution between amino acids. Applied to the S1A serine proteases, the analysis indicates a decomposition of the protein into three quasi-independent groups of correlated amino acids that we term “protein sectors”. Each sector is physically connected in the tertiary structure, has a distinct functional role, and constitutes an independent mode of sequence divergence in the protein family. Functionally relevant sectors are evident in other protein families as well, suggesting that they may be general features of proteins. We propose that sectors represent a structural organization of proteins that reflects their evolutionary histories. PMID:19703402

The uncertain foundation of neo-Darwinism: metaphysical and epistemological pluralism in the evolutionary synthesis.

PubMed

Delisle, Richard G

2009-06-01

The Evolutionary Synthesis is often seen as a unification process in evolutionary biology, one which provided this research area with a solid common theoretical foundation. As such, neo-Darwinism is believed to constitute from this time onward a single, coherent, and unified movement offering research guidelines for investigations. While this may be true if evolutionary biology is solely understood as centred around evolutionary mechanisms, an entirely different picture emerges once other aspects of the founding neo-Darwinists' views are taken into consideration, aspects potentially relevant to the elaboration of an evolutionary worldview: the tree of life, the ontological distinctions of the main cosmic entities (inert matter, biological organisms, mind), the inherent properties of self-organizing matter, evolutionary ethics, and so on. Profound tensions and inconsistencies are immediately revealed in the neo-Darwinian movement once this broader perspective is adopted. This pluralism is such that it is possible to identify at least three distinct and quasi-incommensurable epistemological/metaphysical frameworks as providing a proper foundation for neo-Darwinism. The analysis of the views of Theodosius Dobzhansky, Bernhard Rensch, and Ernst Mayr will illustrate this untenable pluralism, one which requires us to conceive of the neo-Darwinian research agenda as being conducted in more than one research programme or research tradition at the same time.

Laboratory evolution of the migratory polymorphism in the sand cricket: combining physiology with quantitative genetics.

PubMed

Roff, Derek A; Fairbairn, Daphne J

2007-01-01

Predicting evolutionary change is the central goal of evolutionary biology because it is the primary means by which we can test evolutionary hypotheses. In this article, we analyze the pattern of evolutionary change in a laboratory population of the wing-dimorphic sand cricket Gryllus firmus resulting from relaxation of selection favoring the migratory (long-winged) morph. Based on a well-characterized trade-off between fecundity and flight capability, we predict that evolution in the laboratory environment should result in a reduction in the proportion of long-winged morphs. We also predict increased fecundity and reduced functionality and weight of the major flight muscles in long-winged females but little change in short-winged (flightless) females. Based on quantitative genetic theory, we predict that the regression equation describing the trade-off between ovary weight and weight of the major flight muscles will show a change in its intercept but not in its slope. Comparisons across generations verify all of these predictions. Further, using values of genetic parameters estimated from previous studies, we show that a quantitative genetic simulation model can account for not only the qualitative changes but also the evolutionary trajectory. These results demonstrate the power of combining quantitative genetic and physiological approaches for understanding the evolution of complex traits.

Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes

PubMed Central

Timinskas, Kęstutis; Balvočiūtė, Monika; Timinskas, Albertas; Venclovas, Česlovas

2014-01-01

The analysis of ∼2000 bacterial genomes revealed that they all, without a single exception, encode one or more DNA polymerase III α-subunit (PolIIIα) homologs. Classified into C-family of DNA polymerases they come in two major forms, PolC and DnaE, related by ancient duplication. While PolC represents an evolutionary compact group, DnaE can be further subdivided into at least three groups (DnaE1-3). We performed an extensive analysis of various sequence, structure and surface properties of all four polymerase groups. Our analysis suggests a specific evolutionary pathway leading to PolC and DnaE from the last common ancestor and reveals important differences between extant polymerase groups. Among them, DnaE1 and PolC show the highest conservation of the analyzed properties. DnaE3 polymerases apparently represent an ‘impaired’ version of DnaE1. Nonessential DnaE2 polymerases, typical for oxygen-using bacteria with large GC-rich genomes, have a number of features in common with DnaE3 polymerases. The analysis of polymerase distribution in genomes revealed three major combinations: DnaE1 either alone or accompanied by one or more DnaE2s, PolC + DnaE3 and PolC + DnaE1. The first two combinations are present in Escherichia coli and Bacillus subtilis, respectively. The third one (PolC + DnaE1), found in Clostridia, represents a novel, so far experimentally uncharacterized, set. PMID:24106089

Two-step evolution of endosymbiosis between hydra and algae.

PubMed

Ishikawa, Masakazu; Shimizu, Hiroshi; Nozawa, Masafumi; Ikeo, Kazuho; Gojobori, Takashi

2016-10-01

In the Hydra vulgaris group, only 2 of the 25 strains in the collection of the National Institute of Genetics in Japan currently show endosymbiosis with green algae. However, whether the other non-symbiotic strains also have the potential to harbor algae remains unknown. The endosymbiotic potential of non-symbiotic strains that can harbor algae may have been acquired before or during divergence of the strains. With the aim of understanding the evolutionary process of endosymbiosis in the H. vulgaris group, we examined the endosymbiotic potential of non-symbiotic strains of the H. vulgaris group by artificially introducing endosymbiotic algae. We found that 12 of the 23 non-symbiotic strains were able to harbor the algae until reaching the grand-offspring through the asexual reproduction by budding. Moreover, a phylogenetic analysis of mitochondrial genome sequences showed that all the strains with endosymbiotic potential grouped into a single cluster (cluster γ). This cluster contained two strains (J7 and J10) that currently harbor algae; however, these strains were not the closest relatives. These results suggest that evolution of endosymbiosis occurred in two steps; first, endosymbiotic potential was gained once in the ancestor of the cluster γ lineage; second, strains J7 and J10 obtained algae independently after the divergence of the strains. By demonstrating the evolution of the endosymbiotic potential in non-symbiotic H. vulgaris group strains, we have clearly distinguished two evolutionary steps. The step-by-step evolutionary process provides significant insight into the evolution of endosymbiosis in cnidarians. Copyright © 2016 Elsevier Inc. All rights reserved.

Generating high-speed dynamic running gaits in a quadruped robot using an evolutionary search.

PubMed

Krasny, Darren P; Orin, David E

2004-08-01

Over the past several decades, there has been a considerable interest in investigating high-speed dynamic gaits for legged robots. While much research has been published, both in the biomechanics and engineering fields regarding the analysis of these gaits, no single study has adequately characterized the dynamics of high-speed running as can be achieved in a realistic, yet simple, robotic system. The goal of this paper is to find the most energy-efficient, natural, and unconstrained gallop that can be achieved using a simulated quadrupedal robot with articulated legs, asymmetric mass distribution, and compliant legs. For comparison purposes, we also implement the bound and canter. The model used here is planar, although we will show that it captures much of the predominant dynamic characteristics observed in animals. While it is not our goal to prove anything about biological locomotion, the dynamic similarities between the gaits we produce and those found in animals does indicate a similar underlying dynamic mechanism. Thus, we will show that achieving natural, efficient high-speed locomotion is possible even with a fairly simple robotic system. To generate the high-speed gaits, we use an efficient evolutionary algorithm called set-based stochastic optimization. This algorithm finds open-loop control parameters to generate periodic trajectories for the body. Several alternative methods are tested to generate periodic trajectories for the legs. The combined solutions found by the evolutionary search and the periodic-leg methods, over a range of speeds up to 10.0 m/s, reveal "biological" characteristics that are emergent properties of the underlying gaits.

Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont.

