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Sample records for molecular darwinian evolution

  1. Darwinian Evolution and Fractals

    NASA Astrophysics Data System (ADS)

    Carr, Paul H.

    2009-05-01

    Did nature's beauty emerge by chance or was it intelligently designed? Richard Dawkins asserts that evolution is blind aimless chance. Michael Behe believes, on the contrary, that the first cell was intelligently designed. The scientific evidence is that nature's creativity arises from the interplay between chance AND design (laws). Darwin's ``Origin of the Species,'' published 150 years ago in 1859, characterized evolution as the interplay between variations (symbolized by dice) and the natural selection law (design). This is evident in recent discoveries in DNA, Madelbrot's Fractal Geometry of Nature, and the success of the genetic design algorithm. Algorithms for generating fractals have the same interplay between randomness and law as evolution. Fractal statistics, which are not completely random, characterize such phenomena such as fluctuations in the stock market, the Nile River, rainfall, and tree rings. As chaos theorist Joseph Ford put it: God plays dice, but the dice are loaded. Thus Darwin, in discovering the evolutionary interplay between variations and natural selection, was throwing God's dice!

  2. Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution.

    PubMed

    Skinner, Michael K

    2015-04-26

    Environment has a critical role in the natural selection process for Darwinian evolution. The primary molecular component currently considered for neo-Darwinian evolution involves genetic alterations and random mutations that generate the phenotypic variation required for natural selection to act. The vast majority of environmental factors cannot directly alter DNA sequence. Epigenetic mechanisms directly regulate genetic processes and can be dramatically altered by environmental factors. Therefore, environmental epigenetics provides a molecular mechanism to directly alter phenotypic variation generationally. Lamarck proposed in 1802 the concept that environment can directly alter phenotype in a heritable manner. Environmental epigenetics and epigenetic transgenerational inheritance provide molecular mechanisms for this process. Therefore, environment can on a molecular level influence the phenotypic variation directly. The ability of environmental epigenetics to alter phenotypic and genotypic variation directly can significantly impact natural selection. Neo-Lamarckian concept can facilitate neo-Darwinian evolution. A unified theory of evolution is presented to describe the integration of environmental epigenetic and genetic aspects of evolution.

  3. How Darwinian is cultural evolution?

    PubMed

    Claidière, Nicolas; Scott-Phillips, Thomas C; Sperber, Dan

    2014-05-19

    Darwin-inspired population thinking suggests approaching culture as a population of items of different types, whose relative frequencies may change over time. Three nested subtypes of populational models can be distinguished: evolutionary, selectional and replicative. Substantial progress has been made in the study of cultural evolution by modelling it within the selectional frame. This progress has involved idealizing away from phenomena that may be critical to an adequate understanding of culture and cultural evolution, particularly the constructive aspect of the mechanisms of cultural transmission. Taking these aspects into account, we describe cultural evolution in terms of cultural attraction, which is populational and evolutionary, but only selectional under certain circumstances. As such, in order to model cultural evolution, we must not simply adjust existing replicative or selectional models but we should rather generalize them, so that, just as replicator-based selection is one form that Darwinian selection can take, selection itself is one of several different forms that attraction can take. We present an elementary formalization of the idea of cultural attraction.

  4. How Darwinian is cultural evolution?

    PubMed Central

    Claidière, Nicolas; Scott-Phillips, Thomas C.; Sperber, Dan

    2014-01-01

    Darwin-inspired population thinking suggests approaching culture as a population of items of different types, whose relative frequencies may change over time. Three nested subtypes of populational models can be distinguished: evolutionary, selectional and replicative. Substantial progress has been made in the study of cultural evolution by modelling it within the selectional frame. This progress has involved idealizing away from phenomena that may be critical to an adequate understanding of culture and cultural evolution, particularly the constructive aspect of the mechanisms of cultural transmission. Taking these aspects into account, we describe cultural evolution in terms of cultural attraction, which is populational and evolutionary, but only selectional under certain circumstances. As such, in order to model cultural evolution, we must not simply adjust existing replicative or selectional models but we should rather generalize them, so that, just as replicator-based selection is one form that Darwinian selection can take, selection itself is one of several different forms that attraction can take. We present an elementary formalization of the idea of cultural attraction. PMID:24686939

  5. Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution

    PubMed Central

    Bhandari, Vaibhav; Naushad, Hafiz S.; Gupta, Radhey S.

    2012-01-01

    The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies. PMID

  6. Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution.

    PubMed

    Bhandari, Vaibhav; Naushad, Hafiz S; Gupta, Radhey S

    2012-01-01

    The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies.

  7. Quantum Darwinian Evolution Implies Tumor Origination

    NASA Astrophysics Data System (ADS)

    Cooper, W. Grant

    2011-03-01

    Quantum uncertainty limits operating on metastable amino DNA protons drive the arrangement, keto-amino ? enol-imine, which contributes to time-dependent stochastic mutations. Product enol-imine protons participate in coupled quantum oscillations at frequencies of about 1013 s-1 until ``measured by'' an evolutionarily selected quantum reader, the transcriptase. This introduces entanglement states between coherent protons and transcriptase components, which ultimately yield an ensemble of decohered, non-reequilibrated enol and imine isomers that participate in ``molecular clock'' base substitutions at G'-C' and *G-*C sites. This introduces a quantum Darwinian evolution model which (a) simulates incidence of cancer data and (b) implies insight into quantum origins of evolutionary extinction. Data identify an inherited ``genetic space,'' s, which is initially mutation-free and satisfies the inequality, 1 = s = 0.97. When accumulated stochastic mutations cause s-values to approach their evolutionarily allowed threshold limit, s 0.97 + e, age-related degenerative disease is manifested. This implies a gain in evolutionary advantage which protects the gene pool against acquiring unsafe levels of mutation. Data requiring coherent states imply that classical duplex DNA contains an embedded microphysical subset of electron lone-pairs and hydrogen bonded protons that govern time-dependent genetic specificity in terms of quantum probability laws.

  8. Do Galaxies Follow Darwinian Evolution?

    NASA Astrophysics Data System (ADS)

    2006-12-01

    Using VIMOS on ESO's Very Large Telescope, a team of French and Italian astronomers have shown the strong influence the environment exerts on the way galaxies form and evolve. The scientists have for the first time charted remote parts of the Universe, showing that the distribution of galaxies has considerably evolved with time, depending on the galaxies' immediate surroundings. This surprising discovery poses new challenges for theories of the formation and evolution of galaxies. The 'nature versus nurture' debate is a hot topic in human psychology. But astronomers too face similar conundrums, in particular when trying to solve a problem that goes to the very heart of cosmological theories: are the galaxies we see today simply the product of the primordial conditions in which they formed, or did experiences in the past change the path of their evolution? ESO PR Photo 17/06 ESO PR Photo 45/06 Galaxy Distribution in Space In a large, three-year long survey carried out with VIMOS [1], the Visible Imager and Multi-Object Spectrograph on ESO's VLT, astronomers studied more than 6,500 galaxies over a wide range of distances to investigate how their properties vary over different timescales, in different environments and for varying galaxy luminosities [2]. They were able to build an atlas of the Universe in three dimensions, going back more than 9 billion years. This new census reveals a surprising result. The colour-density relation, that describes the relationship between the properties of a galaxy and its environment, was markedly different 7 billion years ago. The astronomers thus found that the galaxies' luminosity, their initial genetic properties, and the environments they reside in have a profound impact on their evolution. "Our results indicate that environment is a key player in galaxy evolution, but there's no simple answer to the 'nature versus nurture' problem in galaxy evolution," said Olivier Le Fèvre from the Laboratoire d'Astrophysique de Marseille

  9. Aptamer Selection by Darwinian Evolution

    NASA Astrophysics Data System (ADS)

    Chauveau, F.; Pestourie, C.; Ducongé, F.; Tavitian, B.

    sequence encodes genetic information, while their wealth of structural potential remains virtually unexploited. In contrast, natural evolution has selected many RNA for their catalytic activities or for their ability to interact with proteins or other classes of molecules.

  10. Teaching Darwinian Evolution: Learning from Religious Education

    NASA Astrophysics Data System (ADS)

    Stolberg, Tonie L.

    2010-06-01

    This article examines what science education might be able to learn from phenomenological religious education’s attempts to teach classes where students hold a plurality of religious beliefs. Recent statements as to how best to accomplish the central pedagogical concept of ‘learning from religion’ as a vehicle for human transformation are explored, and then used to appraise the historical research into how Charles Darwin’s responses to religious ideas influenced and were influenced by his scientific work. The issues identified as crucial for science educators to be aware of when teaching students Darwinian evolution are then outlined and, finally, suggestions are made to enable individual students to examine how their personal religious beliefs might interact with their growing understanding of Darwin’s evolutionary approach.

  11. Is evolution Darwinian or/and Lamarckian?

    PubMed Central

    2009-01-01

    -Lamarckian phenomenon because the induced genomic changes, although random, are triggered by environmental factors and are beneficial to the organism. Conclusion Both Darwinian and Lamarckian modalities of evolution appear to be important, and reflect different aspects of the interaction between populations and the environment. Reviewers this article was reviewed by Juergen Brosius, Valerian Dolja, and Martijn Huynen. For complete reports, see the Reviewers' reports section. PMID:19906303

  12. Darwinian evolution does not rule out the gaia hypothesis.

    PubMed

    Sugimoto, Takeshi

    2002-10-21

    This study explores so-called Darwinian Daisyworlds mathematically rigorously in detail. The original Daisyworld was introduced by Watson & Lovelock (1983) to demonstrate how two species of daisies regulate the global temperature of their planet through competition among these species against the rising solar luminosity, i.e. the Gaia hypothesis. Its variants are Darwinian Daisyworlds in which daisies can adapt themselves to the local temperature. Robertson & Robinson (1998) insist their Darwinian daisies lose the ability for temperature regulation on the basis of their spreadsheet simulations. Lenton & Lovelock (2000) point out that the constraints on adaptation recovers Darwinian daisies' ability of temperature regulation on the basis of their Euler-code simulations. The present study shows there exist the exact and closed-form solutions to these two Daisyworlds. The results contradict the former studies: Robertson and Robinson's daisies do regulate the global temperature even longer than non-adaptive daisies; Lenton and Lovelock's daisies are less adaptive than Robertson and Robinson's daisies because of the constraints on adaptation; the introduction of weak adaptability drives species into a dead end of evolution. Thus, the present results confirm that the Gaia hypothesis and Darwinian evolution can coexist.

  13. Darwinian evolution in the light of genomics

    PubMed Central

    Koonin, Eugene V.

    2009-01-01

    Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future. PMID:19213802

  14. Language evolution as a Darwinian process: computational studies.

    PubMed

    Oudeyer, Pierre-Yves; Kaplan, Frédéric

    2007-03-01

    This paper presents computational experiments that illustrate how one can precisely conceptualize language evolution as a Darwinian process. We show that there is potentially a wide diversity of replicating units and replication mechanisms involved in language evolution. Computational experiments allow us to study systemic properties coming out of populations of linguistic replicators: linguistic replicators can adapt to specific external environments; they evolve under the pressure of the cognitive constraints of their hosts, as well as under the functional pressure of communication for which they are used; one can observe neutral drift; coalitions of replicators may appear, forming higher level groups which can themselves become subject to competition and selection.

  15. Reflections on Darwinian Evolution – Is there a Jewish Perspective?

    PubMed Central

    Jacob, Chaim O.

    2011-01-01

    I present a realistic view of what Darwinian evolution is in its current form and what it is not. I argue that the Torah is not a source of scientific knowledge and all attempts to reconcile its plain text with the data of science are an exercise in futility. The article argues the position that science and the Torah are incommensurable. I argue against using the Torah for attaining knowledge about the nature of the world, or using science for enhancing or denying the truth of the Torah. PMID:23908802

  16. A Heritable Recombination system for synthetic Darwinian evolution in yeast.

    PubMed

    Romanini, Dante W; Peralta-Yahya, Pamela; Mondol, Vanessa; Cornish, Virginia W

    2012-12-21

    Genetic recombination is central to the generation of molecular diversity and enhancement of evolutionary fitness in living systems. Methods such as DNA shuffling that recapitulate this diversity mechanism in vitro are powerful tools for engineering biomolecules with useful new functions by directed evolution. Synthetic biology now brings demand for analogous technologies that enable the controlled recombination of beneficial mutations in living cells. Thus, here we create a Heritable Recombination system centered around a library cassette plasmid that enables inducible mutagenesis via homologous recombination and subsequent combination of beneficial mutations through sexual reproduction in Saccharomyces cerevisiae. Using repair of nonsense codons in auxotrophic markers as a model, Heritable Recombination was optimized to give mutagenesis efficiencies of up to 6% and to allow successive repair of different markers through two cycles of sexual reproduction and recombination. Finally, Heritable Recombination was employed to change the substrate specificity of a biosynthetic enzyme, with beneficial mutations in three different active site loops crossed over three continuous rounds of mutation and selection to cover a total sequence diversity of 10(13). Heritable Recombination, while at an early stage of development, breaks the transformation barrier to library size and can be immediately applied to combinatorial crossing of beneficial mutations for cell engineering, adding important features to the growing arsenal of next generation molecular biology tools for synthetic biology.

  17. Darwinian Docking

    NASA Astrophysics Data System (ADS)

    Kuntz, Irwin D.

    2012-01-01

    The Darwinian model of evolution is an optimization strategy that can be adapted to docking. It differs from the common use of genetic algorithms, primarily in its acceptance of diverse solutions over finding "global" optima. A related problem is selecting compounds using multiple criteria. I discuss these ideas and present the outlines of a protocol for selecting "hits" and "leads" in drug discovery.

  18. Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment.

    PubMed

    Ichihashi, Norikazu; Usui, Kimihito; Kazuta, Yasuaki; Sunami, Takeshi; Matsuura, Tomoaki; Yomo, Tetsuya

    2013-01-01

    The ability to evolve is a key characteristic that distinguishes living things from non-living chemical compounds. The construction of an evolvable cell-like system entirely from non-living molecules has been a major challenge. Here we construct an evolvable artificial cell model from an assembly of biochemical molecules. The artificial cell model contains artificial genomic RNA that replicates through the translation of its encoded RNA replicase. We perform a long-term (600-generation) replication experiment using this system, in which mutations are spontaneously introduced into the RNA by replication error, and highly replicable mutants dominate the population according to Darwinian principles. During evolution, the genomic RNA gradually reinforces its interaction with the translated replicase, thereby acquiring competitiveness against selfish (parasitic) RNAs. This study provides the first experimental evidence that replicating systems can be developed through Darwinian evolution in a cell-like compartment, even in the presence of parasitic replicators.

  19. The genetic code constrains yet facilitates Darwinian evolution.

    PubMed

    Firnberg, Elad; Ostermeier, Marc

    2013-08-01

    An important goal of evolutionary biology is to understand the constraints that shape the dynamics and outcomes of evolution. Here, we address the extent to which the structure of the standard genetic code constrains evolution by analyzing adaptive mutations of the antibiotic resistance gene TEM-1 β-lactamase and the fitness distribution of codon substitutions in two influenza hemagglutinin inhibitor genes. We find that the architecture of the genetic code significantly constrains the adaptive exploration of sequence space. However, the constraints endow the code with two advantages: the ability to restrict access to amino acid mutations with a strong negative effect and, most remarkably, the ability to enrich for adaptive mutations. Our findings support the hypothesis that the standard genetic code was shaped by selective pressure to minimize the deleterious effects of mutation yet facilitate the evolution of proteins through imposing an adaptive mutation bias.

  20. From Darwinian to technological evolution: forgetting the human lottery.

    PubMed

    Tintino, Giorgio

    2014-01-01

    The GRIN technologies (-geno, -robo, -info, -nano) promise to change the inner constitution of human body and its own existence. This transformation involves the structure of our lives and represent a brave new world that we have to explore and to manage. In this sense, the traditional tools of humanism seems very inadequate to think the biotech century and there is a strong demand of a new thought for the evolution and the concrete history of life. The posthuman philosophy tries to take this new path of human existence in all of its novelty since GRIN technologies seem to promise new and unexpected paths of evolution to living beings and, above all, man. For this, the post-human thought, as we see, is a new anthropological overview on the concrete evolution of human being, an overview that involves an epistemological revolution of the categories that humanism uses to conceptualize the journey that divides the Homo sapiens from the man. But, is this right?

  1. Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution

    PubMed Central

    Ling, Shaoping; Hu, Zheng; Yang, Zuyu; Yang, Fang; Li, Yawei; Lin, Pei; Chen, Ke; Dong, Lili; Cao, Lihua; Tao, Yong; Hao, Lingtong; Chen, Qingjian; Gong, Qiang; Wu, Dafei; Li, Wenjie; Zhao, Wenming; Tian, Xiuyun; Hao, Chunyi; Hungate, Eric A.; Catenacci, Daniel V. T.; Hudson, Richard R.; Li, Wen-Hsiung; Lu, Xuemei; Wu, Chung-I

    2015-01-01

    The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 “polymorphic” SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors. PMID:26561581

  2. Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution.