PubMed

Warshan, Denis; Liaimer, Anton; Pederson, Eric; Kim, Sea-Yong; Shapiro, Nicole; Woyke, Tanja; Altermark, Bjørn; Pawlowski, Katharina; Weyman, Philip D; Dupont, Christopher L; Rasmussen, Ulla

2018-05-01

Cyanobacteria belonging to the genus Nostoc comprise free-living strains and also facultative plant symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here, we compared the genomes derived from 11 symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history. A polyphyletic origin was found for Nostoc strains which enter only extracellular symbioses, and inference of transfer events implied that this trait was likely acquired several times in the evolution of the Nostocales. Symbiotic Nostoc strains showed enriched functions in transport and metabolism of organic sulfur, chemotaxis and motility, as well as the uptake of phosphate, branched-chain amino acids, and ammonium. The genomes of the intracellular clade differ from that of other Nostoc strains, with a gain/enrichment of genes encoding proteins to generate l-methionine from sulfite and pathways for the degradation of the plant metabolites vanillin and vanillate, and of the macromolecule xylan present in plant cell walls. These compounds could function as C-sources for members of the intracellular clade. Molecular clock analysis indicated that the intracellular clade emerged ca. 600 Ma, suggesting that intracellular Nostoc symbioses predate the origin of land plants and the emergence of their extant hosts.

Rate of Amino Acid Substitution Is Influenced by the Degree and Conservation of Male-Biased Transcription Over 50 Myr of Drosophila Evolution

PubMed Central

Grath, Sonja; Parsch, John

2012-01-01

Sex-biased gene expression (i.e., the differential expression of genes between males and females) is common among sexually reproducing species. However, genes often differ in their sex-bias classification or degree of sex bias between species. There is also an unequal distribution of sex-biased genes (especially male-biased genes) between the X chromosome and the autosomes. We used whole-genome expression data and evolutionary rate estimates for two different Drosophilid lineages, melanogaster and obscura, spanning an evolutionary time scale of around 50 Myr to investigate the influence of sex-biased gene expression and chromosomal location on the rate of molecular evolution. In both lineages, the rate of protein evolution correlated positively with the male/female expression ratio. Genes with highly male-biased expression, genes expressed specifically in male reproductive tissues, and genes with conserved male-biased expression over long evolutionary time scales showed the fastest rates of evolution. An analysis of sex-biased gene evolution in both lineages revealed evidence for a “fast-X” effect in which the rate of evolution was greater for X-linked than for autosomal genes. This pattern was particularly pronounced for male-biased genes. Genes located on the obscura “neo-X” chromosome, which originated from a recent X-autosome fusion, showed rates of evolution that were intermediate between genes located on the ancestral X-chromosome and the autosomes. This suggests that the shift to X-linkage led to an increase in the rate of molecular evolution. PMID:22321769

Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont

PubMed Central

Liaimer, Anton; Pederson, Eric; Kim, Sea-Yong; Shapiro, Nicole; Woyke, Tanja; Altermark, Bjørn; Pawlowski, Katharina; Weyman, Philip D; Dupont, Christopher L

2018-01-01

Abstract Cyanobacteria belonging to the genus Nostoc comprise free-living strains and also facultative plant symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here, we compared the genomes derived from 11 symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history. A polyphyletic origin was found for Nostoc strains which enter only extracellular symbioses, and inference of transfer events implied that this trait was likely acquired several times in the evolution of the Nostocales. Symbiotic Nostoc strains showed enriched functions in transport and metabolism of organic sulfur, chemotaxis and motility, as well as the uptake of phosphate, branched-chain amino acids, and ammonium. The genomes of the intracellular clade differ from that of other Nostoc strains, with a gain/enrichment of genes encoding proteins to generate l-methionine from sulfite and pathways for the degradation of the plant metabolites vanillin and vanillate, and of the macromolecule xylan present in plant cell walls. These compounds could function as C-sources for members of the intracellular clade. Molecular clock analysis indicated that the intracellular clade emerged ca. 600 Ma, suggesting that intracellular Nostoc symbioses predate the origin of land plants and the emergence of their extant hosts. PMID:29554291

The evolutionary transition from subsocial to eusocial behaviour in Dictyoptera: phylogenetic evidence for modification of the "shift-in-dependent-care" hypothesis with a new subsocial cockroach.

PubMed

Pellens, Roseli; D'Haese, Cyrille A; Bellés, Xavier; Piulachs, Maria-Dolors; Legendre, Frédéric; Wheeler, Ward C; Grandcolas, Philippe

2007-05-01

Cockroaches have always been used to understand the first steps of social evolution in termites because they are close relatives with less complex and integrated social behaviour. Termites are all eusocial and ingroup comparative analysis would be useless to infer the origin of their social behaviour. The cockroach genus Cryptocercus was used as a so-called "prototermite" model because it shows key-attributes similar to the termites (except Termitidae): wood-feeding, intestinal flagellates and subsocial behaviour. In spite of these comparisons between this subsocial cockroach and eusocial termites, the early and remote origin of eusocial behaviour in termites is not well understood yet and the study of other relevant "prototermite" models is however needed. A molecular phylogenetic analysis was carried out to validate a new "prototermite" model, Parasphaeria boleiriana which shows a peculiar combination of these key-attributes. It shows that these attributes of Parasphaeria boleiriana have an independent origin from those of other wood-eating cockroaches and termites. The case of P. boleiriana suggests that a short brood care was selected for with life on an ephemeral wood resource, even with the need for transmission of flagellates. These new phylogenetic insights modify evolutionary hypotheses, contradicting the assumption made with Cryptocercus model that a long brood care is necessary for cooperation between broods in the "shift-in-dependent-care" hypothesis. An ephemeral wood resource is suggested to prompt generation overlap and the evolution of cooperation, even if brood care is shortened.

Variability of metapodials in primates with rudimentary digits: Ateles geoffroyi, Colobus guereza, and Perodicticus potto.

PubMed

Tague, Robert G

2002-03-01

A tenet of evolutionary theory is that, within a species, phenotypic variability is inversely related to the intensity of stabilizing selection. A corollary is that a rudimentary or vestigial structure should be highly variable. This relationship between rudimentation and variability, however, may simply be part of a continuum, as several studies have shown that variability and size of a structure are inversely related. This study tests whether the first metacarpal (MC1) in Ateles geoffroyi and Colobus guereza and the second metacarpal (MC2) in Perodicticus potto are highly variable in their lengths relative to their other metapodials. The former two species have rudimentary thumbs, and the latter species has a rudimentary index finger. Fourteen other species of primates are included in the comparison. The results show that MC1 in A. geoffroyi and C. guereza and MC2 in P. potto are the relatively shortest first and second metapodials, respectively, in this sample of primates. However, an intraspecific analysis shows that neither MC1 in A. geoffroyi and C. guereza nor MC2 in P. potto is significantly more variable than the other metapodials. Nevertheless, an interspecific analysis shows that MC1 in A. geoffroyi and C. guereza is relatively the most variable among the first metapodials (i.e., MC1 and first metatarsal) in this study. MC2 in P. potto, however, is of relatively low variability compared with the other primates. These contrasting results are interpreted in terms of the developmental and evolutionary biology of digits. Copyright 2002 Wiley-Liss, Inc.

Assessing facial attractiveness: individual decisions and evolutionary constraints

PubMed Central

Kocsor, Ferenc; Feldmann, Adam; Bereczkei, Tamas; Kállai, János

2013-01-01

Background Several studies showed that facial attractiveness, as a highly salient social cue, influences behavioral responses. It has also been found that attractive faces evoke distinctive neural activation compared to unattractive or neutral faces. Objectives Our aim was to design a face recognition task where individual preferences for facial cues are controlled for, and to create conditions that are more similar to natural circumstances in terms of decision making. Design In an event-related functional magnetic resonance imaging (fMRI) experiment, subjects were shown attractive and unattractive faces, categorized on the basis of their own individual ratings. Results Statistical analysis of all subjects showed elevated brain activation for attractive opposite-sex faces in contrast to less attractive ones in regions that previously have been reported to show enhanced activation with increasing attractiveness level (e.g. the medial and superior occipital gyri, fusiform gyrus, precentral gyrus, and anterior cingular cortex). Besides these, females showed additional brain activation in areas thought to be involved in basic emotions and desires (insula), detection of facial emotions (superior temporal gyrus), and memory retrieval (hippocampus). Conclusions From these data, we speculate that because of the risks involving mate choice faced by women during evolutionary times, selection might have preferred the development of an elaborated neural system in females to assess the attractiveness and social value of male faces. PMID:24693356

In silico identification and analysis of phytoene synthase genes in plants.