    PubMed

    Ling, Shaoping; Hu, Zheng; Yang, Zuyu; Yang, Fang; Li, Yawei; Lin, Pei; Chen, Ke; Dong, Lili; Cao, Lihua; Tao, Yong; Hao, Lingtong; Chen, Qingjian; Gong, Qiang; Wu, Dafei; Li, Wenjie; Zhao, Wenming; Tian, Xiuyun; Hao, Chunyi; Hungate, Eric A; Catenacci, Daniel V T; Hudson, Richard R; Li, Wen-Hsiung; Lu, Xuemei; Wu, Chung-I

    2015-11-24

    The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 "polymorphic" SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors.

  3. Comparative Structural Models of Similarities and Differences between "Vehicle" and "Target" in Order to Teach Darwinian "Evolution"

    ERIC Educational Resources Information Center

    Marcelos, Maria Fatima; Nagem, Ronaldo L.

    2010-01-01

    Our objective is to contribute to the teaching of Classical Darwinian "Evolution" by means of a study of analogies and metaphors. Throughout the history of knowledge about "Evolution" and in Science teaching, tree structures have been used an analogs to refer to "Evolution," such as by Darwin in the "Tree of Life" passage contained in "On The…

  4. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals

    PubMed Central

    Swanson, Willie J.; Yang, Ziheng; Wolfner, Mariana F.; Aquadro, Charles F.

    2001-01-01

    Rapid evolution driven by positive Darwinian selection is a recurrent theme in male reproductive protein evolution. In contrast, positive selection has never been demonstrated for female reproductive proteins. Here, we perform phylogeny-based tests on three female mammalian fertilization proteins and demonstrate positive selection promoting their divergence. Two of these female fertilization proteins, the zona pellucida glycoproteins ZP2 and ZP3, are part of the mammalian egg coat. Several sites identified in ZP3 as likely to be under positive selection are located in a region previously demonstrated to be involved in species-specific sperm-egg interaction, suggesting the selective pressure is related to male-female interaction. The results provide long-sought evidence for two evolutionary hypotheses: sperm competition and sexual conflict. PMID:11226269

  5. Adaptive evolution of cooperation through Darwinian dynamics in Public Goods games.

    PubMed

    Deng, Kuiying; Chu, Tianguang

    2011-01-01

    The linear or threshold Public Goods game (PGG) is extensively accepted as a paradigmatic model to approach the evolution of cooperation in social dilemmas. Here we explore the significant effect of nonlinearity of the structures of public goods on the evolution of cooperation within the well-mixed population by adopting Darwinian dynamics, which simultaneously consider the evolution of populations and strategies on a continuous adaptive landscape, and extend the concept of evolutionarily stable strategy (ESS) as a coalition of strategies that is both convergent-stable and resistant to invasion. Results show (i) that in the linear PGG contributing nothing is an ESS, which contradicts experimental data, (ii) that in the threshold PGG contributing the threshold value is a fragile ESS, which cannot resist the invasion of contributing nothing, and (iii) that there exists a robust ESS of contributing more than half in the sigmoid PGG if the return rate is relatively high. This work reveals the significant effect of the nonlinearity of the structures of public goods on the evolution of cooperation, and suggests that, compared with the linear or threshold PGG, the sigmoid PGG might be a more proper model for the evolution of cooperation within the well-mixed population.

  6. The search for minimum-energy atomic configurations on a lattice: Lamarckian twist on Darwinian Evolution

    NASA Astrophysics Data System (ADS)

    D'Avezac, Mayeul; Zunger, Alex

    2008-03-01

    We examine how two different mechanisms proposed historically for biological evolution compare for the determination of crystal structures from random initial lattice-configurations. The Darwinian theory of evolution contends that the genetic makeup inherited at birth is the one passed on to offsprings. Lamarck surmised additionally that offspring can inherit acquired traits. In the case of lattice-configurations, such improvements consist in A<->B transmutations of atomic sites as guided by ``Virtual Atom'' energy-gradients(M. d'Avezac and Alex Zunger, J. Phys.: Cond. Matt. 19, 402201 (2007)). This hybrid evolution is shown to provide an efficient solution to a generalized Ising Hamiltonian, illustrated by finding the ground-states of face-centered cubic Au1-xPdx using a cluster-expansion functional fitted to first-principles total-energies. For example, finding all minimum-energy structures of a 32-atom supercell with 95,% confidence requires evaluating 750, 000 configurations using local improvements only, 150, 000 using a reciprocal-space genetic algorithm only, and 14,000 using the hybrid approach. We consider applying the lamarckian search to further functionals.

  7. Evolution Born of Moisture: Analogies and Parallels Between Anaximander's Ideas on Origin of Life and Man and Later Pre-Darwinian and Darwinian Evolutionary Concepts.

    PubMed

    Kočandrle, Radim; Kleisner, Karel

    2013-01-01

    This study focuses on the origin of life as presented in the thought of Anaximander of Miletus but also points to some parallel motifs found in much later conceptions of both the pre-Darwinian German romantic science and post-Darwinian biology. According to Anaximander, life originated in the moisture associated with earth (mud). This moist environment hosted the first living creatures that later populated the dry land. In these descriptions, one can trace the earliest hints of the notion of environmental adaptation. The origin of humans was seen as connected in some way with fish: ancient humans were supposed to have developed inside fish-like animals. Anaximander took into account changes in the development of living creatures (adaptations) and speculated on the origins of humans. Similar ideas are found also in the writings of much later, eighteenth and nineteenth century authors who were close to the tradition of German romantic science. We do not argue that these later concepts are in any way directly linked with those of the pre-Socratics, but they show surprising parallels in, e.g., the hypothesis that life originated in a moist environment or the supposition that human developed from fish-like ancestors. These transformations are seen as a consequence of timeless logic rather than as evolution in historical terms. Despite the accent on the origin of living things, both Anaximander and the later Naturphilosophen lack in their notions the element most characteristic of Darwin's thought, that is, the emphasis on historicity and uniqueness of all that comes into being.

  8. Iterative saturation mutagenesis: a powerful approach to engineer proteins by systematically simulating Darwinian evolution.

    PubMed

    Acevedo-Rocha, Carlos G; Hoebenreich, Sabrina; Reetz, Manfred T

    2014-01-01

    Iterative saturation mutagenesis (ISM) is a widely applicable and powerful strategy for the efficient directed evolution of enzymes. First, one or more amino acid positions from the chosen enzyme are assigned to multi-residue sites (i.e., groups of amino acids or "multisites"). Then, the residues in each multisite are mutated with a user-defined randomization scheme to all canonical amino acids or a reduced amino acid alphabet. Subsequently, the genes of chosen variants (usually the best but not necessarily) are used as templates for saturation mutagenesis at other multisites, and the process is repeated until the desired degree of biocatalyst improvement has been achieved. Addressing multisites iteratively results in a so-called ISM scheme or tree with various upward branches or pathways. The systematic character of ISM simulates in vitro the natural process of Darwinian evolution: variation (library creation), selection (library screening), and amplification (template chosen for the next round of randomization). However, the main feature of ISM that distinguishes it from other directed evolution methods is the systematic probing of a defined segment of the protein sequence space, as it has been shown that ISM is much more efficient in terms of biocatalyst optimization than random methods such as error-prone PCR. In addition, ISM trees have also shed light on the emergence of epistasis, thereby rationally improving the strategies for evolving better enzymes. ISM was developed to improve catalytic properties such as rate, substrate scope, stereo- and regioselectivity using the Combinatorial Active-site Saturation Test (CAST), as well as chemical and thermal stability employing the B-Factor Iterative Test (B-FIT). However, ISM can also be invoked to manipulate such protein properties as binding affinity among other possibilities, including protein-protein interactions. Herein, we provide general guidelines for ISM, using CAST as the case study in the quest to

  9. Mode and tempo in the evolution of socio-political organization: reconciling 'Darwinian' and 'Spencerian' evolutionary approaches in anthropology.

    PubMed

    Currie, Thomas E; Mace, Ruth

    2011-04-12

    Traditional investigations of the evolution of human social and political institutions trace their ancestry back to nineteenth century social scientists such as Herbert Spencer, and have concentrated on the increase in socio-political complexity over time. More recent studies of cultural evolution have been explicitly informed by Darwinian evolutionary theory and focus on the transmission of cultural traits between individuals. These two approaches to investigating cultural change are often seen as incompatible. However, we argue that many of the defining features and assumptions of 'Spencerian' cultural evolutionary theory represent testable hypotheses that can and should be tackled within a broader 'Darwinian' framework. In this paper we apply phylogenetic comparative techniques to data from Austronesian-speaking societies of Island South-East Asia and the Pacific to test hypotheses about the mode and tempo of human socio-political evolution. We find support for three ideas often associated with Spencerian cultural evolutionary theory: (i) political organization has evolved through a regular sequence of forms, (ii) increases in hierarchical political complexity have been more common than decreases, and (iii) political organization has co-evolved with the wider presence of hereditary social stratification.

  10. Darwinian Liberal Education

    ERIC Educational Resources Information Center

    Arnhart, Larry

    2006-01-01

    Be it metaphysics, theology, or some other unifying framework, humans have long sought to determine "first principles" underlying knowledge. Larry Arnhart continues in this vein, positing a Darwinian web of genetic, cultural, and cognitive evolution to explain our social behavior in terms of human nature as governed by biology. He leaves it to us…

  11. Research program for a search of the origin of Darwinian evolution. Research program for a vesicle-based model of the origin of Darwinian evolution on prebiotic early Earth

    NASA Astrophysics Data System (ADS)

    Tessera, Marc

    2017-03-01

    The search for origin of `life' is made even more complicated by differing definitions of the subject matter, although a general consensus is that an appropriate definition should center on Darwinian evolution (Cleland and Chyba 2002). Within a physical approach which has been defined as a level-4 evolution (Tessera and Hoelzer 2013), one mechanism could be described showing that only three conditions are required to allow natural selection to apply to populations of different system lineages. This approach leads to a vesicle- based model with the necessary properties. Of course such a model has to be tested. Thus, after a brief presentation of the model an experimental program is proposed that implements the different steps able to show whether this new direction of the research in the field is valid and workable.

  12. Research program for a search of the origin of Darwinian evolution : Research program for a vesicle-based model of the origin of Darwinian evolution on prebiotic early Earth.

    PubMed

    Tessera, Marc

    2017-03-01

    The search for origin of 'life' is made even more complicated by differing definitions of the subject matter, although a general consensus is that an appropriate definition should center on Darwinian evolution (Cleland and Chyba 2002). Within a physical approach which has been defined as a level-4 evolution (Tessera and Hoelzer 2013), one mechanism could be described showing that only three conditions are required to allow natural selection to apply to populations of different system lineages. This approach leads to a vesicle- based model with the necessary properties. Of course such a model has to be tested. Thus, after a brief presentation of the model an experimental program is proposed that implements the different steps able to show whether this new direction of the research in the field is valid and workable.

  13. Darwinian fitness.

    PubMed

    Demetrius, Lloyd; Ziehe, Martin

    2007-11-01

    The term Darwinian fitness refers to the capacity of a variant type to invade and displace the resident population in competition for available resources. Classical models of this dynamical process claim that competitive outcome is a deterministic event which is regulated by the population growth rate, called the Malthusian parameter. Recent analytic studies of the dynamics of competition in terms of diffusion processes show that growth rate predicts invasion success only in populations of infinite size. In populations of finite size, competitive outcome is a stochastic process--contingent on resource constraints--which is determined by the rate at which a population returns to its steady state condition after a random perturbation in the individual birth and death rates. This return rate, a measure of robustness or population stability, is analytically characterized by the demographic parameter, evolutionary entropy, a measure of the uncertainty in the age of the mother of a randomly chosen newborn. This article appeals to computational and numerical methods to contrast the predictive power of the Malthusian and the entropic principles. The computational analysis rejects the Malthusian model and is consistent with of the entropic principle. These studies thus provide support for the general claim that entropy is the appropriate measure of Darwinian fitness and constitutes an evolutionary parameter with broad predictive and explanatory powers.

  14. From prebiotic chemistry to cellular metabolism--the chemical evolution of metabolism before Darwinian natural selection.

    PubMed

    Meléndez-Hevia, Enrique; Montero-Gómez, Nancy; Montero, Francisco

    2008-06-07

    It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin.

  15. Alfred Russel Wallace (1823-1913): the forgotten co-founder of the Neo-Darwinian theory of biological evolution.

    PubMed

    Kutschera, Ulrich; Hossfeld, Uwe

    2013-12-01

    The British naturalist Alfred Russel Wallace (1823-1913), who had to leave school aged 14 and never attended university, did extensive fieldwork, first in the Amazon River basin (1848-1852) and then in Southeast Asia (1854-1862). Based on this experience, and after reading the corresponding scientific literature, Wallace postulated that species were not created, but are modified descendants of pre-existing varieties (Sarawak Law paper, 1855). Evolution is brought about by a struggle for existence via natural selection, which results in the adaptation of those individuals in variable populations who survive and reproduce (Ternate essay, 1858). In his monograph Darwinism (1889), and in subsequent publications, Wallace extended the contents of Darwin's Origin of Species (1859) into the Neo-Darwinian theory of biological evolution, with reference to the work of August Weismann (1834-1914). Wallace also became the (co)-founder of biogeography, biodiversity research, astrobiology and evolutionary anthropology. Moreover, he envisioned what was later called the anthropocene (i.e., the age of human environmental destructiveness). However, since Wallace believed in atheistic spiritualism and mixed up scientific facts and supernatural speculations in some of his writings, he remains a controversial figure in the history of biology.

  16. Darwinian Controversies: An Historiographical Recounting

    ERIC Educational Resources Information Center

    Depew, David J.

    2010-01-01

    This essay reviews key controversies in the history of the Darwinian research tradition: the Wilberforce-Huxley debate in 1860, early twentieth-century debates about the heritability of acquired characteristics and the consistency of Mendelian genetics with natural selection; the 1925 Scopes trial about teaching evolution; tensions about race,…

  17. The 2009 Garrod lecture: the evolution of antimicrobial resistance: a Darwinian perspective.

    PubMed

    Sykes, Richard

    2010-09-01

    Microbes have evolved over 3.5 billion years and are arguably the most adaptable organisms on earth. Restricted genetically by their inability to reproduce sexually, bacteria have acquired several additional mechanisms by which to exchange genetic material horizontally. Such mechanisms have allowed bacteria to inhabit some of the most inhospitable environments on earth. It is thus hardly surprising that when faced with a barrage of inimical chemicals (antibiotics) they have responded with an equal and opposite force. This article compares and contrasts the evolution of antimicrobial resistance to beta-lactam antibiotics over the last 70 years in two bacterial species, namely Staphylococcus aureus, a highly evolved human pathogen, and Pseudomonas aeruginosa, an opportunistic nosocomial pathogen.

  18. In Darwinian evolution, feedback from natural selection leads to biased mutations.

    PubMed

    Caporale, Lynn Helena; Doyle, John

    2013-12-01

    Natural selection provides feedback through which information about the environment and its recurring challenges is captured, inherited, and accumulated within genomes in the form of variations that contribute to survival. The variation upon which natural selection acts is generally described as "random." Yet evidence has been mounting for decades, from such phenomena as mutation hotspots, horizontal gene transfer, and highly mutable repetitive sequences, that variation is far from the simplifying idealization of random processes as white (uniform in space and time and independent of the environment or context).  This paper focuses on what is known about the generation and control of mutational variation, emphasizing that it is not uniform across the genome or in time, not unstructured with respect to survival, and is neither memoryless nor independent of the (also far from white) environment. We suggest that, as opposed to frequentist methods, Bayesian analysis could capture the evolution of nonuniform probabilities of distinct classes of mutation, and argue not only that the locations, styles, and timing of real mutations are not correctly modeled as generated by a white noise random process, but that such a process would be inconsistent with evolutionary theory.

  19. Darwinian Daisyworld.

    PubMed

    Roberston, D; Robinson, J

    1998-11-07

    The Daisyworld model was developed to show that organisms can collectively regulate the global environment without assuming conscious or altruistic behaviour, i.e. that Gaia is feasible. We studied the effects of adaptive evolution of Daisyworld by allowing daisies to shift their optimal growth temperatures toward the prevailing temperature. This estimates Daisyworld's homeostatic ability, suggesting a trade-off between the ability of organisms to collectively regulate the environment and the abilities of evolving genotypes to adapt to it.

  20. Darwinian medicine and psoriasis.

    PubMed

    Romaní de Gabriel, J

    2015-04-01

    Darwinian medicine, or evolutionary medicine, regards some pathological conditions as attempts by the organism to solve a problem or develop defense mechanisms. At certain stages of human evolution, some diseases may have conferred a selective advantage. Psoriasis is a high-penetrance multigenic disorder with prevalence among whites of up to 3%. Psoriatic lesions have been linked with enhanced wound-healing qualities and greater capacity to fight infection. Leprosy, tuberculosis, and infections caused by viruses similar to human immunodeficiency virus have been postulated as environmental stressors that may have selected for psoriasis-promoting genes in some human populations. The tendency of patients with severe psoriasis to develop metabolic syndrome may reflect the body's attempt to react to environmental stresses and warning signs by triggering insulin resistance and fat storage.

  1. Mistakes and Molecular Evolution.

    ERIC Educational Resources Information Center

    Trevors, J. T.

    1998-01-01

    Examines the role mistakes play in the molecular evolution of bacteria. Discusses the interacting physical, chemical, and biological factors that cause changes in DNA and play a role in prokaryotic evolution. (DDR)

  2. Workshop on Molecular Evolution

    NASA Technical Reports Server (NTRS)

    Cummings, Michael P.

    2004-01-01

    Molecular evolution has become the nexus of many areas of biological research. It both brings together and enriches such areas as biochemistry, molecular biology, microbiology, population genetics, systematics, developmental biology, genomics, bioinformatics, in vitro evolution, and molecular ecology. The Workshop provides an important contribution to these fields in that it promotes interdisciplinary research and interaction, and thus provides a glue that sticks together disparate fields. Due to the wide range of fields addressed by the study of molecular evolution, it is difficult to offer a comprehensive course in a university setting. It is rare for a single institution to maintain expertise in all necessary areas. In contrast, the Workshop is uniquely able to provide necessary breadth and depth by utilizing a large number of faculty with appropriate expertise. Furthermore, the flexible nature of the Workshop allows for rapid adaptation to changes in the dynamic field of molecular evolution. For example, the 2003 Workshop included recently emergent research areas of molecular evolution of development and genomics.

  3. Evolving learnable neutral networks under changing environments with various rates of inheritance of acquired characters: comparison between Darwinian and Lamarckian evolution.

    PubMed

    Sasaki, T; Tokoro, M

    1999-01-01

    The processes of adaptation in natural organisms consist of two complementary phases: learning, occurring within each individual's lifetime, and evolution, occurring over successive generations of the population. In this article, we study the relationship between learning and evolution in a simple abstract model, where neural networks capable of learning are evolved using genetic algorithms (GAs). Individuals try to maximize their life energy by learning certain rules that distinguish between two groups of materials: food and poison. The connective weights of individuals' neural networks undergo modification, that is, certain characters will be acquired, through their lifetime learning. By setting various rates for the heritability of acquired characters, which is a motive force of Lamarckian evolution, we observe adaptational processes of populations over successive generations. Paying particular attention to behaviors under changing environments, we show the following results. Populations with lower rates of heritability not only show more stable behavior against environmental changes, but also maintain greater adaptability with respect to such changing environments. Consequently, the population with zero heritability, that is, the Darwinian population, attains the highest level of adaptation to dynamic environments.

  4. The instinctual nation-state: non-Darwinian theories, state science and ultra-nationalism in Oka Asajirō's Evolution and Human Life.

    PubMed

    Sullivan, Gregory

    2011-01-01

    In his anthology of socio-political essays, Evolution and Human Life, Oka Asajirō (1868-1944), early twentieth century Japan's foremost advocate of evolutionism, developed a biological vision of the nation-state as super-organism that reflected the concerns and aims of German-inspired Meiji statism and anticipated aspects of radical ultra-nationalism. Drawing on non-Darwinian doctrines, Oka attempted to realize such a fused or organic state by enhancing social instincts that would bind the minzoku (ethnic nation) and state into a single living entity. Though mobilization during the Russo-Japanese War seemed to evince this super-organism, the increasingly contentious and complex society that emerged in the war's aftermath caused Oka to turn first to Lamarckism and eventually to orthogenesis in the hopes of preserving the instincts needed for a viable nation-state. It is especially in the state interventionist measures that Oka finally came to endorse in order to forestall orthogenetically-driven degeneration that the technocratic proclivities of his statist orientation become most apparent. The article concludes by suggesting that Oka's emphasis on degeneration, autarkic expansion, and, most especially, totalitarian submersion of individuals into the statist collectivity indicates a complex relationship between his evolutionism and fascist ideology, what recent scholarship has dubbed radical Shinto ultra-nationalism.

  5. Selectionism and Neutralism in Molecular Evolution

    PubMed Central

    Nei, Masatoshi

    2006-01-01

    Charles Darwin proposed that evolution occurs primarily by natural selection, but this view has been controversial from the beginning. Two of the major opposing views have been mutationism and neutralism. Early molecular studies suggested that most amino acid substitutions in proteins are neutral or nearly neutral and the functional change of proteins occurs by a few key amino acid substitutions. This suggestion generated an intense controversy over selectionism and neutralism. This controversy is partially caused by Kimura's definition of neutrality, which was too strict (|2Ns| ≤ 1). If we define neutral mutations as the mutations that do not change the function of gene products appreciably, many controversies disappear because slightly deleterious and slightly advantageous mutations are engulfed by neutral mutations. The ratio of the rate of nonsynonymous nucleotide substitution to that of synonymous substitution is a useful quantity to study positive Darwinian selection operating at highly variable genetic loci, but it does not necessarily detect adaptively important codons. Previously, multigene families were thought to evolve following the model of concerted evolution, but new evidence indicates that most of them evolve by a birth-and-death process of duplicate genes. It is now clear that most phenotypic characters or genetic systems such as the adaptive immune system in vertebrates are controlled by the interaction of a number of multigene families, which are often evolutionarily related and are subject to birth-and-death evolution. Therefore, it is important to study the mechanisms of gene family interaction for understanding phenotypic evolution. Because gene duplication occurs more or less at random, phenotypic evolution contains some fortuitous elements, though the environmental factors also play an important role. The randomness of phenotypic evolution is qualitatively different from allele frequency changes by random genetic drift. However, there is

  6. Usefulness of a Darwinian System in a Biotechnological Application: Evolution of Optical Window Fluorescent Protein Variants under Selective Pressure

    PubMed Central

    Ng, David; Pauli, Jutta; Resch-Genger, Ute; Kühn, Enrico; Heuer, Steffen; Beisker, Wolfgang; Köster, Reinhard W.; Zitzelsberger, Horst; Caldwell, Randolph B

    2014-01-01

    With rare exceptions, natural evolution is an extremely slow process. One particularly striking exception in the case of protein evolution is in the natural production of antibodies. Developing B cells activate and diversify their immunoglobulin (Ig) genes by recombination, gene conversion (GC) and somatic hypermutation (SHM). Iterative cycles of hypermutation and selection continue until antibodies of high antigen binding specificity emerge (affinity maturation). The avian B cell line DT40, a cell line which is highly amenable to genetic manipulation and exhibits a high rate of targeted integration, utilizes both GC and SHM. Targeting the DT40's diversification machinery onto transgenes of interest inserted into the Ig loci and coupling selective pressure based on the desired outcome mimics evolution. Here we further demonstrate the usefulness of this platform technology by selectively pressuring a large shift in the spectral properties of the fluorescent protein eqFP615 into the highly stable and advanced optical imaging expediting fluorescent protein Amrose. The method is advantageous as it is time and cost effective and no prior knowledge of the outcome protein's structure is necessary. Amrose was evolved to have high excitation at 633 nm and excitation/emission into the far-red, which is optimal for whole-body and deep tissue imaging as we demonstrate in the zebrafish and mouse model. PMID:25192257

  7. Evolution of molecular clouds

    NASA Technical Reports Server (NTRS)

    Sevenster, M.

    1993-01-01

    The evolution of interstellar molecular hydrogen was studied, with a special interest for the formation and evolution of molecular clouds and star formation within them, by a two-dimensional hydrodynamical simulation performed on a rectangular grid of physical sizes on the order of 100 pc. It is filled with an initial density of approx. 1 cm(exp -3), except for one cell (approx. 1 pc(exp 2)) at the center of the grid where an accretion core of 1-10(exp 3) solar masses is placed. The grid is co-moving with the gridcenter that is on a circular orbit around the Galactic center and that also is the guiding center of epicyclic approximation of orbits of the matter surrounding it. The initial radial velocity is zero; to account for differential rotation the initial tangential velocity (i.e. the movement around the galactic center) is proportional to the radial distance to the grid center. The rate is comparable to the rotation rate at the Local Standard of Rest. The influence of galactic rotation is noticed by spiral or elliptical forms, but on much longer time scales than self gravitation and cooling processes. Density and temperature are kept constant at the boundaries and no inflow is allowed along the tangential boundaries.

  8. The Molecular Basis of Evolution.

    ERIC Educational Resources Information Center

    Wilson, Allan C.

    1985-01-01

    Discovery that mutations accumulate at steady rates over time in the genes of all lineages of plants and animals has led to new insights into evolution at the molecular and organismal levels. Discusses molecular evolution, examining deoxyribonuclei acid (DNA) sequences, morphological distances, and codon rate of change. (DH)

  9. Darwinian Controversies: An Historiographical Recounting

    NASA Astrophysics Data System (ADS)

    Depew, David J.

    2010-05-01

    This essay reviews key controversies in the history of the Darwinian research tradition: the Wilberforce-Huxley debate in 1860, early twentieth-century debates about the heritability of acquired characteristics and the consistency of Mendelian genetics with natural selection; the 1925 Scopes trial about teaching evolution; tensions about race, culture, and eugenics at the 1959 centenary celebration Darwin’s Origin of Species; adaptationism and its critics in the Sociobiology debate of 1970s and, more recently, Evolutionary Psychology; and current disputes about Intelligent Design. These controversies, I argue, are etched into public memory because they occur at the emotionally charged boundaries between public-political, technical-scientific, and personal-religious spheres of discourse. Over most of them falls the shadow of eugenics. The main lesson is that the history of Darwinism cannot be told except by showing the mutual influence of the different norms of discourse that obtain in the personal, technical, and public spheres. Nor can evolutionary biology successfully be taught to citizens and citizens-to-be until the fractious intersections between spheres of discourse have been made explicit. In the course of showing why, I take rival evolutionary approaches to be dynamical historical research traditions rather than static theories. Accordingly, I distinguish Darwin’s version of Darwinism from its later transformations. I pay special attention to the role Darwin assigned to development in evolution, which was marginalized by twentieth-century population genetical Darwinism, but has recently resurfaced in new forms. I also show how the disputed phrases “survival of the fittest” and “social Darwinism” have shaped personal anxieties about “Darwinism,” have provoked public opposition to teaching evolution in public schools, and have cast a shadow over efforts to effectively communicate to the public largely successful technical efforts to make

  10. Darwinian Model Building

    SciTech Connect

    Kester, Do; Bontekoe, Romke

    2011-03-14

    We present a way to generate heuristic mathematical models based on the Darwinian principles of variation and selection in a pool of individuals over many generations. Each individual has a genotype (the hereditary properties) and a phenotype (the expression of these properties in the environment). Variation is achieved by cross-over and mutation operations on the genotype which consists in the present case of a single chromosome. The genotypes 'live' in the environment of the data. Nested Sampling is used to optimize the free parameters of the models given the data, thus giving rise to the phenotypes. Selection is based on the phenotypes.The evidences which naturally follow from the Nested Sampling Algorithm are used in a second level of Nested Sampling to find increasingly better models.The data in this paper originate from the Leiden Cytology and Pathology Laboratory (LCPL), which screens pap smears for cervical cancer. We have data for 1750 women who on average underwent 5 tests each. The data on individual women are treated as a small time series. We will try to estimate the next value of the prime cancer indicator from previous tests of the same woman.

  11. Darwinian Model Building

    NASA Astrophysics Data System (ADS)

    Kester, Do; Bontekoe, Romke

    2011-03-01

    We present a way to generate heuristic mathematical models based on the Darwinian principles of variation and selection in a pool of individuals over many generations. Each individual has a genotype (the hereditary properties) and a phenotype (the expression of these properties in the environment). Variation is achieved by cross-over and mutation operations on the genotype which consists in the present case of a single chromosome. The genotypes `live' in the environment of the data. Nested Sampling is used to optimize the free parameters of the models given the data, thus giving rise to the phenotypes. Selection is based on the phenotypes. The evidences which naturally follow from the Nested Sampling Algorithm are used in a second level of Nested Sampling to find increasingly better models. The data in this paper originate from the Leiden Cytology and Pathology Laboratory (LCPL), which screens pap smears for cervical cancer. We have data for 1750 women who on average underwent 5 tests each. The data on individual women are treated as a small time series. We will try to estimate the next value of the prime cancer indicator from previous tests of the same woman.

  12. Chemical evolution of molecular clouds

    NASA Technical Reports Server (NTRS)

    Prasad, Sheo S.; Tarafdar, Sankar P.; Villere, Karen R.; Huntress, Wesley T., Jr.

    1987-01-01

    The principles behind the coupled chemical-dynamical evolution of molecular clouds are described. Particular attention is given to current problems involving the simplest species (i.e., C. CO, O2, and H2) in quiescent clouds. The results of a comparison made between the molecular abundances in the Orion ridge and the hot core (Blake, 1986) are presented.

  13. The Janus face of Darwinian competition.

    PubMed

    Hintze, Arend; Phillips, Nathaniel; Hertwig, Ralph

    2015-09-10

    Without competition, organisms would not evolve any meaningful physical or cognitive abilities. Competition can thus be understood as the driving force behind Darwinian evolution. But does this imply that more competitive environments necessarily evolve organisms with more sophisticated cognitive abilities than do less competitive environments? Or is there a tipping point at which competition does more harm than good? We examine the evolution of decision strategies among virtual agents performing a repetitive sampling task in three distinct environments. The environments differ in the degree to which the actions of a competitor can affect the fitness of the sampling agent, and in the variance of the sample. Under weak competition, agents evolve decision strategies that sample often and make accurate decisions, which not only improve their own fitness, but are good for the entire population. Under extreme competition, however, the dark side of the Janus face of Darwinian competition emerges: Agents are forced to sacrifice accuracy for speed and are prevented from sampling as often as higher variance in the environment would require. Modest competition is therefore a good driver for the evolution of cognitive abilities and of the population as a whole, whereas too much competition is devastating.

  14. The Problem with a Darwinian View of Humanity

    ERIC Educational Resources Information Center

    Cunningham, Paul F.

    2009-01-01

    Comments on the special issue on Charles Darwin and psychology (Dewsbury, February-March 2009), in which the authors present evidence supporting the validity of Charles Darwin's theory of evolution and how generations of psychologists have viewed the natural world through its light, taking Darwinian theories for granted as being a literal…

  15. The Malthusian-Darwinian dynamic and the trajectory of civilization

    USGS Publications Warehouse

    Nekola, Jeffrey C.; Allen, Craig D.; Brown, James H.; Burger, Joseph R.; Davidson, Ana D.; Fristoe, Trevor S.; Hamilton, Marcus J.; Hammond, Sean T.; Kodric-Brown, Astrid; Mercado-Silva, Norman; Okie, Jordan G.

    2013-01-01

    Two interacting forces influence all populations: the Malthusian dynamic of exponential growth until resource limits are reached, and the Darwinian dynamic of innovation and adaptation to circumvent these limits through biological and/or cultural evolution. The specific manifestations of these forces in modern human society provide an important context for determining how humans can establish a sustainable relationship with the finite Earth.

  16. Toward Darwinian fisheries management

    PubMed Central

    Dunlop, Erin S; Enberg, Katja; Jørgensen, Christian; Heino, Mikko

    2009-01-01

    There is increasing evidence that fishing may cause rapid contemporary evolution in freshwater and marine fish populations. This has led to growing concern about the possible consequences such evolutionary change might have for aquatic ecosystems and the utility of those ecosystems to society. This special issue contains contributions from a symposium on fisheries-induced evolution held at the American Fisheries Society Annual Meeting in August 2008. Contributions include primary studies and reviews of field-based and experimental evidence, and several theoretical modeling studies advancing life-history theory and investigating potential management options. In this introduction we review the state of research in the field, discuss current controversies, and identify contributions made by the papers in this issue to the knowledge of fisheries-induced evolution. We end by suggesting directions for future research. PMID:25567878

  17. The search for purpose in a post-Darwinian universe: George Bernard Shaw, 'creative evolution', and Shavian eugenics: 'The dark side of the force'.

    PubMed

    Hale, Piers J

    2006-01-01

    The Irish playwright and socialist George Bernard Shaw has been of marginal concern for historians of biology because his vitalist Lamarckism has been viewed as out of step with contemporary science. However, Julian Huxley and J.B.S. Haldane were certainly of the opinion that Shaw was a man of influence in this regard and took pains to counter his views in their own attempts to engage the public in science. Previously, Shaw's colleague and friend H.G. Wells had also agued with Shaw from his own mechanistic neo-Darwinian perspective. The very public debate between Shaw and Wells, which continued to concern Huxley and Haldane, shows that public concern over the moral implications of Darwinism has a long history. Taking into account the opinions of John Maynard Smith on this matter, I suggest that a consideration of Shaw in this context can give us an understanding of the historical popularity of vitalist teleology as well as of the persistent ambivalence to the non-normative character of Darwinism.