PubMed

Han, Y; Zheng, Q S; Wei, Y P; Chen, J; Liu, R; Wan, H J

2015-08-14

In this study, we examined phytoene synthetase (PSY), the first key limiting enzyme in the synthesis of carotenoids and catalyzing the formation of geranylgeranyl pyrophosphate in terpenoid biosynthesis. We used known amino acid sequences of the PSY gene in tomato plants to conduct a genome-wide search and identify putative candidates in 34 sequenced plants. A total of 101 homologous genes were identified. Phylogenetic analysis revealed that PSY evolved independently in algae as well as monocotyledonous and dicotyledonous plants. Our results showed that the amino acid structures exhibited 5 motifs (motifs 1 to 5) in algae and those in higher plants were highly conserved. The PSY gene structures showed that the number of intron in algae varied widely, while the number of introns in higher plants was 4 to 5. Identification of PSY genes in plants and the analysis of the gene structure may provide a theoretical basis for studying evolutionary relationships in future analyses.

Carpological analysis of Phoenix (Arecaceae): contributions to the taxonomy and evolutionary history of the genus

USDA-ARS?s Scientific Manuscript database

The main purpose of this study was, first, to analyze the morphology of seeds of Phoenix spp. and relevant cultivars and to assess the taxonomic value of the information generated as a means of studying the systematics and evolutionary history of the genus Phoenix. We then analyzed seed morphologica...

Evolutionary Maps: A New Model for the Analysis of Conceptual Development, with Application to the Diurnal Cycle

ERIC Educational Resources Information Center

Navarro, Manuel

2014-01-01

This paper presents a model of how children generate concrete concepts from perception through processes of differentiation and integration. The model informs the design of a novel methodology ("evolutionary maps" or "emaps"), whose implementation on certain domains unfolds the web of itineraries that children may follow in the…

A Novel Handwritten Letter Recognizer Using Enhanced Evolutionary Neural Network

NASA Astrophysics Data System (ADS)

Mahmoudi, Fariborz; Mirzashaeri, Mohsen; Shahamatnia, Ehsan; Faridnia, Saed

This paper introduces a novel design for handwritten letter recognition by employing a hybrid back-propagation neural network with an enhanced evolutionary algorithm. Feeding the neural network consists of a new approach which is invariant to translation, rotation, and scaling of input letters. Evolutionary algorithm is used for the global search of the search space and the back-propagation algorithm is used for the local search. The results have been computed by implementing this approach for recognizing 26 English capital letters in the handwritings of different people. The computational results show that the neural network reaches very satisfying results with relatively scarce input data and a promising performance improvement in convergence of the hybrid evolutionary back-propagation algorithms is exhibited.

Evaluation of Generation Alternation Models in Evolutionary Robotics

NASA Astrophysics Data System (ADS)

Oiso, Masashi; Matsumura, Yoshiyuki; Yasuda, Toshiyuki; Ohkura, Kazuhiro

For efficient implementation of Evolutionary Algorithms (EA) to a desktop grid computing environment, we propose a new generation alternation model called Grid-Oriented-Deletion (GOD) based on comparison with the conventional techniques. In previous research, generation alternation models are generally evaluated by using test functions. However, their exploration performance on the real problems such as Evolutionary Robotics (ER) has not been made very clear yet. Therefore we investigate the relationship between the exploration performance of EA on an ER problem and its generation alternation model. We applied four generation alternation models to the Evolutionary Multi-Robotics (EMR), which is the package-pushing problem to investigate their exploration performance. The results show that GOD is more effective than the other conventional models.

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

PubMed Central

Harms, Michael J.; Thornton, Joseph W.

2014-01-01

The repertoire of proteins and nucleic acids in the living world is determined by evolution; their properties are determined by the laws of physics and chemistry. Explanations of these two kinds of causality — the purviews of evolutionary biology and biochemistry, respectively — are typically pursued in isolation, but many fundamental questions fall squarely at the interface of fields. Here we articulate the paradigm of evolutionary biochemistry, which aims to dissect the physical mechanisms and evolutionary processes by which biological molecules diversified and to reveal how their physical architecture facilitates and constrains their evolution. We show how an integration of evolution with biochemistry moves us towards a more complete understanding of why biological molecules have the properties that they do. PMID:23864121

The great opportunity: Evolutionary applications to medicine and public health.

PubMed

Nesse, Randolph M; Stearns, Stephen C

2008-02-01

Evolutionary biology is an essential basic science for medicine, but few doctors and medical researchers are familiar with its most relevant principles. Most medical schools have geneticists who understand evolution, but few have even one evolutionary biologist to suggest other possible applications. The canyon between evolutionary biology and medicine is wide. The question is whether they offer each other enough to make bridge building worthwhile. What benefits could be expected if evolution were brought fully to bear on the problems of medicine? How would studying medical problems advance evolutionary research? Do doctors need to learn evolution, or is it valuable mainly for researchers? What practical steps will promote the application of evolutionary biology in the areas of medicine where it offers the most? To address these questions, we review current and potential applications of evolutionary biology to medicine and public health. Some evolutionary technologies, such as population genetics, serial transfer production of live vaccines, and phylogenetic analysis, have been widely applied. Other areas, such as infectious disease and aging research, illustrate the dramatic recent progress made possible by evolutionary insights. In still other areas, such as epidemiology, psychiatry, and understanding the regulation of bodily defenses, applying evolutionary principles remains an open opportunity. In addition to the utility of specific applications, an evolutionary perspective fundamentally challenges the prevalent but fundamentally incorrect metaphor of the body as a machine designed by an engineer. Bodies are vulnerable to disease - and remarkably resilient - precisely because they are not machines built from a plan. They are, instead, bundles of compromises shaped by natural selection in small increments to maximize reproduction, not health. Understanding the body as a product of natural selection, not design, offers new research questions and a framework for making medical education more coherent. We conclude with recommendations for actions that would better connect evolutionary biology and medicine in ways that will benefit public health. It is our hope that faculty and students will send this article to their undergraduate and medical school Deans, and that this will initiate discussions about the gap, the great opportunity, and action plans to bring the full power of evolutionary biology to bear on human health problems.

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

An evolutionary game approach for determination of the structural conflicts in signed networks

PubMed Central

Tan, Shaolin; Lü, Jinhu

2016-01-01

Social or biochemical networks can often divide into two opposite alliances in response to structural conflicts between positive (friendly, activating) and negative (hostile, inhibiting) interactions. Yet, the underlying dynamics on how the opposite alliances are spontaneously formed to minimize the structural conflicts is still unclear. Here, we demonstrate that evolutionary game dynamics provides a felicitous possible tool to characterize the evolution and formation of alliances in signed networks. Indeed, an evolutionary game dynamics on signed networks is proposed such that each node can adaptively adjust its choice of alliances to maximize its own fitness, which yet leads to a minimization of the structural conflicts in the entire network. Numerical experiments show that the evolutionary game approach is universally efficient in quality and speed to find optimal solutions for all undirected or directed, unweighted or weighted signed networks. Moreover, the evolutionary game approach is inherently distributed. These characteristics thus suggest the evolutionary game dynamic approach as a feasible and effective tool for determining the structural conflicts in large-scale on-line signed networks. PMID:26915581

A Novel Multiobjective Evolutionary Algorithm Based on Regression Analysis

PubMed Central

Song, Zhiming; Wang, Maocai; Dai, Guangming; Vasile, Massimiliano

2015-01-01

As is known, the Pareto set of a continuous multiobjective optimization problem with m objective functions is a piecewise continuous (m − 1)-dimensional manifold in the decision space under some mild conditions. However, how to utilize the regularity to design multiobjective optimization algorithms has become the research focus. In this paper, based on this regularity, a model-based multiobjective evolutionary algorithm with regression analysis (MMEA-RA) is put forward to solve continuous multiobjective optimization problems with variable linkages. In the algorithm, the optimization problem is modelled as a promising area in the decision space by a probability distribution, and the centroid of the probability distribution is (m − 1)-dimensional piecewise continuous manifold. The least squares method is used to construct such a model. A selection strategy based on the nondominated sorting is used to choose the individuals to the next generation. The new algorithm is tested and compared with NSGA-II and RM-MEDA. The result shows that MMEA-RA outperforms RM-MEDA and NSGA-II on the test instances with variable linkages. At the same time, MMEA-RA has higher efficiency than the other two algorithms. A few shortcomings of MMEA-RA have also been identified and discussed in this paper. PMID:25874246

Testing convergent and parallel adaptations in talpids humeral mechanical performance by means of geometric morphometrics and finite element analysis.