  18. Three Laws in Darwinian Evolutionary Theory

    NASA Astrophysics Data System (ADS)

    Ao, Ping

    2006-03-01

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

  19. The evolution of molecular clouds

    NASA Technical Reports Server (NTRS)

    Shu, Frank H.; Lizano, Susana

    1988-01-01

    The problem of the structure and evolution of molecular clouds is reviewed, with particular emphasis given to the relationship with star formation. The basic hypothesis is that magnetic fields are the primary agents for supporting molecular clouds, although damped Alfven waves may play an important role in the direction parallel to the field lines. This picture naturally leads to a conception of 'bimodal star formation'. It is proposed that high-mass stars form from the overall gravitational collapse of a supercritical cloud, whereas low-mass stars form from small individual cores that slowly condense by ambipolar diffusion from a more extended envelope until they pass the brink of graviational instability and begin to collapse dynamically from 'inside-out'. The evidence that the infall stage of protostellar evolution is terminated by the development of a powerful stellar wind is reviewed.

  20. Antagonistic coevolution accelerates molecular evolution

    PubMed Central

    Paterson, Steve; Vogwill, Tom; Buckling, Angus; Benmayor, Rebecca; Spiers, Andrew J.; Thomson, Nicholas R.; Quail, Mike; Smith, Frances; Walker, Danielle; Libberton, Ben; Fenton, Andrew; Hall, Neil; Brockhurst, Michael A.

    2013-01-01

    The Red Queen hypothesis proposes that coevolution of interacting species (such as hosts and parasites) should drive molecular evolution through continual natural selection for adaptation and counter-adaptation1–3. Although the divergence observed at some host-resistance4–6 and parasite-infectivity7–9 genes is consistent with this, the long time periods typically required to study coevolution have so far prevented any direct empirical test. Here we show, using experimental populations of the bacterium Pseudomonas fluorescens SBW25 and its viral parasite, phage Φ2 (refs 10, 11), that the rate of molecular evolution in the phage was far higher when both bacterium and phage coevolved with each other than when phage evolved against a constant host genotype. Coevolution also resulted in far greater genetic divergence between replicate populations, which was correlated with the range of hosts that coevolved phage were able to infect. Consistent with this, the most rapidly evolving phage genes under coevolution were those involved in host infection. These results demonstrate, at both the genomic and phenotypic level, that antagonistic coevolution is a cause of rapid and divergent evolution, and is likely to be a major driver of evolutionary change within species. PMID:20182425

  1. Adaptive evolution of molecular phenotypes

    NASA Astrophysics Data System (ADS)

    Held, Torsten; Nourmohammad, Armita; Lässig, Michael

    2014-09-01

    Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.

  2. Maternal Effects in Molecular Evolution

    NASA Astrophysics Data System (ADS)

    Wilke, Claus O.

    2002-02-01

    We introduce a model of molecular evolution in which the fitness of an individual depends both on its own and on the parent's genotype. The model can be solved by means of a nonlinear mapping onto the standard quasispecies model. The dependency on the parental genotypes cancels from the mean fitness, but not from the individual sequence concentrations. For finite populations, the position of the error threshold is very sensitive to the influence from parent genotypes. In addition to biological applications, our model is important for understanding the dynamics of self-replicating computer programs.

  3. A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution

    PubMed Central

    Hartl, Daniel L.

    2016-01-01

    Much of the public lacks a proper understanding of Darwinian evolution, a problem that can be addressed with new learning and teaching approaches to be implemented both inside the classroom and in less formal settings. Few analogies have been as successful in communicating the basics of molecular evolution as John Maynard Smith’s protein space analogy (1970), in which he compared protein evolution to the transition between the terms WORD and GENE, changing one letter at a time to yield a different, meaningful word (in his example, the preferred path was WORD → WORE → GORE → GONE → GENE). Using freely available computer science tools (Google Books Ngram Viewer), we offer an update to Maynard Smith’s analogy and explain how it might be developed into an exploratory and pedagogical device for understanding the basics of molecular evolution and, more specifically, the adaptive landscape concept. We explain how the device works through several examples and provide resources that might facilitate its use in multiple settings, ranging from public engagement activities to formal instruction in evolution, population genetics, and computational biology. PMID:27736867

  4. A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution.

    PubMed

    Ogbunugafor, C Brandon; Hartl, Daniel L

    2016-10-01

    Much of the public lacks a proper understanding of Darwinian evolution, a problem that can be addressed with new learning and teaching approaches to be implemented both inside the classroom and in less formal settings. Few analogies have been as successful in communicating the basics of molecular evolution as John Maynard Smith's protein space analogy (1970), in which he compared protein evolution to the transition between the terms WORD and GENE, changing one letter at a time to yield a different, meaningful word (in his example, the preferred path was WORD → WORE → GORE → GONE → GENE). Using freely available computer science tools (Google Books Ngram Viewer), we offer an update to Maynard Smith's analogy and explain how it might be developed into an exploratory and pedagogical device for understanding the basics of molecular evolution and, more specifically, the adaptive landscape concept. We explain how the device works through several examples and provide resources that might facilitate its use in multiple settings, ranging from public engagement activities to formal instruction in evolution, population genetics, and computational biology.

  5. Directional Darwinian Selection in proteins

    PubMed Central

    2013-01-01

    Background Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins. Methods Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test. Results Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations. Conclusions Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time. PMID:24267049

  6. Anarchy, socialism and a Darwinian left.

    PubMed

    Clarke, Ellen

    2006-03-01

    In A Darwinian left Peter Singer aims to reconcile Darwinian theory with left wing politics, using evolutionary game theory and in particular a model proposed by Robert Axelrod, which shows that cooperation can be an evolutionarily successful strategy. In this paper I will show that whilst Axelrod's model can give support to a kind of left wing politics, it is not the kind that Singer himself envisages. In fact, it is shown that there are insurmountable problems for the idea of increasing Axelrodian cooperation within a welfare state. My surprising conclusion will be that a Darwinian left worthy of the name would be anarchistic.

  7. Molecular evolution and the latitudinal biodiversity gradient

    PubMed Central

    Dowle, E J; Morgan-Richards, M; Trewick, S A

    2013-01-01

    Species density is higher in the tropics (low latitude) than in temperate regions (high latitude) resulting in a latitudinal biodiversity gradient (LBG). The LBG must be generated by differential rates of speciation and/or extinction and/or immigration among regions, but the role of each of these processes is still unclear. Recent studies examining differences in rates of molecular evolution have inferred a direct link between rate of molecular evolution and rate of speciation, and postulated these as important drivers of the LBG. Here we review the molecular genetic evidence and examine the factors that might be responsible for differences in rates of molecular evolution. Critical to this is the directionality of the relationship between speciation rates and rates of molecular evolution. PMID:23486082

  8. Molecular evolution and thermal adaptation

    NASA Astrophysics Data System (ADS)

    Chen, Peiqiu

    2011-12-01

    In this thesis, we address problems in molecular evolution, thermal adaptation, and the kinetics of adaptation of bacteria and viruses to elevated environmental temperatures. We use a nearly neutral fitness model where the replication speed of an organism is proportional to the copy number of folded proteins. Our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. We find that species with high mutation rates tend to have less stable proteins compared to species with low mutation rate. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: striking asymmetry of thermal response curves, the absence of evolutionary trade-off which was expected but not found in experiments, correlation between denaturation temperature for several protein families and the Optimal Growth Temperature (OGT) of their carrier organisms, and proximity of bacterial or viral OGTs to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species. The model also addresses the key to adaptation is in weak-link genes (WLG), which encode least thermodynamically stable essential proteins in the proteome. We observe, as in experiment, a two-stage adaptation process. The first stage is a Luria-Delbruck type of selection, whereby rare WLG alleles, whose proteins are more stable than WLG proteins of the majority of the population (either due to standing genetic variation or due to an early acquired mutation), rapidly rise to fixation. The second stage constitutes subsequent slow accumulation of mutations in an adapted population. As adaptation progresses, selection regime changes from positive to neutral: Selection coefficient of beneficial mutations scales as a negative power of number of

  9. Teaching Darwinian Evolution: Learning from Religious Education

    ERIC Educational Resources Information Center

    Stolberg, Tonie L.

    2010-01-01

    This article examines what science education might be able to learn from phenomenological religious education's attempts to teach classes where students hold a plurality of religious beliefs. Recent statements as to how best to accomplish the central pedagogical concept of "learning from religion" as a vehicle for human transformation are…

  10. The Theory of Evolution: An Educational Perspective.

    ERIC Educational Resources Information Center

    Johnson, William L.; Johnson, Annabel M.

    The article's thesis is that evolution's intellectual foundations have been steadily eroding, and that few new findings in embryology, taxonomy, fossil remains, and molecular biology are bringing us very near to a formal, logical disproof of Darwinian claims. The paper begins by discussing the evidence of a prehistoric world, then they discuss…

  11. Model of evolution of molecular sequences

    NASA Astrophysics Data System (ADS)

    Luo, Liaofu; Tsai, Lu; Lee, Weijiang

    1990-05-01

    A simplified model of the evolution of molecular sequences is proposed. An ensemble of strings is considered that consists of two letters and undergoes random point mutations and natural selections. A set of evolution equations is deduced. From the solution it is found that the first-order (second-order) informational parameters (redundancies) D1 decrease (D2 increase) in the course of evolution. Furthermore, the statistical correlations of the letters (bases) in the sequences are investigated in detail and the short-distance correlation is demonstrated. These results give a preliminary explanation of some physical aspects in the evolution of nucleic acid sequences.

  12. Study on a Possible Darwinian Origin of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Baladrón, C.

    2011-03-01

    A sketchy subquantum theory deeply influenced by Wheeler's ideas (Am. J. Phys. 51:398-404, 1983) and by the de Broglie-Bohm interpretation (Goldstein in Stanford Encyclopedia of Philosophy, 2006) of quantum mechanics is further analyzed. In this theory a fundamental system is defined as a dual entity formed by bare matter and a methodological probabilistic classical Turing machine. The evolution of the system would be determined by three Darwinian informational regulating principles. Some progress in the derivation of the postulates of quantum mechanics from these regulating principles is reported. The entanglement in a bipartite system is preliminarily considered.

  13. A biophysical perspective on molecular evolution

    NASA Astrophysics Data System (ADS)

    Wilke, Claus

    2014-03-01

    The field of molecular evolution investigates how genes and genomes evolve over time. It has its origin in the late 1960s, when the first DNA and protein sequences were becoming available. With rapid progress in sequencing technologies came ever increasing demand for computational tools to study molecular evolution. Today, molecular evolution is among the largest subfields of evolutionary biology, and arguably one of the most computationally advanced. A side effect of the strong emphasis on developing sophisticated methods for sequence analysis has been that the underlying biophysical objects represented by the sequences, DNA molecules, RNA molecules, and proteins, have taken a back-seat in much computational molecular-evolution work. The vast majority of algorithms for sequence analysis, for example, operate purely on strings of letters, and don't incorporate any information of the biophysical reality that these letters represent. However, DNA, RNA, and proteins are three-dimensional physical objects composed of many interacting particles. We thus expect that their genetic evolution over time is shaped to some extent by these physical properties. Here, I will discuss the extent to which biophysical properties of proteins shape genetic evolution, and how we can use these properties to improve evolutionary analyses.

  14. Near-Neutrality: the Leading Edge of the Neutral Theory of Molecular Evolution

    PubMed Central

    Hughes, Austin L.

    2009-01-01

    The nearly-neutral theory represents a development of Kimura’s Neutral Theory of Molecular Evolution that makes testable predictions that go beyond a mere null model. Recent evidence has strongly supported several of these predictions, including the prediction that slightly deleterious variants will accumulate in a species that has undergone a severe bottleneck or in cases where recombination is reduced or absent. Because bottlenecks often occur in speciation and slightly deleterious mutations in coding regions will usually be nonsynonymous, we should expect that the ratio of nonsynonymous to synonymous fixed differences between species should often exceed the ratio of nonsynonymous to synonymous polymorphisms within species. Numerous data support this prediction, although they have often been wrongly interpreted as evidence for positive Darwinian selection. The use of conceptually flawed tests for positive selection has become widespread in recent years, seriously harming the quest for an understanding of genome evolution. When properly analyzed, many (probably most) claimed cases of positive selection will turn out to involve the fixation of slightly deleterious mutations by genetic drift in bottlenecked populations. Slightly deleterious variants are a transient feature of evolution in the long term, but they have had substantial impact on contemporary species, including our own. PMID:18559820

  15. JavaGenes Molecular Evolution

    NASA Technical Reports Server (NTRS)

    Lohn, Jason; Smith, David; Frank, Jeremy; Globus, Al; Crawford, James

    2007-01-01

    JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.

  16. What makes Darwinian hydrology "Darwinian"? Asking a different kind of question about landscapes

    NASA Astrophysics Data System (ADS)

    Harman, C.; Troch, P. A.

    2014-02-01

    There have been repeated calls for a Darwinian approach to hydrologic science, or for a synthesis of Darwinian and Newtonian approaches, to deepen understanding of the hydrologic system in the larger landscape context, and so develop a better basis for predictions now and in an uncertain future. But what exactly makes a Darwinian approach to hydrology "Darwinian"? While there have now been a number of discussions of Darwinian approaches, many referencing Harte (2002), the term is potentially a source of confusion because its connections to Darwin remain allusive rather than explicit. Here we suggest that the Darwinian approach to hydrology follows the example of Charles Darwin by focusing attention on the patterns of variation in populations and seeking hypotheses that explain these patterns in terms of the mechanisms and conditions that determine their historical development. These hypotheses do not simply catalog patterns or predict them statistically - they connect the present structure with processes operating in the past. Nor are they explanations presented without independent evidence or critical analysis - Darwin's hypotheses about the mechanisms underlying present-day variation could be independently tested and validated. With a Darwinian framework in mind, it is easy to see that a great deal of hydrologic research has already been done that contributes to a Darwinian hydrology - whether deliberately or not. We discuss some practical and philosophical issues with this approach to hydrologic science: how are explanatory hypotheses generated? What constitutes a good hypothesis? How are hypotheses tested? "Historical" sciences - including paleohydrology - have long grappled with these questions, as must a Darwinian hydrologic science. We can draw on Darwin's own example for some answers, though there are ongoing debates about the philosophical nature of his methods and reasoning. Darwin used a range of methods of historical reasoning to develop explanatory

  17. Molecular evolution tracks macroevolutionary transitions in Cetacea.

    PubMed

    McGowen, Michael R; Gatesy, John; Wildman, Derek E

    2014-06-01

    Cetacea (whales, dolphins, and porpoises) is a model group for investigating the molecular signature of macroevolutionary transitions. Recent research has begun to reveal the molecular underpinnings of the remarkable anatomical and behavioral transformation in this clade. This shift from terrestrial to aquatic environments is arguably the best-understood major morphological transition in vertebrate evolution. The ancestral body plan and physiology were extensively modified and, in many cases, these crucial changes are recorded in cetacean genomes. Recent studies have highlighted cetaceans as central to understanding adaptive molecular convergence and pseudogene formation. Here, we review current research in cetacean molecular evolution and the potential of Cetacea as a model for the study of other macroevolutionary transitions from a genomic perspective.

  18. Sexual selection: Another Darwinian process.

    PubMed

    Gayon, Jean

    2010-02-01

    the Darwin-Wallace controversy was that most Darwinian biologists avoided the subject of sexual selection until at least the 1950s, Ronald Fisher being a major exception. This controversy still deserves attention from modern evolutionary biologists, because the modern approach inherits from both Darwin and Wallace. The modern approach tends to present sexual selection as a special aspect of the theory of natural selection, although it also recognizes the big difficulties resulting from the inevitable interaction between these two natural processes of selection. And contra Wallace, it considers mate choice as a major process that deserves a proper evolutionary treatment. The paper's conclusion explains why sexual selection can be taken as a test case for a proper assessment of "Darwinism" as a scientific tradition. Darwin's and Wallace's attitudes towards sexual selection reveal two different interpretations of the principle of natural selection: Wallace's had an environmentalist conception of natural selection, whereas Darwin was primarily sensitive to the element of competition involved in the intimate mechanism of any natural process of selection. Sexual selection, which can lack adaptive significance, reveals this exemplarily.

  19. Positive darwinian selection at the imprinted MEDEA locus in plants.

    PubMed

    Spillane, Charles; Schmid, Karl J; Laoueillé-Duprat, Sylvia; Pien, Stéphane; Escobar-Restrepo, Juan-Miguel; Baroux, Célia; Gagliardini, Valeria; Page, Damian R; Wolfe, Kenneth H; Grossniklaus, Ueli

    2007-07-19

    In mammals and seed plants, a subset of genes is regulated by genomic imprinting where an allele's activity depends on its parental origin. The parental conflict theory suggests that genomic imprinting evolved after the emergence of an embryo-nourishing tissue (placenta and endosperm), resulting in an intragenomic parental conflict over the allocation of nutrients from mother to offspring. It was predicted that imprinted genes, which arose through antagonistic co-evolution driven by a parental conflict, should be subject to positive darwinian selection. Here we show that the imprinted plant gene MEDEA (MEA), which is essential for seed development, originated during a whole-genome duplication 35 to 85 million years ago. After duplication, MEA underwent positive darwinian selection consistent with neo-functionalization and the parental conflict theory. MEA continues to evolve rapidly in the out-crossing species Arabidopsis lyrata but not in the self-fertilizing species Arabidopsis thaliana, where parental conflicts are reduced. The paralogue of MEA, SWINGER (SWN; also called EZA1), is not imprinted and evolved under strong purifying selection because it probably retained the ancestral function of the common precursor gene. The evolution of MEA suggests a late origin of genomic imprinting within the Brassicaceae, whereas imprinting is thought to have originated early within the mammalian lineage.

  20. Molecular Evolution of Grass Stomata.

    PubMed

    Chen, Zhong-Hua; Chen, Guang; Dai, Fei; Wang, Yizhou; Hills, Adrian; Ruan, Yong-Ling; Zhang, Guoping; Franks, Peter J; Nevo, Eviatar; Blatt, Michael R

    2017-02-01

    Grasses began to diversify in the late Cretaceous Period and now dominate more than one third of global land area, including three-quarters of agricultural land. We hypothesize that their success is likely attributed to the evolution of highly responsive stomata capable of maximizing productivity in rapidly changing environments. Grass stomata harness the active turgor control mechanisms present in stomata of more ancient plant lineages, maximizing several morphological and developmental features to ensure rapid responses to environmental inputs. The evolutionary development of grass stomata appears to have been a gradual progression. Therefore, understanding the complex structures, developmental events, regulatory networks, and combinations of ion transporters necessary to drive rapid stomatal movement may inform future efforts towards breeding new crop varieties.

  1. Molecular evolution of the ependymin protein family: a necessary update

    PubMed Central

    Suárez-Castillo, Edna C; García-Arrarás, José E

    2007-01-01

    Background Ependymin (Epd), the predominant protein in the cerebrospinal fluid of teleost fishes, was originally associated with neuroplasticity and regeneration. Ependymin-related proteins (Epdrs) have been identified in other vertebrates, including amphibians and mammals. Recently, we reported the identification and characterization of an Epdr in echinoderms, showing that there are ependymin family members in non-vertebrate deuterostomes. We have now explored multiple databases to find Epdrs in different metazoan species. Using these sequences we have performed genome mapping, molecular phylogenetic analyses using Maximum Likelihood and Bayesian methods, and statistical tests of tree topologies, to ascertain the phylogenetic relationship among ependymin proteins. Results Our results demonstrate that ependymin genes are also present in protostomes. In addition, as a result of the putative fish-specific genome duplication event and posterior divergence, the ependymin family can be divided into four groups according to their amino acid composition and branching pattern in the gene tree: 1) a brain-specific group of ependymin sequences that is unique to teleost fishes and encompasses the originally described ependymin; 2) a group expressed in non-brain tissue in fishes; 3) a group expressed in several tissues that appears to be deuterostome-specific, and 4) a group found in invertebrate deuterostomes and protostomes, with a broad pattern of expression and that probably represents the evolutionary origin of the ependymins. Using codon-substitution models to statistically assess the selective pressures acting over the ependymin protein family, we found evidence of episodic positive Darwinian selection and relaxed selective constraints in each one of the postduplication branches of the gene tree. However, purifying selection (with among-site variability) appears to be the main influence on the evolution of each subgroup within the family. Functional divergence among the

  2. Origins of Genius: Darwinian Perspectives on Creativity.

    ERIC Educational Resources Information Center

    Simonton, Dean Keith

    This study of creative genius argues that creativity can best be understood as a Darwinian process of variation and selection. The artist or scientist generates a wealth of ideas, and then subjects these ideas to aesthetic or scientific judgment, selecting only those that have the best chance to survive and reproduce. The book draws on the latest…

  3. The Nature of the Darwinian Revolution

    ERIC Educational Resources Information Center

    Mayr, Ernst

    1972-01-01

    Analysis of the writings of anti-evolutionists contemporary with Darwin reveals that there were many objections that had to be overcome and that the Darwinian revolution" does not conform to the simple model of a scientific revolution as outlined by T. S. Kuhn. (AL)

  4. Proteins, exons and molecular evolution.

    PubMed

    Holland, S K; Blake, C C

    1987-01-01

    The discovery of the eukaryotic gene structure has prompted research into the potential relationship between protein structure and function and the corresponding exon/intron patterns. The exon shuffling hypothesis put forward by Gilbert and Blake suggests the encodement of structural and functional protein elements by exons which can recombine to create novel proteins. This provides an explanation for the relatively rapid evolution of proteins from a few primordial molecules. As the number of gene and protein structures increases, evidence of exon shuffling is becoming more apparent and examples are presented both from modern multi-domain proteins and ancient proteins. Recent work into the chemical properties and catalytic functions of RNA have led to hypotheses based upon the early existence of RNA. These theories suggest that the split gene structure originated in the primordial soup as a result of random RNA synthesis. Stable regions of RNA, or exons, were utilised as primitive enzymes. In response to selective pressures for information storage, the activity was directly transferred from the RNA enzymes or ribozymes, to proteins. These short polypeptides fused together to create larger proteins with a wide range of functions. Recent research into RNA processing and exon size, discussed in this review, provides a clearer insight into the evolutionary development of the gene and protein structure.

  5. Molecular cloud evolution and star formation

    NASA Technical Reports Server (NTRS)

    Silk, J.

    1985-01-01

    The present state of knowledge of the relationship between molecular clouds and young stars is reviewed. The determination of physical parameters from molecular line observations is summarized, and evidence for fragmentation of molecular clouds is discussed. Hierarchical fragmentation is reviewed, minimum fragment scales are derived, and the stability against fragmentation of both spherically and anisotropically collapsing clouds is discussed. Observational evidence for high-velocity flows in clouds is summarized, and the effects of winds from pre-main sequence stars on molecular gas are discussed. The triggering of cloud collapse by enhanced pressure is addressed, as is the formation of dense shells by spherical outflows and their subsequent breakup. A model for low-mass star formation is presented, and constraints on star formation from the initial mass function are examined. The properties of giant molecular clouds and massive star formation are described. The implications of magnetic fields for cloud evolution and star formation are addressed.

  6. The Post-Darwinian Controversies

    NASA Astrophysics Data System (ADS)

    Moore, James R.

    1981-11-01

    Preface; Introduction: the terrain of revision; Part I. Historians and Historiography: 1. Draper, White, and the military metaphor; 2. Politics, polemics, and the military milieu; 3. Warfare's toll in historical interpretation; 4. Towards a non-violent history; Part II. Darwinism and Evolutionary Thought: 5. Darwinism in transition; 6. The challenge of Lamarckian evolution; 7. The vogue of Herbert Spencer; 8. Darwinism and Neo-Darwinism; Part III. Theology and Evolution: 9. Christian anti-Darwinism: the realm of certainty and fixity; 10. Christian Darwinism: the role of providence and progress; 11. Christian Darwinism: the relevance of orthodox theology; 12. Darwinism and Darwinisticism in theology; Conclusion; Notes to the text; Bibliography; Index.

  7. Positive Darwinian selection at single amino acid sites conferring plant virus resistance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Explicit evaluation of the accuracy and power of Maximum Likelihood and Bayesian methods for detecting site-specific positive Darwinian selection presents a challenge because selective consequences of single amino acid changes are generally unknown. We exploit extensive molecular and functional cha...

  8. Making a Theist out of Darwin: Asa Gray's Post-Darwinian Natural Theology

    NASA Astrophysics Data System (ADS)

    Russell Hunter, T.

    2012-07-01

    In March of 1860 the eminent Harvard Botanist and orthodox Christian Asa Gray began promoting the Origin of Species in hopes of securing a fair examination of Darwin's evolutionary theory among theistic naturalists. To this end, Gray sought to demonstrate that Darwin had not written atheistically and that his theory of evolution by natural selection had not presented any new scientific or theological difficulties for traditional Christian belief. From his personal correspondence with the author of the Origin, Gray well knew that Darwin did not affirm God's "particular" design of nature but conceded to the possibility that evolution proceeded according to "designed laws." From this concession, Gray attempted to develop a post-Darwinian natural theology which encouraged theistic naturalists to view God's design of nature through the evolutionary process in a manner similar to the way in which they viewed God's Providential interaction with human history. Indeed, securing a fair reading of the Origin was not Gray's sole aim as a promoter of Darwinian ideas. In Darwin's theory of natural selection, Gray believed he had discovered the means by which a more robust natural theological conception of the living and evolving natural world could be developed. In this paper I outline Gray's efforts to produce and popularize a theistic interpretation of Darwinian theory in order to correct various misconceptions concerning Gray's natural theological views and their role in the Darwinian Revolution.

  9. Evolution of molecular phenotypes under stabilizing selection

    NASA Astrophysics Data System (ADS)

    Nourmohammad, Armita; Schiffels, Stephan; Lässig, Michael

    2013-01-01

    Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype’s genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes.

  10. Molecular evolution in bacterial endosymbionts of fungi.

    PubMed

    Castillo, Dean M; Pawlowska, Teresa E

    2010-03-01

    The prediction that progressive coupling of host and symbiont metabolic and reproductive interests leads to reduced mixing of symbiont lineages has been verified extensively in maternally transmitted bacterial endosymbionts of insects. To test whether this prediction is also applicable to associations of bacteria with fungi, we explored patterns of molecular evolution in two lineages of mutualistic endosymbionts of fungi: the Burkholderia endosymbionts of Rhizopus microsporus (Mucormycotina) and Candidatus Glomeribacter gigasporarum endosymbionts of arbuscular mycorrhizal fungi (Glomeromycota). We compared these two lineages with the closely related Candidatus Tremblaya princeps endosymbionts of mealybugs (Hemiptera, Coccoidea, Pseudococcidae) and to free-living Burkholderia species. To make inferences about the life histories of the endosymbionts, we relied on the empirically validated predictions of the nearly neutral theory of molecular evolution that a reduction of the effective population size increases the rate of fixation of slightly deleterious mutations. Our analyses showed that the slightly deleterious mutation accumulation patterns in the Burkholderia endosymbionts of Rhizopus were nearly indistinguishable from those in their free-living relatives. In contrast, Ca. Glomeribacter showed unique patterns of molecular evolution that differentiated them from both the Burkholderia endosymbionts of Rhizopus and from the Ca. Tremblaya endosymbionts of insects. These findings imply that reduced mixing of symbiont lineages is not a universal feature of symbioses between fungi and endocellular bacteria.

  11. Molecular epidemiology, phylogeny and evolution of dermatophytes.

    PubMed

    Cafarchia, Claudia; Iatta, Roberta; Latrofa, Maria Stefania; Gräser, Yvonne; Otranto, Domenico

    2013-12-01

    Dermatophytes are fungi that invade and propagate in the keratinized skin of mammals, including humans, often causing contagious infections. The species of medical concern belong to the genera Microsporum, Trichophyton, Epidermophyton (in their anamorphic state) and Arthroderma (in their telomorphic state), which were traditionally identified based on their morphology and biochemical characters. Nonetheless, limitations linked to the differentiation of closely related agents at species and strains level have been recently overcome by molecular studies. Indeed, an accurate identification of dermatophytes is pivotal for the establishment of effective control and prevention programs as well as for determining the most appropriate and effective antifungal therapies to be applied. This article reviews the DNA techniques and the molecular markers used to identify and to characterize dermatophyte species, as well as aspects of their phylogeny and evolution. The applications of typing molecular strain to both basic and applied research (e.g., taxonomy, ecology, typing of infection, antifungal susceptibility) have also been discussed.

  12. Darwinian natural selection: its enduring explanatory power

    PubMed Central

    2012-01-01

    Evolutionary theory has never had a stronger scientific foundation than it does today. In a short review I hope to portray the deep commitment of today's biologists to Darwinian natural selection and to discoveries made since Darwin's time. In spite of the scientific advances in the century and a half since the publication of On the Origin of Species, Darwin still remains the principal author of modern evolutionary theory. He is one of the greatest contributors of all time to our understanding of nature. PMID:22481845

  13. Integrating influenza antigenic dynamics with molecular evolution

    PubMed Central

    Bedford, Trevor; Suchard, Marc A; Lemey, Philippe; Dudas, Gytis; Gregory, Victoria; Hay, Alan J; McCauley, John W; Russell, Colin A; Smith, Derek J; Rambaut, Andrew

    2014-01-01

    Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001 PMID:24497547

  14. Molecular Evolution of Phosphoprotein Phosphatases in Drosophila

    PubMed Central

    Miskei, Márton; Ádám, Csaba; Kovács, László; Karányi, Zsolt; Dombrádi, Viktor

    2011-01-01

    Phosphoprotein phosphatases (PPP), these ancient and important regulatory enzymes are present in all eukaryotic organisms. Based on the genome sequences of 12 Drosophila species we traced the evolution of the PPP catalytic subunits and noted a substantial expansion of the gene family. We concluded that the 18–22 PPP genes of Drosophilidae were generated from a core set of 8 indispensable phosphatases that are present in most of the insects. Retropositons followed by tandem gene duplications extended the phosphatase repertoire, and sporadic gene losses contributed to the species specific variations in the PPP complement. During the course of these studies we identified 5, up till now uncharacterized phosphatase retrogenes: PpY+, PpD5+, PpD6+, Pp4+, and Pp6+ which are found only in some ancient Drosophila. We demonstrated that all of these new PPP genes exhibit a distinct male specific expression. In addition to the changes in gene numbers, the intron-exon structure and the chromosomal localization of several PPP genes was also altered during evolution. The G−C content of the coding regions decreased when a gene moved into the heterochromatic region of chromosome Y. Thus the PPP enzymes exemplify the various types of dynamic rearrangements that accompany the molecular evolution of a gene family in Drosophilidae. PMID:21789237

  15. Evolution, phylogeny, and molecular epidemiology of Chlamydia.

    PubMed

    Nunes, Alexandra; Gomes, João P

    2014-04-01

    The Chlamydiaceae are a family of obligate intracellular bacteria characterized by a unique biphasic developmental cycle. It encompasses the single genus Chlamydia, which involves nine species that affect a wide range of vertebral hosts, causing infections with serious impact on human health (mainly due to Chlamydia trachomatis infections) and on farming and veterinary industries. It is believed that Chlamydiales originated ∼700mya, whereas C. trachomatis likely split from the other Chlamydiaceae during the last 6mya. This corresponds to the emergence of modern human lineages, with the first descriptions of chlamydial infections as ancient as four millennia. Chlamydiaceae have undergone a massive genome reduction, on behalf of the deletional bias "use it or lose it", stabilizing at 1-1.2Mb and keeping a striking genome synteny. Their phylogeny reveals species segregation according to biological properties, with huge differences in terms of host range, tissue tropism, and disease outcomes. Genome differences rely on the occurrence of mutations in the >700 orthologous genes, as well as on events of recombination, gene loss, inversion, and paralogous expansion, affecting both a hypervariable region named the plasticity zone, and genes essentially encoding polymorphic and transmembrane head membrane proteins, type III secretion effectors and some metabolic pathways. Procedures for molecular typing are still not consensual but have allowed the knowledge of molecular epidemiology patterns for some species as well as the identification of outbreaks and emergence of successful clones for C. trachomatis. This manuscript intends to provide a comprehensive review on the evolution, phylogeny, and molecular epidemiology of Chlamydia.

  16. The chemical evolution of molecular clouds

    NASA Technical Reports Server (NTRS)

    Iglesias, E.

    1977-01-01

    The nonequilibrium chemistry of dense molecular clouds (10,000 to 1 million hydrogen molecules per cu cm) is studied in the framework of a model that includes the latest published chemical data and most of the recent theoretical advances. In this model the only important external source of ionization is assumed to be high-energy cosmic-ray bombardment; standard charge-transfer reactions are taken into account as well as reactions that transfer charge from molecular ions to trace-metal atoms. Schemes are proposed for the synthesis of such species as NCO, HNCO, and CN. The role played by adsorption and condensation of molecules on the surface of dust grains is investigated, and effects on the chemical evolution of a dense molecular cloud are considered which result from varying the total density or the elemental abundances and from assuming negligible or severe condensation of gaseous species on dust grains. It is shown that the chemical-equilibrium time scale is given approximately by the depletion times of oxygen and nitrogen when the condensation efficiency is negligible; that this time scale is probably in the range from 1 to 4 million years, depending on the elemental composition and initial conditions in the cloud; and that this time scale is insensitive to variations in the total density.

  17. Introducing the fractional order robotic Darwinian PSO

    NASA Astrophysics Data System (ADS)

    Couceiro, Micael S.; Martins, Fernando M. L.; Rocha, Rui P.; Ferreira, Nuno M. F.

    2012-11-01

    The Darwinian Particle Swarm Optimization (DPSO) is an evolutionary algorithm that extends the Particle Swarm Optimization using natural selection to enhance the ability to escape from sub-optimal solutions. An extension of the DPSO to multi-robot applications has been recently proposed and denoted as Robotic Darwinian PSO (RDPSO), benefiting from the dynamical partitioning of the whole population of robots, hence decreasing the amount of required information exchange among robots. This paper further extends the previously proposed algorithm using fractional calculus concepts to control the convergence rate, while considering the robot dynamical characteristics. Moreover, to improve the convergence analysis of the RDPSO, an adjustment of the fractional coefficient based on mobile robot constraints is presented and experimentally assessed with 2 real platforms. Afterwards, this novel fractional-order RDPSO is evaluated in 12 physical robots being further explored using a larger population of 100 simulated mobile robots within a larger scenario. Experimental results show that changing the fractional coefficient does not significantly improve the final solution but presents a significant influence in the convergence time because of its inherent memory property.