PubMed

Piras, P; Sansalone, G; Teresi, L; Kotsakis, T; Colangelo, P; Loy, A

2012-07-01

The shape and mechanical performance in Talpidae humeri were studied by means of Geometric Morphometrics and Finite Element Analysis, including both extinct and extant taxa. The aim of this study was to test whether the ability to dig, quantified by humerus mechanical performance, was characterized by convergent or parallel adaptations in different clades of complex tunnel digger within Talpidae, that is, Talpinae+Condylura (monophyletic) and some complex tunnel diggers not belonging to this clade. Our results suggest that the pattern underlying Talpidae humerus evolution is evolutionary parallelism. However, this insight changed to true convergence when we tested an alternative phylogeny based on molecular data, with Condylura moved to a more basal phylogenetic position. Shape and performance analyses, as well as specific comparative methods, provided strong evidence that the ability to dig complex tunnels reached a functional optimum in distantly related taxa. This was also confirmed by the lower phenotypic variance in complex tunnel digger taxa, compared to non-complex tunnel diggers. Evolutionary rates of phenotypic change showed a smooth deceleration in correspondence with the most recent common ancestor of the Talpinae+Condylura clade. Copyright © 2012 Wiley Periodicals, Inc.

Prediction of stock markets by the evolutionary mix-game model

NASA Astrophysics Data System (ADS)

Chen, Fang; Gou, Chengling; Guo, Xiaoqian; Gao, Jieping

2008-06-01

This paper presents the efforts of using the evolutionary mix-game model, which is a modified form of the agent-based mix-game model, to predict financial time series. Here, we have carried out three methods to improve the original mix-game model by adding the abilities of strategy evolution to agents, and then applying the new model referred to as the evolutionary mix-game model to forecast the Shanghai Stock Exchange Composite Index. The results show that these modifications can improve the accuracy of prediction greatly when proper parameters are chosen.

Hotspots and the conservation of evolutionary history

PubMed Central

Sechrest, Wes; Brooks, Thomas M.; da Fonseca, Gustavo A. B.; Konstant, William R.; Mittermeier, Russell A.; Purvis, Andy; Rylands, Anthony B.; Gittleman, John L.

2002-01-01

Species diversity is unevenly distributed across the globe, with terrestrial diversity concentrated in a few restricted biodiversity hotspots. These areas are associated with high losses of primary vegetation and increased human population density, resulting in growing numbers of threatened species. We show that conservation of these hotspots is critical because they harbor even greater amounts of evolutionary history than expected by species numbers alone. We used supertrees for carnivores and primates to estimate that nearly 70% of the total amount of evolutionary history represented in these groups is found in 25 biodiversity hotspots. PMID:11854502

The evolutionary psychology of hunger.

PubMed

Al-Shawaf, Laith

2016-10-01

An evolutionary psychological perspective suggests that emotions can be understood as coordinating mechanisms whose job is to regulate various psychological and physiological programs in the service of solving an adaptive problem. This paper suggests that it may also be fruitful to approach hunger from this coordinating mechanism perspective. To this end, I put forward an evolutionary task analysis of hunger, generating novel a priori hypotheses about the coordinating effects of hunger on psychological processes such as perception, attention, categorization, and memory. This approach appears empirically fruitful in that it yields a bounty of testable new hypotheses. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolutionary genetics of insect innate immunity.

PubMed

Viljakainen, Lumi

2015-11-01

Patterns of evolution in immune defense genes help to understand the evolutionary dynamics between hosts and pathogens. Multiple insect genomes have been sequenced, with many of them having annotated immune genes, which paves the way for a comparative genomic analysis of insect immunity. In this review, I summarize the current state of comparative and evolutionary genomics of insect innate immune defense. The focus is on the conserved and divergent components of immunity with an emphasis on gene family evolution and evolution at the sequence level; both population genetics and molecular evolution frameworks are considered. © The Author 2015. Published by Oxford University Press.

Evolutionary pattern search algorithms

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

Hart, W.E.

1995-09-19

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

Gene-Culture Coevolution in a Social Cetacean: Integrating Acoustic and Genetic Data to Understand Population Structure in the Short-Finned Pilot Whale (Globicephala macrorhynchus)

NASA Astrophysics Data System (ADS)

Van Cise, Amy

The evolutionary ecology of a species is driven by a combination of random events, ecological and environmental mechanisms, and social behavior. Gene-culture coevolutionary theory attempts to understand the evolutionary trajectory of a species by examining the interactions between these potential drivers. Further, our choice of data type will affect the patterns we observe, therefore by integrating several types of data we achieve a holistic understanding of the various aspects of evolutionary ecology within a species. In order to understand population structure in short-finned pilot whales, I use a combination of genetic and acoustic data to examine structure on evolutionary (genetic) and cultural (acoustic) timescales. I first examine structure among geographic populations in the Pacific Ocean. Using genetic sequences from the mitochondrial control region, I show that two genetically and morphologically distinct types of short-finned pilot whale, described off the coast of Japan, have non-overlapping distributions throughout their range in the Pacific Ocean. Analysis of the acoustic features of their social calls indicates that they are acoustically differentiated, possibly due to limited communication between the two types. This evidence supports the hypothesis that the two types may be separate species or subspecies. Next, I examine structure among island communities and social groups within the Hawaiian Island population of short-finned pilot whales. Using a combination of mitochondrial and nuclear DNA, I showed that the hierarchical social structure in Hawaiian pilot whales is driven by genetic relatedness; individuals remain in groups with their immediate family members, and preferentially associate with relatives. Similarly, social structure affects genetic differentiation, likely by restricting access to mates. Acoustic differentiation among social groups indicates that social structure may also restrict the flow of cultural information, such as vocal repertoire or dialect. The qualitative correlation between social structure, cultural information transfer, and genetic structure suggest that gene-culture coevolution may be an important mechanism to the evolutionary ecology of short-finned pilot whales. Further research may reveal a similar structure in the transmission of ecological behaviors, such as diet preference, habitat use, or movements. The results of this research underscore the applicability of gene-culture coevolutionary theory to non-human taxa.

Evolutionary robotics simulations help explain why reciprocity is rare in nature

PubMed Central

André, Jean-Baptiste; Nolfi, Stefano

2016-01-01

The relative rarity of reciprocity in nature, contrary to theoretical predictions that it should be widespread, is currently one of the major puzzles in social evolution theory. Here we use evolutionary robotics to solve this puzzle. We show that models based on game theory are misleading because they neglect the mechanics of behavior. In a series of experiments with simulated robots controlled by artificial neural networks, we find that reciprocity does not evolve, and show that this results from a general constraint that likely also prevents it from evolving in the wild. Reciprocity can evolve if it requires very few mutations, as is usually assumed in evolutionary game theoretic models, but not if, more realistically, it requires the accumulation of many adaptive mutations. PMID:27616139

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

PubMed

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

2015-06-10

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

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

PubMed Central

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

2015-01-01

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

Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium.

PubMed

Kweon, Ohgew; Kim, Seong-Jae; Blom, Jochen; Kim, Sung-Kwan; Kim, Bong-Soo; Baek, Dong-Heon; Park, Su Inn; Sutherland, John B; Cerniglia, Carl E

2015-02-14

The bacterial genus Mycobacterium is of great interest in the medical and biotechnological fields. Despite a flood of genome sequencing and functional genomics data, significant gaps in knowledge between genome and phenome seriously hinder efforts toward the treatment of mycobacterial diseases and practical biotechnological applications. In this study, we propose the use of systematic, comparative functional pan-genomic analysis to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon (PAH) metabolism in the genus Mycobacterium. Phylogenetic, phenotypic, and genomic information for 27 completely genome-sequenced mycobacteria was systematically integrated to reconstruct a mycobacterial phenotype network (MPN) with a pan-genomic concept at a network level. In the MPN, mycobacterial phenotypes show typical scale-free relationships. PAH degradation is an isolated phenotype with the lowest connection degree, consistent with phylogenetic and environmental isolation of PAH degraders. A series of functional pan-genomic analyses provide conserved and unique types of genomic evidence for strong epistatic and pleiotropic impacts on evolutionary trajectories of the PAH-degrading phenotype. Under strong natural selection, the detailed gene gain/loss patterns from horizontal gene transfer (HGT)/deletion events hypothesize a plausible evolutionary path, an epistasis-based birth and pleiotropy-dependent death, for PAH metabolism in the genus Mycobacterium. This study generated a practical mycobacterial compendium of phenotypic and genomic changes, focusing on the PAH-degrading phenotype, with a pan-genomic perspective of the evolutionary events and the environmental challenges. Our findings suggest that when selection acts on PAH metabolism, only a small fraction of possible trajectories is likely to be observed, owing mainly to a combination of the ambiguous phenotypic effects of PAHs and the corresponding pleiotropy- and epistasis-dependent evolutionary adaptation. Evolutionary constraints on the selection of trajectories, like those seen in PAH-degrading phenotypes, are likely to apply to the evolution of other phenotypes in the genus Mycobacterium.

Physical properties of high-mass star-forming clumps in different evolutionary stages from the Bolocam Galactic Plane Survey

NASA Astrophysics Data System (ADS)

Svoboda, Brian; Shirley, Yancy; Rosolowsky, Erik; Dunham, Miranda; Ellsworth-Bowers, Timothy; Ginsburg, Adam

2013-07-01

High mass stars play a key role in the physical and chemical evolution of the interstellar medium, yet the evolutionary sequence for high mass star forming regions is poorly understood. Recent Galactic plane surveys are providing the first systematic view of high-mass star-forming regions in all evolutionary phases across the Milky Way. We present observations of the 22.23 GHz H2O maser transition J(Ka,Kc) = 6(1,6)→5(2,3) transition toward 1398 clumps identified in the Bolocam Galactic Plane Survey using the 100m Green Bank Telescope (GBT). We detect 392 H2O masers, 279 (71%) newly discovered. We show that H2O masers can identify the presence of protostars which were not previously identified by Spitzer/MSX Galactic plane IR surveys: 25% of IR-dark clumps have an H2O maser. We compare the physical properties of the clumps in the Bolocam Galactic Plane Survey (BGPS) with observations of diagnostics of star formation activity: 8 and 24 um YSO candidates, H2O and CH3OH masers, shocked H2, EGOs, and UCHII regions. We identify a sub-sample of 400 clumps with no star formation indicators representing the largest and most robust sample of pre-protocluster candidates from an unbiased survey to date. The different evolutionary stages show strong separations in HCO+ linewidth and integrated intensity, surface mass density, and kinetic temperature. Monte Carlo techniques are applied to distance probability distribution functions (DPDFs) in order to marginalize over the kinematic distance ambiguity and calculate the distribution of derived quantities for clumps in different evolutionary stages. Surface area and dust mass show weak separations above > 2 pc^2 and > 3x10^3 solar masses. An observed breakdown occurs in the size-linewidth relationship with no differentiation by evolutionary stage. Future work includes adding evolutionary indicators (MIPSGAL, HiGal, MMB) and expanding DPDF priors (HI self-absorption, Galactic structure) for more well-resolved KDAs.

Dynamics of body time, social time and life history at adolescence.

PubMed

Worthman, Carol M; Trang, Kathy

2018-02-21

Recent opposing trends towards earlier physical maturation and later social maturation present a conundrum of apparent biological-social mismatch. Here we use life history analysis from evolutionary ecology to identify forces that drive these shifts. Together with findings in developmental science, our life history analysis indicates that adolescence is a distinctive period for biological embedding of culture. Ethnographic evidence shows that mass education is a novel feature of the globalizing cultural configurations of adolescence, which are driven by transformations in labour, livelihood and lifestyle. Evaluation of the life history trade-offs and sociocultural ecologies that are experienced by adolescents may offer a practical basis for enhancing their development.

Dynamics of body time, social time and life history at adolescence

NASA Astrophysics Data System (ADS)

Worthman, Carol M.; Trang, Kathy

2018-02-01

Recent opposing trends towards earlier physical maturation and later social maturation present a conundrum of apparent biological-social mismatch. Here we use life history analysis from evolutionary ecology to identify forces that drive these shifts. Together with findings in developmental science, our life history analysis indicates that adolescence is a distinctive period for biological embedding of culture. Ethnographic evidence shows that mass education is a novel feature of the globalizing cultural configurations of adolescence, which are driven by transformations in labour, livelihood and lifestyle. Evaluation of the life history trade-offs and sociocultural ecologies that are experienced by adolescents may offer a practical basis for enhancing their development.

Antibody Epitope Analysis to Investigate Folded Structure, Allosteric Conformation, and Evolutionary Lineage of Proteins.

PubMed

Wong, Sienna; Jin, J-P

2017-01-01

Study of folded structure of proteins provides insights into their biological functions, conformational dynamics and molecular evolution. Current methods of elucidating folded structure of proteins are laborious, low-throughput, and constrained by various limitations. Arising from these methods is the need for a sensitive, quantitative, rapid and high-throughput method not only analysing the folded structure of proteins, but also to monitor dynamic changes under physiological or experimental conditions. In this focused review, we outline the foundation and limitations of current protein structure-determination methods prior to discussing the advantages of an emerging antibody epitope analysis for applications in structural, conformational and evolutionary studies of proteins. We discuss the application of this method using representative examples in monitoring allosteric conformation of regulatory proteins and the determination of the evolutionary lineage of related proteins and protein isoforms. The versatility of the method described herein is validated by the ability to modulate a variety of assay parameters to meet the needs of the user in order to monitor protein conformation. Furthermore, the assay has been used to clarify the lineage of troponin isoforms beyond what has been depicted by sequence homology alone, demonstrating the nonlinear evolutionary relationship between primary structure and tertiary structure of proteins. The antibody epitope analysis method is a highly adaptable technique of protein conformation elucidation, which can be easily applied without the need for specialized equipment or technical expertise. When applied in a systematic and strategic manner, this method has the potential to reveal novel and biomedically meaningful information for structure-function relationship and evolutionary lineage of proteins. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Experiential Thinking in Creationism—A Textual Analysis

PubMed Central

Nieminen, Petteri; Ryökäs, Esko; Mustonen, Anne-Mari

2015-01-01

Creationism is a religiously motivated worldview in denial of biological evolution that has been very resistant to change. We performed a textual analysis by examining creationist and pro-evolutionary texts for aspects of “experiential thinking”, a cognitive process different from scientific thought. We observed characteristics of experiential thinking as follows: testimonials (present in 100% of sampled creationist texts), such as quotations, were a major form of proof. Confirmation bias (100% of sampled texts) was represented by ignoring or dismissing information that would contradict the creationist hypothesis. Scientifically irrelevant or flawed information was re-interpreted as relevant for the falsification of evolution (75–90% of sampled texts). Evolutionary theory was associated to moral issues by demonizing scientists and linking evolutionary theory to atrocities (63–93% of sampled texts). Pro-evolutionary rebuttals of creationist claims also contained testimonials (93% of sampled texts) and referred to moral implications (80% of sampled texts) but displayed lower prevalences of stereotypical thinking (47% of sampled texts), confirmation bias (27% of sampled texts) and pseudodiagnostics (7% of sampled texts). The aspects of experiential thinking could also be interpreted as argumentative fallacies. Testimonials lead, for instance, to ad hominem and appeals to authorities. Confirmation bias and simplification of data give rise to hasty generalizations and false dilemmas. Moral issues lead to guilt by association and appeals to consequences. Experiential thinking and fallacies can contribute to false beliefs and the persistence of the claims. We propose that science educators would benefit from the systematic analysis of experiential thinking patterns and fallacies in creationist texts and pro-evolutionary rebuttals in order to concentrate on scientific misconceptions instead of the scientifically irrelevant aspects of the creationist—evolutionist debate. PMID:25734650

Experiential thinking in creationism--a textual analysis.