  18. Pervasive Cryptic Epistasis in Molecular Evolution

    PubMed Central

    Lunzer, Mark; Golding, G. Brian; Dean, Antony M.

    2010-01-01

    The functional effects of most amino acid replacements accumulated during molecular evolution are unknown, because most are not observed naturally and the possible combinations are too numerous. We created 168 single mutations in wild-type Escherichia coli isopropymalate dehydrogenase (IMDH) that match the differences found in wild-type Pseudomonas aeruginosa IMDH. 104 mutant enzymes performed similarly to E. coli wild-type IMDH, one was functionally enhanced, and 63 were functionally compromised. The transition from E. coli IMDH, or an ancestral form, to the functional wild-type P. aeruginosa IMDH requires extensive epistasis to ameliorate the combined effects of the deleterious mutations. This result stands in marked contrast with a basic assumption of molecular phylogenetics, that sites in sequences evolve independently of each other. Residues that affect function are scattered haphazardly throughout the IMDH structure. We screened for compensatory mutations at three sites, all of which lie near the active site and all of which are among the least active mutants. No compensatory mutations were found at two sites indicating that a single site may engage in compound epistatic interactions. One complete and three partial compensatory mutations of the third site are remote and lie in a different domain. This demonstrates that epistatic interactions can occur between distant (>20Å) sites. Phylogenetic analysis shows that incompatible mutations were fixed in different lineages. PMID:20975933

  19. Molecular epidemiology and evolution of fish Novirhabdoviruses

    USGS Publications Warehouse

    Kurath, Gael

    2014-01-01

    The genus Novirhabdoviridae contains several of the important rhabdoviruses that infect fish hosts. There are four established virus species: Infectious hematopoietic necrosis virus (IHNV), Viral hemorrhagic septicemia virus (VHSV), Hirame rhabdovirus(HIRRV), and Snakehead rhabdovirus (SHRV). Viruses of these species vary in host and geographic range, and they have all been studied at the molecular and genomic level. As globally significant pathogens of cultured fish, IHNV and VHSV have been particularly well studied in terms of molecular epidemiology and evolution. Phylogenic analyses of hundreds of field isolates have defined five major genogroups of IHNV and four major genotypes of VHSV worldwide. These phylogenies are informed by the known histories of IHNV and VHSV, each involving a series of viral emergence events that are sometimes associated with host switches, most often into cultured rainbow trout. In general, IHNV has relatively low genetic diversity and a narrow host range, and has been spread from its endemic source in North American to Europe and Asia due to aquaculture activities. In contrast, VHSV has broad host range and high genetic diversity, and the source of emergence events is virus in widespread marine fish reservoirs in the northern Atlantic and Pacific Oceans. Common mechanisms of emergence and host switch events include use of raw feed, proximity to wild fish reservoirs of virus, and geographic translocations of virus or naive fish hosts associated with aquaculture.

  20. Molecular Evolution of PTEN Pseudogenes in Mammals

    PubMed Central

    Tang, Jingsi; Ning, Ruihong; Zeng, Bo; Li, Ying

    2016-01-01

    Phosphatase and tensin homolog (PTEN) is a tumor-suppressor gene. PTEN pseudogene (PTENp) acts as an endogenous RNA, which regulates its parental gene by competitively binding to the 3’ UTR of PTEN gene in the human. Despite the importance of this pseudogene, little is known about the molecular evolution of PTENp in mammals. In this study, we identified 37 pseudogenes from 65 mammalian genomes. Among them, 32 were from rodents or primates. Phylogenetic analyse showed a complex evolutionary history of this gene family. Some PTENps were shared both in primates and rodents. However, some PTENps were shown to be species-specific, such as the tasmanian devil PTENp1, nine banded armadillo PTENp1 and gibbon PTENp1. Most interestingly, the naked mole rat (NMR), an anticancer model organism, possessed 17 copies of PTENps, which were classified into four clades based on the phylogenetic analyses. Furthermore, we found that all the 3’UTR of PTEN and PTENps shared common microRNA (MicroRNA) binding sites in NMR, based on our prediction of specific MicroRNA binding sites. Our findings suggested that multiple gene duplications have occurred in the formation of PTEN/PTENp gene family during the evolution of mammals. Some PTENps were relatively ancient and were shared by primates and rodents; others were newly originated through species- specific gene duplications. PTENps in NMR may function as competitive endogenous RNAs (ceRNAs) to regulate their counterpart genes by competing for common MicroRNAs, which may be one of the interpretations for the cancer resistance in NMR. PMID:27936183

  1. Molecular musings in microbial ecology and evolution

    PubMed Central

    2011-01-01

    A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology. The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology. The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology). The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies

  2. The relativity of Darwinian populations and the ecology of endosymbiosis.

    PubMed

    Stencel, Adrian

    If there is a single discipline of science calling the basic concepts of biology into question, it is without doubt microbiology. Indeed, developments in microbiology have recently forced us to rethink such fundamental concepts as the organism, individual, and genome. In this paper I show how microorganisms are changing our understanding of natural aggregations and develop the concept of a Darwinian population to embrace these discoveries. I start by showing that it is hard to set the boundaries of a Darwinian population, and I suggest thinking of a Darwinian population as a relative property of a Darwinian individual. Then I argue, in contrast to the commonly held view, that Darwinian populations are multispecies units, and that in order to accept the multispecies account of Darwinian populations we have to separate fitness from natural selection. Finally, I show how all these ideas provide a theoretical framework leading to a more precise understanding of the ecology of endosymbiosis than is afforded by poetic metaphors such as 'slavery'.

  3. Theory of recombination in directed molecular evolution

    NASA Astrophysics Data System (ADS)

    Peng, Weiqun; Hwa, Terence; Levine, Herbert; Kessler, David A.

    2003-03-01

    Recombination is a fundamental process driving the evolution of biological organisms in nature. It is also a very efficient method being used in in vitro directed evolution of molecules. Here we propose a simple model for the directed evolution of protein-binding DNA sequences subject to recombination, substitution, and competitive selection. This turns out to be a rare model of involving recombination which is analytically tractable. We characterize the dynamical and steady-state behaviors of this model and verify them numerically. We discuss the manner in which recombination drastically speeds up the evolutionary process.

  4. Imaging the Temporal Evolution of Molecular Orbitals during Ultrafast Dissociation

    NASA Astrophysics Data System (ADS)

    Sann, H.; Havermeier, T.; Müller, C.; Kim, H.-K.; Trinter, F.; Waitz, M.; Voigtsberger, J.; Sturm, F.; Bauer, T.; Wallauer, R.; Schneider, D.; Weller, M.; Goihl, C.; Tross, J.; Cole, K.; Wu, J.; Schöffler, M. S.; Schmidt-Böcking, H.; Jahnke, T.; Simon, M.; Dörner, R.

    2016-12-01

    We investigate the temporal evolution of molecular frame angular distributions of Auger electrons emitted during ultrafast dissociation of HCl following a resonant single-photon excitation. The electron emission pattern changes its shape from that of a molecular σ orbital to that of an atomic p state as the system evolves from a molecule into two separated atoms.

  5. The Darwinian revolution: rethinking its meaning and significance.

    PubMed

    Ruse, Michael

    2009-06-16

    The Darwinian revolution is generally taken to be one of the key events in the history of Western science. In recent years, however, the very notion of a scientific revolution has come under attack, and in the specific case of Charles Darwin and his Origin of Species there are serious questions about the nature of the change (if there was such) and the specifically Darwinian input. This article considers these issues by addressing these questions: Was there a Darwinian revolution? That is, was there a revolution at all? Was there a Darwinian revolution? That is, what was the specific contribution of Charles Darwin? Was there a Darwinian revolution? That is, what was the conceptual nature of what occurred on and around the publication of the Origin? I argue that there was a major change, both scientifically and in a broader metaphysical sense; that Charles Darwin was the major player in the change, although one must qualify the nature and the extent of the change, looking particularly at things in a broader historical context than just as an immediate event; and that the revolution was complex and we need the insights of rather different philosophies of scientific change to capture the whole phenomenon. In some respects, indeed, the process of analysis is still ongoing and unresolved.

  6. The Darwinian revolution: Rethinking its meaning and significance

    PubMed Central

    Ruse, Michael

    2009-01-01

    The Darwinian revolution is generally taken to be one of the key events in the history of Western science. In recent years, however, the very notion of a scientific revolution has come under attack, and in the specific case of Charles Darwin and his Origin of Species there are serious questions about the nature of the change (if there was such) and the specifically Darwinian input. This article considers these issues by addressing these questions: Was there a Darwinian revolution? That is, was there a revolution at all? Was there a Darwinian revolution? That is, what was the specific contribution of Charles Darwin? Was there a Darwinian revolution? That is, what was the conceptual nature of what occurred on and around the publication of the Origin? I argue that there was a major change, both scientifically and in a broader metaphysical sense; that Charles Darwin was the major player in the change, although one must qualify the nature and the extent of the change, looking particularly at things in a broader historical context than just as an immediate event; and that the revolution was complex and we need the insights of rather different philosophies of scientific change to capture the whole phenomenon. In some respects, indeed, the process of analysis is still ongoing and unresolved. PMID:19528652

  7. Automatic Evolution of Molecular Nanotechnology Designs

    NASA Technical Reports Server (NTRS)

    Globus, Al; Lawton, John; Wipke, Todd; Saini, Subhash (Technical Monitor)

    1998-01-01

    This paper describes strategies for automatically generating designs for analog circuits at the molecular level. Software maps out the edges and vertices of potential nanotechnology systems on graphs, then selects appropriate ones through evolutionary or genetic paradigms.

  8. Molecular clouds. [significance in stellar evolution

    NASA Technical Reports Server (NTRS)

    Thaddeus, P.

    1977-01-01

    An attempt is made to understand star formation in the context of the dense interstellar molecular gas from which stars are made. Attention is given to how molecular observations (e.g., UV spectroscopy and radio 21-cm and recombination line observations) provide data on the physical state of the dense interstellar gas; observations of H II regions, stellar associations, and dark nebulae are discussed. CO clouds are studied with reference to radial velocity, temperature, density, ionization, magnetic field.

  9. Brassinosteroid action in flowering plants: a Darwinian perspective.

    PubMed

    Kutschera, Ulrich; Wang, Zhi-Yong

    2012-06-01

    The year 2012 marks the 150th anniversary of the publication of Charles Darwin's first botanical book, on the fertilization of orchids (1862), wherein he described pollen grains and outlined his evolutionary principles with respect to plant research. Five decades later, the growth-promoting effect of extracts of Orchid pollen on coleoptile elongation was documented. These studies led to the discovery of a new class of phytohormones, the brassinosteroids (BRs) that were isolated from rapeseed (Brassica napus) pollen. These growth-promoting steroids, which regulate height, fertility, and seed-filling in crop plants such as rice (Oryza sativa), also induce stress- and disease resistance in green algae and angiosperms. The origin and current status of BR-research is described here, with reference to BR-action and -signal transduction, and it is shown that modern high-yield rice varieties with erect leaves are deficient in endogenous BRs. Since brassinosteroids induce pathogen resistance in rice plants and hence can suppress rice blast- and bacterial blight-diseases, genetic manipulation of BR-biosynthesis or -perception may be a means to increase crop production. Basic research on BR activity in plants, such as Arabidopsis and rice, has the potential to increase crop yields further as part of a 21th century 'green biotech-revolution' that can be traced back to Darwin's classical breeding experiments. It is concluded that 'Nothing in brassinosteroid research makes sense except in the light of Darwinian evolution' and the value of basic science is highlighted, with reference to the genetic engineering of better food crops that may become resistant to a variety of plant diseases.

  10. Molecular Evolution of Threonine Dehydratase in Bacteria

    PubMed Central

    Yu, Xuefei; Li, Ye; Wang, Xiaoyuan

    2013-01-01

    Threonine dehydratase converts L-threonine to 2-ketobutyrate. Several threonine dehydratases exist in bacteria, but their origins and evolutionary pathway are unknown. Here we analyzed all the available threonine dehydratases in bacteria and proposed an evolutionary pathway leading to the genes encoding three different threonine dehydratases CTD, BTD1 and BTD2. The ancestral threonine dehydratase might contain only a catalytic domain, but one or two ACT-like subdomains were fused during the evolution, resulting BTD1 and BTD2, respectively. Horizontal gene transfer, gene fusion, gene duplication, and gene deletion may occur during the evolution of this enzyme. The results are important for understanding the functions of various threonine dehydratases found in bacteria. PMID:24324624

  11. Temperature Evolution of Molecular Clouds in the Central Molecular Zone

    NASA Astrophysics Data System (ADS)

    Krieger, Nico; Ott, Jürgen; Walter, Fabian; Kruijssen, J. M. Diederik; Beuther, Henrik

    2017-01-01

    We infer the absolute time dependence of kinematic gas temperature along a proposed orbit of molecular clouds in the Central Molecular Zone (CMZ) of the Galactic Center (GC). Ammonia gas temperature maps are one of the results of the ``Survey of Water and Ammonia in the Galactic Center'' (SWAG, PI: J. Ott); the dynamical model of molecular clouds in the CMZ was taken from Kruijssen et al. (2015). We find that gas temperatures increase as a function of time in both regimes before and after the cloud passes pericenter on its orbit in the GC potential. This is consistent with the recent proposal that pericenter passage triggers gravitational collapse. Other investigated quantities (line width, column density, opacity) show no strong sign of time dependence but are likely dominated by cloud-to-cloud variations.

  12. Analytical Biases Associated with GC-Content in Molecular Evolution

    PubMed Central

    Romiguier, Jonathan; Roux, Camille

    2017-01-01

    Molecular evolution is being revolutionized by high-throughput sequencing allowing an increased amount of genome-wide data available for multiple species. While base composition summarized by GC-content is one of the first metrics measured in genomes, its genomic distribution is a frequently neglected feature in downstream analyses based on DNA sequence comparisons. Here, we show how base composition heterogeneity among loci and taxa can bias common molecular evolution analyses such as phylogenetic tree reconstruction, detection of natural selection and estimation of codon usage. We then discuss the biological, technical and methodological causes of these GC-associated biases and suggest approaches to overcome them. PMID:28261263

  13. Slow rate of molecular evolution in high-elevation hummingbirds.

    PubMed

    Bleiweiss, R

    1998-01-20

    Estimates of relative rates of molecular evolution from a DNA-hybridization phylogeny for 26 hummingbird species provide evidence for a negative association between elevation and rate of single-copy genome evolution. This effect of elevation on rate remains significant even after taking into account a significant negative association between body mass and molecular rate. Population-level processes do not appear to account for these patterns because (i) all hummingbirds breed within their first year and (ii) the more extensive subdivision and speciation of bird populations living at high elevations predicts a positive association between elevation and rate. The negative association between body mass and molecular rate in other organisms has been attributed to higher mutation rates in forms with higher oxidative metabolism. As ambient oxygen tensions and temperature decrease with elevation, the slow rate of molecular evolution in high-elevation hummingbirds also may have a metabolic basis. A slower rate of single-copy DNA change at higher elevations suggests that the dynamics of molecular evolution cannot be separated from the environmental context.

  14. Molecular evolution of cryptochromes in fishes.

    PubMed

    Mei, Qiming; Sadovy, Yvonne; Dvornyk, Volodymyr

    2015-12-10

    Circadian rhythmicity is an endogenous biological cycle of about 24h, which exists in cyanobacteria and fungi, plants and animals. Circadian rhythms improve the adaptability of organisms in both constant and changing environments. The cryptochrome (CRY) is a key element of the circadian system in various animal groups including fishes. We studied evolution of cryptochromes in the phylogenetically and ecologically diverse fish taxa. The phylogenetic tree of fish Cry features two major clades: Cry1 and Cry2. Teleosts possess extra copies of Cry1 due to the genome duplication, which resulted in 3 main paralogous subfamilies (1A, 1B and 1C). Cry1 experienced further diversification through additional duplications in some taxa. 1A of Cry1 is more conserved than the other paralogs (dN=0.010 ± 0.003, π=0.119 ± 0.058). The analysis of selection indicated that, while the Cry homologs in fish evolved under the different levels of selection pressure, strong purifying selection (average ω=0.017) dominated in their evolution.