PubMed

Nieminen, Petteri; Ryökäs, Esko; Mustonen, Anne-Mari

2015-01-01

Creationism is a religiously motivated worldview in denial of biological evolution that has been very resistant to change. We performed a textual analysis by examining creationist and pro-evolutionary texts for aspects of "experiential thinking", a cognitive process different from scientific thought. We observed characteristics of experiential thinking as follows: testimonials (present in 100% of sampled creationist texts), such as quotations, were a major form of proof. Confirmation bias (100% of sampled texts) was represented by ignoring or dismissing information that would contradict the creationist hypothesis. Scientifically irrelevant or flawed information was re-interpreted as relevant for the falsification of evolution (75-90% of sampled texts). Evolutionary theory was associated to moral issues by demonizing scientists and linking evolutionary theory to atrocities (63-93% of sampled texts). Pro-evolutionary rebuttals of creationist claims also contained testimonials (93% of sampled texts) and referred to moral implications (80% of sampled texts) but displayed lower prevalences of stereotypical thinking (47% of sampled texts), confirmation bias (27% of sampled texts) and pseudodiagnostics (7% of sampled texts). The aspects of experiential thinking could also be interpreted as argumentative fallacies. Testimonials lead, for instance, to ad hominem and appeals to authorities. Confirmation bias and simplification of data give rise to hasty generalizations and false dilemmas. Moral issues lead to guilt by association and appeals to consequences. Experiential thinking and fallacies can contribute to false beliefs and the persistence of the claims. We propose that science educators would benefit from the systematic analysis of experiential thinking patterns and fallacies in creationist texts and pro-evolutionary rebuttals in order to concentrate on scientific misconceptions instead of the scientifically irrelevant aspects of the creationist-evolutionist debate.

Coevolving memetic algorithms: a review and progress report.

PubMed

Smith, Jim E

2007-02-01

Coevolving memetic algorithms are a family of metaheuristic search algorithms in which a rule-based representation of local search (LS) is coadapted alongside candidate solutions within a hybrid evolutionary system. Simple versions of these systems have been shown to outperform other nonadaptive memetic and evolutionary algorithms on a range of problems. This paper presents a rationale for such systems and places them in the context of other recent work on adaptive memetic algorithms. It then proposes a general structure within which a population of LS algorithms can be evolved in tandem with the solutions to which they are applied. Previous research started with a simple self-adaptive system before moving on to more complex models. Results showed that the algorithm was able to discover and exploit certain forms of structure and regularities within the problems. This "metalearning" of problem features provided a means of creating highly scalable algorithms. This work is briefly reviewed to highlight some of the important findings and behaviors exhibited. Based on this analysis, new results are then presented from systems with more flexible representations, which, again, show significant improvements. Finally, the current state of, and future directions for, research in this area is discussed.

KEPLER ECLIPSING BINARIES WITH DELTA SCUTI/GAMMA DORADUS PULSATING COMPONENTS. I. KIC 9851944

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

Guo, Zhao; Gies, Douglas R.; Matson, Rachel A.

2016-07-20

KIC 9851944 is a short-period ( P = 2.16 days) eclipsing binary in the Kepler field of view. By combining the analysis of Kepler photometry and phase-resolved spectra from Kitt Peak National Observatory and Lowell Observatory, we determine the atmospheric and physical parameters of both stars. The two components have very different radii (2.27 R {sub ⊙}, 3.19 R {sub ⊙}) but close masses (1.76 M {sub ⊙}, 1.79 M {sub ⊙}) and effective temperatures (7026, 6902 K), indicating different evolutionary stages. The hotter primary is still on the main sequence (MS), while the cooler and larger secondary star hasmore » evolved to the post-MS, burning hydrogen in a shell. A comparison with coeval evolutionary models shows that it requires solar metallicity and a higher mass ratio to fit the radii and temperatures of both stars simultaneously. Both components show δ Scuti-type pulsations, which we interpret as p -modes and p and g mixed modes. After a close examination of the evolution of δ Scuti pulsational frequencies, we make a comparison of the observed frequencies with those calculated from MESA/GYRE.« less

Evolutionary game theory meets social science: is there a unifying rule for human cooperation?

PubMed

Rosas, Alejandro

2010-05-21

Evolutionary game theory has shown that human cooperation thrives in different types of social interactions with a PD structure. Models treat the cooperative strategies within the different frameworks as discrete entities and sometimes even as contenders. Whereas strong reciprocity was acclaimed as superior to classic reciprocity for its ability to defeat defectors in public goods games, recent experiments and simulations show that costly punishment fails to promote cooperation in the IR and DR games, where classic reciprocity succeeds. My aim is to show that cooperative strategies across frameworks are capable of a unified treatment, for they are governed by a common underlying rule or norm. An analysis of the reputation and action rules that govern some representative cooperative strategies both in models and in economic experiments confirms that the different frameworks share a conditional action rule and several reputation rules. The common conditional rule contains an option between costly punishment and withholding benefits that provides alternative enforcement methods against defectors. Depending on the framework, individuals can switch to the appropriate strategy and method of enforcement. The stability of human cooperation looks more promising if one mechanism controls successful strategies across frameworks. Published by Elsevier Ltd.

Quantitative food web analysis supports the energy-limitation hypothesis in cave stream ecosystems.

PubMed

Venarsky, Michael P; Huntsman, Brock M; Huryn, Alexander D; Benstead, Jonathan P; Kuhajda, Bernard R

2014-11-01

Energy limitation has long been the primary assumption underlying conceptual models of evolutionary and ecological processes in cave ecosystems. However, the prediction that cave communities are actually energy-limited in the sense that constituent populations are consuming all or most of their resource supply is untested. We assessed the energy-limitation hypothesis in three cave streams in northeastern Alabama (USA) by combining measurements of animal production, demand, and resource supplies (detritus, primarily decomposing wood particles). Comparisons of animal consumption and detritus supply rates in each cave showed that all, or nearly all, available detritus was required to support macroinvertebrate production. Furthermore, only a small amount of macroinvertebrate prey production remained to support other predatory taxa (i.e., cave fish and salamanders) after accounting for crayfish consumption. Placing the energy demands of a cave community within the context of resource supply rates provided quantitative support for the energy-limitation hypothesis, confirming the mechanism (limited energy surpluses) that likely influences the evolutionary processes and population dynamics that shape cave communities. Detritus-based surface ecosystems often have large detrital surpluses. Thus, cave ecosystems, which show minimal surpluses, occupy the extreme oligotrophic end of the spectrum of detritus-based food webs.

Selection methods regulate evolution of cooperation in digital evolution

PubMed Central

Lichocki, Paweł; Floreano, Dario; Keller, Laurent

2014-01-01

A key, yet often neglected, component of digital evolution and evolutionary models is the ‘selection method’ which assigns fitness (number of offspring) to individuals based on their performance scores (efficiency in performing tasks). Here, we study with formal analysis and numerical experiments the evolution of cooperation under the five most common selection methods (proportionate, rank, truncation-proportionate, truncation-uniform and tournament). We consider related individuals engaging in a Prisoner's Dilemma game where individuals can either cooperate or defect. A cooperator pays a cost, whereas its partner receives a benefit, which affect their performance scores. These performance scores are translated into fitness by one of the five selection methods. We show that cooperation is positively associated with the relatedness between individuals under all selection methods. By contrast, the change in the performance benefit of cooperation affects the populations’ average level of cooperation only under the proportionate methods. We also demonstrate that the truncation and tournament methods may introduce negative frequency-dependence and lead to the evolution of polymorphic populations. Using the example of the evolution of cooperation, we show that the choice of selection method, though it is often marginalized, can considerably affect the evolutionary dynamics. PMID:24152811

The evolutionarily conserved transcription factor PRDM12 controls sensory neuron development and pain perception.

PubMed

Nagy, Vanja; Cole, Tiffany; Van Campenhout, Claude; Khoung, Thang M; Leung, Calvin; Vermeiren, Simon; Novatchkova, Maria; Wenzel, Daniel; Cikes, Domagoj; Polyansky, Anton A; Kozieradzki, Ivona; Meixner, Arabella; Bellefroid, Eric J; Neely, G Gregory; Penninger, Josef M

2015-01-01

PR homology domain-containing member 12 (PRDM12) belongs to a family of conserved transcription factors implicated in cell fate decisions. Here we show that PRDM12 is a key regulator of sensory neuronal specification in Xenopus. Modeling of human PRDM12 mutations that cause hereditary sensory and autonomic neuropathy (HSAN) revealed remarkable conservation of the mutated residues in evolution. Expression of wild-type human PRDM12 in Xenopus induced the expression of sensory neuronal markers, which was reduced using various human PRDM12 mutants. In Drosophila, we identified Hamlet as the functional PRDM12 homolog that controls nociceptive behavior in sensory neurons. Furthermore, expression analysis of human patient fibroblasts with PRDM12 mutations uncovered possible downstream target genes. Knockdown of several of these target genes including thyrotropin-releasing hormone degrading enzyme (TRHDE) in Drosophila sensory neurons resulted in altered cellular morphology and impaired nociception. These data show that PRDM12 and its functional fly homolog Hamlet are evolutionary conserved master regulators of sensory neuronal specification and play a critical role in pain perception. Our data also uncover novel pathways in multiple species that regulate evolutionary conserved nociception.

Reanalysis Of The PZ Tel System: Arguments For The Reality Of PZ Tel B To Be PZ Tel b

NASA Astrophysics Data System (ADS)

Jenkins, James

2011-09-01

I will present some new analysis of the PZ Tel system, which has recently been shown to host a young companion with a mass of around 30 Jupiter-masses, along with a debris disk of around 0.3 Lunar-masses. We have reanalyzed the iron abundance of the host star using our new spectral synthesis method, and contrary to previous results, we find the star to be super metal-rich, with a metallicity ([Fe/H]) of 0.2 dex. We also find the age of the system from chromospheric activities and pre-main sequence evolutionary models to be around 25Myrs. I will show some comparisons between the companion's bulk properties, such as broadband colours, and some of the latest evolutionary models as a function of metallicity. Finally, I will use these results to show how the companion to PZ Tel could be the first directly imaged extreme-Jovian extrasolar planet and not a low-mass brown dwarf. I acknowledge funding by Fondecyt through grant 3110004 and partial support from Centro de Astrofisica FONDAP 15010003, the GEMINI-CONICYT FUND and from the Comite Mixto ESO-GOBIERNO DE CHILE.

Darwinism and cultural change.

PubMed

Godfrey-Smith, Peter

2012-08-05

Evolutionary models of cultural change have acquired an important role in attempts to explain the course of human evolution, especially our specialization in knowledge-gathering and intelligent control of environments. In both biological and cultural change, different patterns of explanation become relevant at different 'grains' of analysis and in contexts associated with different explanatory targets. Existing treatments of the evolutionary approach to culture, both positive and negative, underestimate the importance of these distinctions. Close attention to grain of analysis motivates distinctions between three possible modes of cultural evolution, each associated with different empirical assumptions and explanatory roles.

Darwinism in quantum systems?

NASA Astrophysics Data System (ADS)

Iqbal, A.; Toor, A. H.

2002-03-01

We investigate the role of quantum mechanical effects in the central stability concept of evolutionary game theory, i.e., an evolutionarily stable strategy (ESS). Using two and three-player symmetric quantum games we show how the presence of quantum phenomenon of entanglement can be crucial to decide the course of evolutionary dynamics in a population of interacting individuals.

Phylogenetic context determines the role of competition in adaptive radiation

PubMed Central

Tan, Jiaqi; Slattery, Matthew R.; Yang, Xian; Jiang, Lin

2016-01-01

Understanding ecological mechanisms regulating the evolution of biodiversity is of much interest to ecologists and evolutionary biologists. Adaptive radiation constitutes an important evolutionary process that generates biodiversity. Competition has long been thought to influence adaptive radiation, but the directionality of its effect and associated mechanisms remain ambiguous. Here, we report a rigorous experimental test of the role of competition on adaptive radiation using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting with multiple bacterial species that differed in their phylogenetic distance to the diversifying bacterium. We showed that the inhibitive effect of competitors on the adaptive radiation of P. fluorescens decreased as their phylogenetic distance increased. To explain this phylogenetic dependency of adaptive radiation, we linked the phylogenetic distance between P. fluorescens and its competitors to their niche and competitive fitness differences. Competitive fitness differences, which showed weak phylogenetic signal, reduced P. fluorescens abundance and thus diversification, whereas phylogenetically conserved niche differences promoted diversification. These results demonstrate the context dependency of competitive effects on adaptive radiation, and highlight the importance of past evolutionary history for ongoing evolutionary processes. PMID:27335414

Controlling Tensegrity Robots Through Evolution

NASA Technical Reports Server (NTRS)

Iscen, Atil; Agogino, Adrian; SunSpiral, Vytas; Tumer, Kagan

2013-01-01

Tensegrity structures (built from interconnected rods and cables) have the potential to offer a revolutionary new robotic design that is light-weight, energy-efficient, robust to failures, capable of unique modes of locomotion, impact tolerant, and compliant (reducing damage between the robot and its environment). Unfortunately robots built from tensegrity structures are difficult to control with traditional methods due to their oscillatory nature, nonlinear coupling between components and overall complexity. Fortunately this formidable control challenge can be overcome through the use of evolutionary algorithms. In this paper we show that evolutionary algorithms can be used to efficiently control a ball-shaped tensegrity robot. Experimental results performed with a variety of evolutionary algorithms in a detailed soft-body physics simulator show that a centralized evolutionary algorithm performs 400 percent better than a hand-coded solution, while the multi-agent evolution performs 800 percent better. In addition, evolution is able to discover diverse control solutions (both crawling and rolling) that are robust against structural failures and can be adapted to a wide range of energy and actuation constraints. These successful controls will form the basis for building high-performance tensegrity robots in the near future.

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.

Evolution of toll-like receptors in the context of terrestrial ungulates and cetaceans diversification.

PubMed

Ishengoma, Edson; Agaba, Morris

2017-02-16

Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined. In addition, comparison of the patterning of key TLR motifs and domains between giraffe and related species was performed. The quantification of selection pressure and divergence on TLRs among terrestrial ungulates and cetaceans was also performed. Sequence analysis shows that giraffe has 94-99% nucleotide identity with okapi and cattle for all TLRs analyzed. Variations in the number of Leucine-rich repeats were observed in some of TLRs between giraffe, okapi and cattle. Patterning of key TLR domains did not reveal any significant differences in the domain architecture among giraffe, okapi and cattle. Molecular evolutionary analysis for selection pressure identifies positive selection on key sites for all TLRs examined suggesting that pervasive evolutionary pressure has taken place during the evolution of terrestrial ungulates and cetaceans. Analysis of positively selected sites showed some site to be part of Leucine-rich motifs suggesting functional relevance in species-specific recognition of pathogen associated molecular patterns. Notably, clade analysis reveals significant selection divergence between terrestrial ungulates and cetaceans in viral sensing TLR3. Mapping of giraffe TLR3 key substitutions to the structure of the receptor indicates that at least one of giraffe altered sites coincides with TLR3 residue known to play a critical role in receptor signaling activity. There is overall structural conservation in TLRs among giraffe, okapi and cattle indicating that the mechanism for innate immune response utilizing TLR pathways may not have changed very much during the evolution of these species. However, a broader phylogenetic analysis revealed signatures of adaptive evolution among terrestrial ungulates and cetaceans, including the observed selection divergence in TLR3. This suggests that long term ecological dynamics has led to species-specific innovation and functional variation in the mechanisms mediating innate immunity in terrestrial ungulates and cetaceans.

Performance comparison of the Prophecy (forecasting) Algorithm in FFT form for unseen feature and time-series prediction

NASA Astrophysics Data System (ADS)

Jaenisch, Holger; Handley, James

2013-06-01

We introduce a generalized numerical prediction and forecasting algorithm. We have previously published it for malware byte sequence feature prediction and generalized distribution modeling for disparate test article analysis. We show how non-trivial non-periodic extrapolation of a numerical sequence (forecast and backcast) from the starting data is possible. Our ancestor-progeny prediction can yield new options for evolutionary programming. Our equations enable analytical integrals and derivatives to any order. Interpolation is controllable from smooth continuous to fractal structure estimation. We show how our generalized trigonometric polynomial can be derived using a Fourier transform.