  15. The Jukes-Cantor Model of Molecular Evolution

    ERIC Educational Resources Information Center

    Erickson, Keith

    2010-01-01

    The material in this module introduces students to some of the mathematical tools used to examine molecular evolution. This topic is standard fare in many mathematical biology or bioinformatics classes, but could also be suitable for classes in linear algebra or probability. While coursework in matrix algebra, Markov processes, Monte Carlo…

  16. Molecular characterization of the evolution of phagosomes

    PubMed Central

    Boulais, Jonathan; Trost, Matthias; Landry, Christian R; Dieckmann, Régis; Levy, Emmanuel D; Soldati, Thierry; Michnick, Stephen W; Thibault, Pierre; Desjardins, Michel

    2010-01-01

    Amoeba use phagocytosis to internalize bacteria as a source of nutrients, whereas multicellular organisms utilize this process as a defense mechanism to kill microbes and, in vertebrates, initiate a sustained immune response. By using a large-scale approach to identify and compare the proteome and phosphoproteome of phagosomes isolated from distant organisms, and by comparative analysis over 39 taxa, we identified an ‘ancient' core of phagosomal proteins around which the immune functions of this organelle have likely organized. Our data indicate that a larger proportion of the phagosome proteome, compared with the whole cell proteome, has been acquired through gene duplication at a period coinciding with the emergence of innate and adaptive immunity. Our study also characterizes in detail the acquisition of novel proteins and the significant remodeling of the phagosome phosphoproteome that contributed to modify the core constituents of this organelle in evolution. Our work thus provides the first thorough analysis of the changes that enabled the transformation of the phagosome from a phagotrophic compartment into an organelle fully competent for antigen presentation. PMID:20959821

  17. Molecular clocks and the early evolution of metazoan nervous systems

    PubMed Central

    Wray, Gregory A.

    2015-01-01

    The timing of early animal evolution remains poorly resolved, yet remains critical for understanding nervous system evolution. Methods for estimating divergence times from sequence data have improved considerably, providing a more refined understanding of key divergences. The best molecular estimates point to the origin of metazoans and bilaterians tens to hundreds of millions of years earlier than their first appearances in the fossil record. Both the molecular and fossil records are compatible, however, with the possibility of tiny, unskeletonized, low energy budget animals during the Proterozoic that had planktonic, benthic, or meiofaunal lifestyles. Such animals would likely have had relatively simple nervous systems equipped primarily to detect food, avoid inhospitable environments and locate mates. The appearance of the first macropredators during the Cambrian would have changed the selective landscape dramatically, likely driving the evolution of complex sense organs, sophisticated sensory processing systems, and diverse effector systems involved in capturing prey and avoiding predation. PMID:26554040

  18. Molecular clocks and the early evolution of metazoan nervous systems.

    PubMed

    Wray, Gregory A

    2015-12-19

    The timing of early animal evolution remains poorly resolved, yet remains critical for understanding nervous system evolution. Methods for estimating divergence times from sequence data have improved considerably, providing a more refined understanding of key divergences. The best molecular estimates point to the origin of metazoans and bilaterians tens to hundreds of millions of years earlier than their first appearances in the fossil record. Both the molecular and fossil records are compatible, however, with the possibility of tiny, unskeletonized, low energy budget animals during the Proterozoic that had planktonic, benthic, or meiofaunal lifestyles. Such animals would likely have had relatively simple nervous systems equipped primarily to detect food, avoid inhospitable environments and locate mates. The appearance of the first macropredators during the Cambrian would have changed the selective landscape dramatically, likely driving the evolution of complex sense organs, sophisticated sensory processing systems, and diverse effector systems involved in capturing prey and avoiding predation.

  19. Molecular evolution of the gamma-Herpesvirinae.

    PubMed Central

    McGeoch, D J

    2001-01-01

    Genomic sequences available for members of the gamma-Herpesvirinae allow analysis of many aspects of the group's evolution. This paper examines four topics: (i) the phylogeny of the group; (ii) the histories of gamma-herpesvirus-specific genes; (iii) genomic variation of human herpesvirus 8 (HHV-8); and (iv) the relationship between Epstein-Barr virus types 1 and 2 (EBV-1 and EBV-2). A phylogenetic tree based on eight conserved genes has been constructed for eight gamma-herpesviruses and extended to 14 species with smaller gene sets. This gave a generally robust assignment of evolutionary relationships, with the exception of murine herpesvirus 4 (MHV-4), which could not be placed unambiguously on the tree and which has evidently experienced an unusually high rate of genomic change. The gamma-herpesviruses possess a variable complement of genes with cellular homologues. In the clearest cases these virus genes were shown to have originated from host genome lineages in the distant past. HHV-8 possesses at its left genomic terminus a highly diverse gene (K1) and at its right terminus a gene (K15) having two diverged alleles. It was proposed that the high diversity of K1 results from a positive selection on K1 and a hitchhiking effect that reduces diversity elsewhere in the genome. EBV-1 and EBV-2 differ in their alleles of the EBNA-2, EBNA-3A, EBNA-3B and EBNA-3C genes. It was suggested that EBV-1 and EBV-2 may recombine in mixed infections so that their sequences outside these genes remain homogeneous. Models for genesis of the types, by recombination between diverged parents or by local divergence from a single lineage, both present difficulties. PMID:11313003

  20. [Recent progress in protist virology--molecular ecology, taxonomy, molecular evolution].

    PubMed

    Nagasaki, Keizo; Tomaru, Yuji

    2009-06-01

    At present, more than 40 protist-infecting viruses have been isolated and characterized. From the viewpoints of molecular ecology, taxomony and molecular evolution, several new discoveries were made within the last five years. In this minireview, three topics of interest on protist-infecting viruses are introduced: 1) molecular ecological relationships between a bloom-forming dinoflagellate Heterocapsa circularisquama and its ssRNA virus (HcRNAV); 2) findings of new ssRNA- and ssDNA-virus groups infecting diatoms; 3) establishment of a hypothesis concerning the evolution of picornaviruses. The potential of aquatic virus studies is far-reaching and inestimable.

  1. Giant Molecular Cloud Structure and Evolution

    NASA Technical Reports Server (NTRS)

    Hollenbach, David (Technical Monitor); Bodenheimer, P. H.

    2003-01-01

    Bodenheimer and Burkert extended earlier calculations of cloud core models to study collapse and fragmentation. The initial condition for an SPH collapse calculation is the density distribution of a Bonnor-Ebert sphere, with near balance between turbulent plus thermal energy and gravitational energy. The main parameter is the turbulent Mach number. For each Mach number several runs are made, each with a different random realization of the initial turbulent velocity field. The turbulence decays on a dynamical time scale, leading the cloud into collapse. The collapse proceeds isothermally until the density has increased to about 10(exp 13) g cm(exp -3). Then heating is included in the dense regions. The nature of the fragmentation is investigated. About 15 different runs have been performed with Mach numbers ranging from 0.3 to 3.5 (the typical value observed in molecular cloud cores is 0.7). The results show a definite trend of increasing multiplicity with increasing Mach number (M), with the number of fragments approximately proportional to (1 + M). In general, this result agrees with that of Fisher, Klein, and McKee who published three cases with an AMR grid code. However our results show that there is a large spread about this curve. For example, for M=0.3 one case resulted in no fragmentation while a second produced three fragments. Thus it is not only the value of M but also the details of the superposition of the various velocity modes that play a critical role in the formation of binaries. Also, the simulations produce a wide range of separations (10-1000 AU) for the multiple systems, in rough agreement with observations. These results are discussed in two conference proceedings.

  2. HIV-1 evolution: frustrating therapies, but disclosing molecular mechanisms

    PubMed Central

    Das, Atze T.; Berkhout, Ben

    2010-01-01

    Replication of HIV-1 under selective pressure frequently results in the evolution of virus variants that replicate more efficiently under the applied conditions. For example, in patients on antiretroviral therapy, such evolution can result in variants that are resistant to the HIV-1 inhibitors, thus frustrating the therapy. On the other hand, virus evolution can help us to understand the molecular mechanisms that underlie HIV-1 replication. For example, evolution of a defective virus mutant can result in variants that overcome the introduced defect by restoration of the original sequence or by the introduction of additional mutations in the viral genome. Analysis of the evolution pathway can reveal the requirements of the element under study and help to understand its function. Analysis of the escape routes may generate new insight in the viral life cycle and result in the identification of unexpected biological mechanisms. We have developed in vitro HIV-1 evolution into a systematic research tool that allows the study of different aspects of the viral replication cycle. We will briefly review this method of forced virus evolution and provide several examples that illustrate the power of this approach. PMID:20478891

  3. HIV-1 evolution: frustrating therapies, but disclosing molecular mechanisms.

    PubMed

    Das, Atze T; Berkhout, Ben

    2010-06-27

    Replication of HIV-1 under selective pressure frequently results in the evolution of virus variants that replicate more efficiently under the applied conditions. For example, in patients on antiretroviral therapy, such evolution can result in variants that are resistant to the HIV-1 inhibitors, thus frustrating the therapy. On the other hand, virus evolution can help us to understand the molecular mechanisms that underlie HIV-1 replication. For example, evolution of a defective virus mutant can result in variants that overcome the introduced defect by restoration of the original sequence or by the introduction of additional mutations in the viral genome. Analysis of the evolution pathway can reveal the requirements of the element under study and help to understand its function. Analysis of the escape routes may generate new insight in the viral life cycle and result in the identification of unexpected biological mechanisms. We have developed in vitro HIV-1 evolution into a systematic research tool that allows the study of different aspects of the viral replication cycle. We will briefly review this method of forced virus evolution and provide several examples that illustrate the power of this approach.

  4. A good Darwinian? Winwood Reade and the making of a late Victorian evolutionary epic.

    PubMed

    Hesketh, Ian

    2015-06-01

    In 1871 the travel writer and anthropologist W. Winwood Reade (1838-1875) was inspired by his correspondence with Darwin to turn his narrow ethnological research on West African tribes into the broadest history imaginable, one that would show Darwin's great principle of natural selection at work throughout the evolutionary history of humanity, stretching back to the origins of the universe itself. But when Martyrdom of Man was published in 1872, Reade confessed that Darwin would not likely find him a very good Darwinian, as he was unable to show that natural selection was anything more than a secondary law that arranges all details. When it came to historicising humans within the sweeping history of all creation, Reade argued that the primary law was that of development, a less contentious theory of human evolution that was better suited to Reade's progressive and teleological history of life. By focussing on the extensive correspondence between Reade and Darwin, this paper reconstructs the attempt to make an explicitly Darwinian evolutionary epic in order to shed light on the moral and aesthetic demands that worked to give shape to Victorian efforts to historicise humans within a vastly expanding timeframe.

  5. The Mastodon in the room: how Darwinian is neo-Darwinism?

    PubMed

    Brooks, Daniel R

    2011-03-01

    Failing to acknowledge substantial differences between Darwinism and neo-Darwinism impedes evolutionary biology. Darwin described evolution as the outcome of interactions between the nature of the organism and the nature of the conditions, each relatively autonomous but both historically and spatially intertwined. Furthermore, he postulated that the nature of the organism was more important than the nature of the conditions, leading to natural selection as an inevitable emergent product of biological systems. The neo-Darwinian tradition assumed a creative rather than selective view of natural selection, with the nature of the organism determined by the nature of the conditions, rendering the nature of the organism and temporal contingency unnecessary. Contemporary advances in biology, specifically the phylogenetics revolution and evo-devo, underscore the significance of history and the nature of the organism in biology. Darwinism explains more biology better, and better resolves apparent anomalies between living systems and more general natural laws, than does neo-Darwinism. The "extended" or "expanded" synthesis currently called for by neo-Darwinians is Darwinism.

  6. Molecular evolution of cyclin proteins in animals and fungi

    PubMed Central

    2011-01-01

    Background The passage through the cell cycle is controlled by complexes of cyclins, the regulatory units, with cyclin-dependent kinases, the catalytic units. It is also known that cyclins form several families, which differ considerably in primary structure from one eukaryotic organism to another. Despite these lines of evidence, the relationship between the evolution of cyclins and their function is an open issue. Here we present the results of our study on the molecular evolution of A-, B-, D-, E-type cyclin proteins in animals and fungi. Results We constructed phylogenetic trees for these proteins, their ancestral sequences and analyzed patterns of amino acid replacements. The analysis of infrequently fixed atypical amino acid replacements in cyclins evidenced that accelerated evolution proceeded predominantly during paralog duplication or after it in animals and fungi and that it was related to aromorphic changes in animals. It was shown also that evolutionary flexibility of cyclin function may be provided by consequential reorganization of regions on protein surface remote from CDK binding sites in animal and fungal cyclins and by functional differentiation of paralogous cyclins formed in animal evolution. Conclusions The results suggested that changes in the number and/or nature of cyclin-binding proteins may underlie the evolutionary role of the alterations in the molecular structure of cyclins and their involvement in diverse molecular-genetic events. PMID:21798004

  7. Evolution of egg coats: linking molecular biology and ecology.

    PubMed

    Shu, Longfei; Suter, Marc J-F; Räsänen, Katja

    2015-08-01

    One central goal of evolutionary biology is to explain how biological diversity emerges and is maintained in nature. Given the complexity of the phenotype and the multifaceted nature of inheritance, modern evolutionary ecological studies rely heavily on the use of molecular tools. Here, we show how molecular tools help to gain insight into the role of egg coats (i.e. the extracellular structures surrounding eggs and embryos) in evolutionary diversification. Egg coats are maternally derived structures that have many biological functions from mediating fertilization to protecting the embryo from environmental hazards. They show great molecular, structural and functional diversity across species, but intraspecific variability and the role of ecology in egg coat evolution have largely been overlooked. Given that much of the variation that influences egg coat function is ultimately determined by their molecular phenotype, cutting-edge molecular tools (e.g. proteomics, glycomics and transcriptomics), combined with functional assays, are needed for rigorous inferences on their evolutionary ecology. Here, we identify key research areas and highlight emerging molecular techniques that can increase our understanding of the role of egg coats in the evolution of biological diversity, from adaptation to speciation.

  8. Social parasitism and the molecular basis of phenotypic evolution

    PubMed Central

    Cini, Alessandro; Patalano, Solenn; Segonds-Pichon, Anne; Busby, George B. J.; Cervo, Rita; Sumner, Seirian

    2015-01-01

    Contrasting phenotypes arise from similar genomes through a combination of losses, gains, co-option and modifications of inherited genomic material. Understanding the molecular basis of this phenotypic diversity is a fundamental challenge in modern evolutionary biology. Comparisons of the genes and their expression patterns underlying traits in closely related species offer an unrivaled opportunity to evaluate the extent to which genomic material is reorganized to produce novel traits. Advances in molecular methods now allow us to dissect the molecular machinery underlying phenotypic diversity in almost any organism, from single-celled entities to the most complex vertebrates. Here we discuss how comparisons of social parasites and their free-living hosts may provide unique insights into the molecular basis of phenotypic evolution. Social parasites evolve from a eusocial ancestor and are specialized to exploit the socially acquired resources of their closely-related eusocial host. Molecular comparisons of such species pairs can reveal how genomic material is re-organized in the loss of ancestral traits (i.e., of free-living traits in the parasites) and the gain of new ones (i.e., specialist traits required for a parasitic lifestyle). We define hypotheses on the molecular basis of phenotypes in the evolution of social parasitism and discuss their wider application in our understanding of the molecular basis of phenotypic diversity within the theoretical framework of phenotypic plasticity and shifting reaction norms. Currently there are no data available to test these hypotheses, and so we also provide some proof of concept data using the paper wasp social parasite/host system (Polistes sulcifer—Polistes dominula). This conceptual framework and first empirical data provide a spring-board for directing future genomic analyses on exploiting social parasites as a route to understanding the evolution of phenotypic specialization. PMID:25741361

  9. Social parasitism and the molecular basis of phenotypic evolution.

    PubMed

    Cini, Alessandro; Patalano, Solenn; Segonds-Pichon, Anne; Busby, George B J; Cervo, Rita; Sumner, Seirian

    2015-01-01

    Contrasting phenotypes arise from similar genomes through a combination of losses, gains, co-option and modifications of inherited genomic material. Understanding the molecular basis of this phenotypic diversity is a fundamental challenge in modern evolutionary biology. Comparisons of the genes and their expression patterns underlying traits in closely related species offer an unrivaled opportunity to evaluate the extent to which genomic material is reorganized to produce novel traits. Advances in molecular methods now allow us to dissect the molecular machinery underlying phenotypic diversity in almost any organism, from single-celled entities to the most complex vertebrates. Here we discuss how comparisons of social parasites and their free-living hosts may provide unique insights into the molecular basis of phenotypic evolution. Social parasites evolve from a eusocial ancestor and are specialized to exploit the socially acquired resources of their closely-related eusocial host. Molecular comparisons of such species pairs can reveal how genomic material is re-organized in the loss of ancestral traits (i.e., of free-living traits in the parasites) and the gain of new ones (i.e., specialist traits required for a parasitic lifestyle). We define hypotheses on the molecular basis of phenotypes in the evolution of social parasitism and discuss their wider application in our understanding of the molecular basis of phenotypic diversity within the theoretical framework of phenotypic plasticity and shifting reaction norms. Currently there are no data available to test these hypotheses, and so we also provide some proof of concept data using the paper wasp social parasite/host system (Polistes sulcifer-Polistes dominula). This conceptual framework and first empirical data provide a spring-board for directing future genomic analyses on exploiting social parasites as a route to understanding the evolution of phenotypic specialization.