New Genotype of Dengue Type 3 Virus Circulating in Brazil and Colombia Showed a Close Relationship to Old Asian Viruses

PubMed Central

Aquino, Victor Hugo; Amarilla, Alberto Anastacio; Alfonso, Helda Liz; Batista, Weber Cheli; Figueiredo, Luiz Tadeu Moraes

2009-01-01

Dengue type 3 genotype V viruses have been recently detected in Brazil and Colombia. In this study, we described another Brazilian isolate belonging to this genotype. Phylogenetic analysis including dengue type 3 viruses isolated worldwide showed that Brazilian and Colombian viruses were closely related to viruses isolated in Asia more than two decades ago. The characteristic evolutionary pattern of dengue type 3 virus cannot explain the close similarity of new circulating viruses with old viruses. Further studies are needed to confirm the origin of the new dengue type III genotype circulating in Brazil and Colombia. PMID:19823677

Divergent Evolutionary Pattern of Sugar Transporter Genes is Associated with the Difference in Sugar Accumulation between Grasses and Eudicots.

PubMed

Wang, Wei; Zhou, Hui; Ma, Baiquan; Owiti, Albert; Korban, Schuyler S; Han, Yuepeng

2016-06-30

Sugars play a variety of roles in plants, and their accumulation in seeds and/or surrounding pericarp tissues is distinctly different between grasses and eudicots. However, little is known about the evolutionary pattern of genes involved in sugar accumulation in these two major groups of flowering plants. Here, we compared evolutionary rates, gene duplication, and selective patterns of genes involved in sugar metabolism and transport between grasses and eudicots using six grass species and seven eudicot species as materials. Overall, sugar transporter genes exhibit divergent evolutionary patterns, whereas, sugar metabolism genes showing similar evolutionary pattern between monocots and eudicots. Sugar transporter genes have higher frequencies of recent duplication in eudicots than in grasses and their patterns of evolutionary rate are different. Evidence for divergent selection of these two groups of flowering plants is also observed in sugar transporter genes, wherein, these genes have undergone positive selection in eudicots, but not in grasses. Taken together, these findings suggest that sugar transporter genes rather than sugar metabolism genes play important roles in sugar accumulation in plants, and that divergent evolutionary patterns of sugar transporter genes are associated with the difference of sugar accumulation in storage tissues of grasses and eudicots.

Divergent Evolutionary Pattern of Sugar Transporter Genes is Associated with the Difference in Sugar Accumulation between Grasses and Eudicots

PubMed Central

Wang, Wei; Zhou, Hui; Ma, Baiquan; Owiti, Albert; Korban, Schuyler S.; Han, Yuepeng

2016-01-01

Sugars play a variety of roles in plants, and their accumulation in seeds and/or surrounding pericarp tissues is distinctly different between grasses and eudicots. However, little is known about the evolutionary pattern of genes involved in sugar accumulation in these two major groups of flowering plants. Here, we compared evolutionary rates, gene duplication, and selective patterns of genes involved in sugar metabolism and transport between grasses and eudicots using six grass species and seven eudicot species as materials. Overall, sugar transporter genes exhibit divergent evolutionary patterns, whereas, sugar metabolism genes showing similar evolutionary pattern between monocots and eudicots. Sugar transporter genes have higher frequencies of recent duplication in eudicots than in grasses and their patterns of evolutionary rate are different. Evidence for divergent selection of these two groups of flowering plants is also observed in sugar transporter genes, wherein, these genes have undergone positive selection in eudicots, but not in grasses. Taken together, these findings suggest that sugar transporter genes rather than sugar metabolism genes play important roles in sugar accumulation in plants, and that divergent evolutionary patterns of sugar transporter genes are associated with the difference of sugar accumulation in storage tissues of grasses and eudicots. PMID:27356489

An Analytical Framework for Runtime of a Class of Continuous Evolutionary Algorithms.

PubMed

Zhang, Yushan; Hu, Guiwu

2015-01-01

Although there have been many studies on the runtime of evolutionary algorithms in discrete optimization, relatively few theoretical results have been proposed on continuous optimization, such as evolutionary programming (EP). This paper proposes an analysis of the runtime of two EP algorithms based on Gaussian and Cauchy mutations, using an absorbing Markov chain. Given a constant variation, we calculate the runtime upper bound of special Gaussian mutation EP and Cauchy mutation EP. Our analysis reveals that the upper bounds are impacted by individual number, problem dimension number n, searching range, and the Lebesgue measure of the optimal neighborhood. Furthermore, we provide conditions whereby the average runtime of the considered EP can be no more than a polynomial of n. The condition is that the Lebesgue measure of the optimal neighborhood is larger than a combinatorial calculation of an exponential and the given polynomial of n.

Law, evolution and the brain: applications and open questions.

PubMed Central

Jones, Owen D

2004-01-01

This paper discusses several issues at the intersection of law and brain science. It focuses principally on ways in which an improved understanding of how evolutionary processes affect brain function and human behaviour may improve law's ability to regulate behaviour. It explores sample uses of such 'evolutionary analysis in law' and also raises questions about how that analysis might be improved in the future. Among the discussed uses are: (i) clarifying cost-benefit analyses; (ii) providing theoretical foundation and potential predictive power; (iii) assessing comparative effectiveness of legal strategies; and (iv) revealing deep patterns in legal architecture. Throughout, the paper emphasizes the extent to which effective law requires: (i) building effective behavioural models; (ii) integrating life-science perspectives with social-science perspectives; (iii) considering the effects of brain biology on behaviours that law seeks to regulate; and (iv) examining the effects of evolutionary processes on brain design. PMID:15590611

Law, evolution and the brain: applications and open questions.

PubMed

Jones, Owen D

2004-11-29

This paper discusses several issues at the intersection of law and brain science. It focuses principally on ways in which an improved understanding of how evolutionary processes affect brain function and human behaviour may improve law's ability to regulate behaviour. It explores sample uses of such 'evolutionary analysis in law' and also raises questions about how that analysis might be improved in the future. Among the discussed uses are: (i) clarifying cost-benefit analyses; (ii) providing theoretical foundation and potential predictive power; (iii) assessing comparative effectiveness of legal strategies; and (iv) revealing deep patterns in legal architecture. Throughout, the paper emphasizes the extent to which effective law requires: (i) building effective behavioural models; (ii) integrating life-science perspectives with social-science perspectives; (iii) considering the effects of brain biology on behaviours that law seeks to regulate; and (iv) examining the effects of evolutionary processes on brain design.

Perceived consequences of evolution: College students perceive negative personal and social impact in evolutionary theory

NASA Astrophysics Data System (ADS)

Brem, Sarah K.; Ranney, Michael; Schindel, Jennifer

2003-03-01

Evolutionary science has consequences for individuals and society, ranging from the way we interpret human behavior to our notions of spirituality and the purpose of our existence. Popular portrayals of evolution depict a paradoxical theory, a source of knowledge and human connections, but also a threat to our humanity and freedom. Using quantitative and qualitative methodology, we examined how college-educated adults (n = 135) from diverse ethnic and religious backgrounds perceive the impact of evolutionary theory on individuals and society. We identified a continuum of perspectives, ranging from strong creationist to strong evolutionist. Using the model of knowledge as an ecology (Demastes, Good, & Peebles, Science Education, 79, 637-666, 1995; Nardi & O'Day, Information ecologies: Using technology with heart, MIT Press, Cambridge, MA, 1999), we examined the relationships among participants' beliefs, their perceptions regarding the social and personal impact of evolutionary theory, their prior exposure to and knowledge of evolutionary theory, and their opinions regarding the teaching of evolution. Evolutionists and creationists differed in their prior exposure to evolutionary theory, and their opinions about some aspects of teaching, but showed striking similarities regarding perceived impact. All groups viewed the consequences of accepting evolutionary principles in a way that might be considered undesirable: increased selfishness and racism, decreased spirituality, and a decreased sense of purpose and self-determination. From a science education perspective, this one-sided interpretation is troublesome because it runs counter to the available evidence and theories in evolutionary science, and we consider ways of fostering more balanced presentation and appraisal of evolutionary theory.