  10. Widespread convergence in toxin resistance by predictable molecular evolution

    PubMed Central

    Ujvari, Beata; Casewell, Nicholas R.; Sunagar, Kartik; Arbuckle, Kevin; Wüster, Wolfgang; Lo, Nathan; O’Meally, Denis; Beckmann, Christa; King, Glenn F.; Deplazes, Evelyne; Madsen, Thomas

    2015-01-01

    The question about whether evolution is unpredictable and stochastic or intermittently constrained along predictable pathways is the subject of a fundamental debate in biology, in which understanding convergent evolution plays a central role. At the molecular level, documented examples of convergence are rare and limited to occurring within specific taxonomic groups. Here we provide evidence of constrained convergent molecular evolution across the metazoan tree of life. We show that resistance to toxic cardiac glycosides produced by plants and bufonid toads is mediated by similar molecular changes to the sodium-potassium-pump (Na+/K+-ATPase) in insects, amphibians, reptiles, and mammals. In toad-feeding reptiles, resistance is conferred by two point mutations that have evolved convergently on four occasions, whereas evidence of a molecular reversal back to the susceptible state in varanid lizards migrating to toad-free areas suggests that toxin resistance is maladaptive in the absence of selection. Importantly, resistance in all taxa is mediated by replacements of 2 of the 12 amino acids comprising the Na+/K+-ATPase H1–H2 extracellular domain that constitutes a core part of the cardiac glycoside binding site. We provide mechanistic insight into the basis of resistance by showing that these alterations perturb the interaction between the cardiac glycoside bufalin and the Na+/K+-ATPase. Thus, similar selection pressures have resulted in convergent evolution of the same molecular solution across the breadth of the animal kingdom, demonstrating how a scarcity of possible solutions to a selective challenge can lead to highly predictable evolutionary responses. PMID:26372961

  11. Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology.

    PubMed

    Elliott, Briony; Androga, Grace O; Knight, Daniel R; Riley, Thomas V

    2017-04-01

    Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era.

  12. Contrasting Levels of Molecular Evolution on the Mouse X Chromosome.

    PubMed

    Larson, Erica L; Vanderpool, Dan; Keeble, Sara; Zhou, Meng; Sarver, Brice A J; Smith, Andrew D; Dean, Matthew D; Good, Jeffrey M

    2016-08-01

    The mammalian X chromosome has unusual evolutionary dynamics compared to autosomes. Faster-X evolution of spermatogenic protein-coding genes is known to be most pronounced for genes expressed late in spermatogenesis, but it is unclear if these patterns extend to other forms of molecular divergence. We tested for faster-X evolution in mice spanning three different forms of molecular evolution-divergence in protein sequence, gene expression, and DNA methylation-across different developmental stages of spermatogenesis. We used FACS to isolate individual cell populations and then generated cell-specific transcriptome profiles across different stages of spermatogenesis in two subspecies of house mice (Mus musculus), thereby overcoming a fundamental limitation of previous studies on whole tissues. We found faster-X protein evolution at all stages of spermatogenesis and faster-late protein evolution for both X-linked and autosomal genes. In contrast, there was less expression divergence late in spermatogenesis (slower late) on the X chromosome and for autosomal genes expressed primarily in testis (testis-biased). We argue that slower-late expression divergence reflects strong regulatory constraints imposed during this critical stage of sperm development and that these constraints are particularly acute on the tightly regulated sex chromosomes. We also found slower-X DNA methylation divergence based on genome-wide bisulfite sequencing of sperm from two species of mice (M. musculus and M. spretus), although it is unclear whether slower-X DNA methylation reflects development constraints in sperm or other X-linked phenomena. Our study clarifies key differences in patterns of regulatory and protein evolution across spermatogenesis that are likely to have important consequences for mammalian sex chromosome evolution, male fertility, and speciation.

  13. Darwinian Behavior in a Cold, Sporadically Fed Pool of Ribonucleotides

    PubMed Central

    2012-01-01

    Abstract A testable, explicit origin for Darwinian behavior, feasible on a chaotic early Earth, would aid origins discussion. Here I show that a pool receiving unreliable supplies of unstable ribonucleotide precursors can recurrently fill this role. By using numerical integration, the differential equations governing a sporadically fed pool are solved, yielding quantitative constraints for the proliferation of molecules that also have a chemical phenotype. For example, templated triphosphate nucleotide joining is >104 too slow, suggesting that a group more reactive than pyrophosphate activated primordial nucleotides. However, measured literature rates are sufficient if the Initial Darwinian Ancestor (IDA) resembles a 5′-5′ cofactor-like dinucleotide RNA, synthesized via activation with a phosphorimidazolide-like group. A sporadically fed pool offers unforeseen advantages; for example, the pool hosts a novel replicator which is predominantly unpaired, even though it replicates. Such free template is optimized for effective selection during its replication. Pool nucleotides are also subject to a broadly based selection that impels the population toward replication, effective selection, and Darwinian behavior. Such a primordial pool may have left detectable modern traces. A sporadically fed ribonucleotide pool also fits a recognizable early Earth environment, has recognizable modern descendants, and suits the early shape of the phylogenetic tree of Earthly life. Finally, analysis points to particular data now needed to refine the hypothesis. Accordingly, a kinetically explicit chemical hypothesis for a terran IDA can be justified, and informative experiments seem readily accessible. Key Words: Cofactor—RNA—Origin of life—Replication—Initial Darwinian Ancestor (IDA). Astrobiology 12, 870–883. PMID:22946838

  14. [A group of new experiments on molecular evolution].

    PubMed

    Zhu, Xin-Yu; Xie, Xiao-Ling; Chen, Pei-Lin

    2004-07-01

    This paper presents a group of new experiments on molecular evolution. It allows students to get acquaint with the basic process of the reconstruction of phylogenetic tree using DNA or protein sequences, and to acquire the correct viewpoint how to affect the result of reconstruction when different tree-building methods, materials and parameters were used. This group of experiments are also characteristic of the opening and exploring, which accords with the direction and demand of experimental teaching reform.

  15. Reconstructing phylogenies and phenotypes: a molecular view of human evolution

    PubMed Central

    Bradley, Brenda J

    2008-01-01

    This review broadly summarizes how molecular biology has contributed to our understanding of human evolution. Molecular anthropology began in the 1960s with immunological comparisons indicating that African apes and humans were closely related and, indeed, shared a common ancestor as recently as 5 million years ago. Although initially dismissed, this finding has proven robust and numerous lines of molecular evidence now firmly place the human-ape divergence at 4–8 Ma. Resolving the trichotomy among humans, chimpanzees and gorillas took a few more decades. Despite the readily apparent physical similarities shared by African apes to the exclusion of modern humans (body hair, knuckle-walking, thin tooth enamel), the molecular support for a human–chimpanzee clade is now overwhelming. More recently, whole genome sequencing and gene mapping have shifted the focus of molecular anthropology from phylogenetic analyses to phenotypic reconstruction and functional genomics. We are starting to identify the genetic basis of the morphological, physiological and behavioural traits that distinguish modern humans from apes and apes from other primates. Most notably, recent comparative genomic analyses strongly indicate that the marked differences between modern humans and chimpanzees are likely due more to changes in gene regulation than to modifications of the genes themselves, an idea first proposed over 30 years ago. Almost weekly, press releases describe newly identified genes and regulatory elements that seem to have undergone strong positive selection along the human lineage. Loci involved in speech (e.g. FOXP2), brain development (e.g. ASPM), and skull musculature (e.g. MYH16) have been of particular interest, but some surprising candidate loci (e.g. those involved in auditory capabilities) have emerged as well. Exciting new research avenues, such as the Neanderthal Genome Project, promise that molecular analyses will continue to provide novel insights about our evolution

  16. Immune evasion and the evolution of molecular mimicry in parasites.

    PubMed

    Hurford, Amy; Day, Troy

    2013-10-01

    Parasites that are molecular mimics express proteins which resemble host proteins. This resemblance facilitates immune evasion because the immune molecules with the specificity to react with the parasite also cross-react with the host's own proteins, and these lymphocytes are rare. Given this advantage, why are not most parasites molecular mimics? Here we explore potential factors that can select against molecular mimicry in parasites and thereby limit its occurrence. We consider two hypotheses: (1) molecular mimics are more likely to induce autoimmunity in their hosts, and hosts with autoimmunity generate fewer new infections (the "costly autoimmunity hypothesis"); and (2) molecular mimicry compromises protein functioning, lowering the within-host replication rate and leading to fewer new infections (the "mimicry trade-off hypothesis"). Our analysis shows that although both hypotheses may select against molecular mimicry in parasites, unique hallmarks of protein expression identify whether selection is due to the costly autoimmunity hypothesis or the mimicry trade-off hypothesis. We show that understanding the relevant selective forces is necessary to predict how different medical interventions will affect the proportion of hosts that experience the different infection types, and that if parasite evolution is ignored, interventions aimed at reducing infection-induced autoimmunity may ultimately fail.

  17. Molecular hyperdiversity and evolution in very large populations

    PubMed Central

    Cutter, Asher D.; Jovelin, Richard; Dey, Alivia

    2014-01-01

    The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function, and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually-reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation, and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of non-crossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on non-coding regulatory elements. PMID:23506466

  18. Epidemiology, molecular epidemiology and evolution of bovine respiratory syncytial virus.

    PubMed

    Sarmiento-Silva, Rosa Elena; Nakamura-Lopez, Yuko; Vaughan, Gilberto

    2012-11-30

    The bovine respiratory syncytial virus (BRSV) is an enveloped, negative sense, single-stranded RNA virus belonging to the pneumovirus genus within the family Paramyxoviridae. BRSV has been recognized as a major cause of respiratory disease in young calves since the early 1970s. The analysis of BRSV infection was originally hampered by its characteristic lability and poor growth in vitro. However, the advent of numerous immunological and molecular methods has facilitated the study of BRSV enormously. The knowledge gained from these studies has also provided the opportunity to develop safe, stable, attenuated virus vaccine candidates. Nonetheless, many aspects of the epidemiology, molecular epidemiology and evolution of the virus are still not fully understood. The natural course of infection is rather complex and further complicates diagnosis, treatment and the implementation of preventive measures aimed to control the disease. Therefore, understanding the mechanisms by which BRSV is able to establish infection is needed to prevent viral and disease spread. This review discusses important information regarding the epidemiology and molecular epidemiology of BRSV worldwide, and it highlights the importance of viral evolution in virus transmission.

  19. Detection of biological threats. A challenge for directed molecular evolution.

    PubMed

    Petrenko, Valery A; Sorokulova, Iryna B

    2004-08-01

    The probe technique originated from early attempts of Anton van Leeuwenhoek to contrast microorganisms under the microscope using plant juices, successful staining of tubercle bacilli with synthetic dyes by Paul Ehrlich and discovery of a stain for differentiation of gram-positive and gram-negative bacteria by Hans Christian Gram. The technique relies on the principle that pathogens have unique structural features, which can be recognized by specifically labeled organic molecules. A hundred years of extensive screening efforts led to discovery of a limited assortment of organic probes that are used for identification and differentiation of bacteria. A new challenge--continuous monitoring of biological threats--requires long lasting molecular probes capable of tight specific binding of pathogens in unfavorable conditions. To respond to the challenge, probe technology is being revolutionized by utilizing methods of combinatorial chemistry, phage display and directed molecular evolution. This review describes how molecular evolution methods are applied for development of peptide, antibody and phage probes, and summarizes the author's own data on development of landscape phage probes against Salmonella typhimurium. The performance of the probes in detection of Salmonella is illustrated by a precipitation test, enzyme-linked immunosorbent assay (ELISA), fluorescence-activated cell sorting (FACS) and fluorescent, optical and electron microscopy.

  20. Molecular Evolution of Freshwater Snails with Contrasting Mating Systems.

    PubMed

    Burgarella, Concetta; Gayral, Philippe; Ballenghien, Marion; Bernard, Aurélien; David, Patrice; Jarne, Philippe; Correa, Ana; Hurtrez-Boussès, Sylvie; Escobar, Juan; Galtier, Nicolas; Glémin, Sylvain

    2015-09-01

    Because mating systems affect population genetics and ecology, they are expected to impact the molecular evolution of species. Self-fertilizing species experience reduced effective population size, recombination rates, and heterozygosity, which in turn should decrease the efficacy of natural selection, both adaptive and purifying, and the strength of meiotic drive processes such as GC-biased gene conversion. The empirical evidence is only partly congruent with these predictions, depending on the analyzed species, some, but not all, of the expected effects have been observed. One possible reason is that self-fertilization is an evolutionary dead-end, so that most current selfers recently evolved self-fertilization, and their genome has not yet been strongly impacted by selfing. Here, we investigate the molecular evolution of two groups of freshwater snails in which mating systems have likely been stable for several millions of years. Analyzing coding sequence polymorphism, divergence, and expression levels, we report a strongly reduced genetic diversity, decreased efficacy of purifying selection, slower rate of adaptive evolution, and weakened codon usage bias/GC-biased gene conversion in the selfer Galba compared with the outcrosser Physa, in full agreement with theoretical expectations. Our results demonstrate that self-fertilization, when effective in the long run, is a major driver of population genomic and molecular evolutionary processes. Despite the genomic effects of selfing, Galba truncatula seems to escape the demographic consequences of the genetic load. We suggest that the particular ecology of the species may buffer the negative consequences of selfing, shedding new light on the dead-end hypothesis.

  1. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  2. Getting Past the RNA World: The Initial Darwinian Ancestor

    PubMed Central

    Yarus, Michael

    2011-01-01

    SUMMARY A little-noted result of the confirmation of multiple premises of the RNA-world hypothesis is that we now know something about the dawn organisms that followed the origin of life, perhaps over 4 billion years ago. We are therefore in an improved position to reason about the biota just before RNA times, during the era of the first replicators, the first Darwinian creatures on Earth. An RNA congener still prominent in modern biology is a plausible descendent of these first replicators. PMID:20719875

  3. Molecular phylogeny and evolution of the cone snails (Gastropoda, Conoidea).

    PubMed

    Puillandre, N; Bouchet, P; Duda, T F; Kauferstein, S; Kohn, A J; Olivera, B M; Watkins, M; Meyer, C

    2014-09-01

    We present a large-scale molecular phylogeny that includes 320 of the 761 recognized valid species of the cone snails (Conus), one of the most diverse groups of marine molluscs, based on three mitochondrial genes (COI, 16S rDNA and 12S rDNA). This is the first phylogeny of the taxon to employ concatenated sequences of several genes, and it includes more than twice as many species as the last published molecular phylogeny of the entire group nearly a decade ago. Most of the numerous molecular phylogenies published during the last 15years are limited to rather small fractions of its species diversity. Bayesian and maximum likelihood analyses are mostly congruent and confirm the presence of three previously reported highly divergent lineages among cone snails, and one identified here using molecular data. About 85% of the species cluster in the single Large Major Clade; the others are divided between the Small Major Clade (∼12%), the Conus californicus lineage (one species), and a newly defined clade (∼3%). We also define several subclades within the Large and Small major clades, but most of their relationships remain poorly supported. To illustrate the usefulness of molecular phylogenies in addressing specific evolutionary questions, we analyse the evolution of the diet, the biogeography and the toxins of cone snails. All cone snails whose feeding biology is known inject venom into large prey animals and swallow them whole. Predation on polychaete worms is inferred as the ancestral state, and diet shifts to molluscs and fishes occurred rarely. The ancestor of cone snails probably originated from the Indo-Pacific; rather few colonisations of other biogeographic provinces have probably occurred. A new classification of the Conidae, based on the molecular phylogeny, is published in an accompanying paper.

  4. Molecular Evolution of Cytochrome bd Oxidases across Proteobacterial Genomes

    PubMed Central

    Degli Esposti, Mauro; Rosas-Pérez, Tania; Servín-Garcidueñas, Luis Eduardo; Bolaños, Luis Manuel; Rosenblueth, Monica; Martínez-Romero, Esperanza

    2015-01-01

    This work is aimed to resolve the complex molecular evolution of cytochrome bd ubiquinol oxidase, a nearly ubiquitous bacterial enzyme that is involved in redox balance and bioenergetics. Previous studies have created an unclear picture of bd oxidases phylogenesis without considering the existence of diverse types of bd oxidases. Integrated approaches of genomic and protein analysis focused on proteobacteria have generated a molecular classification of diverse types of bd oxidases, which produces a new scenario for interpreting their evolution. A duplication of the original gene cluster of bd oxidase might have occurred in the ancestors of extant α-proteobacteria of the Rhodospirillales order, such as Acidocella, from which the bd-I type of the oxidase might have diffused to other proteobacterial lineages. In contrast, the Cyanide-Insensitive Oxidase type may have differentiated into recognizable subtypes after another gene cluster duplication. These subtypes are widespread in the genomes of α-, β-, and γ-proteobacteria, with occasional instances of lateral gene transfer. In resolving the evolutionary pattern of proteobacterial bd oxidases, this work sheds new light on the basal taxa of α-proteobacteria from which the γ-proteobacterial lineage probably emerged. PMID:25688108

  5. Molecular evolution of Pediculus humanus and the origin of clothing.

    PubMed

    Kittler, Ralf; Kayser, Manfred; Stoneking, Mark

    2003-08-19

    The human head louse (Pediculus humanus capitis) and body louse (P. humanus corporis or P. h. humanus) are strict, obligate human ectoparasites that differ mainly in their habitat on the host : the head louse lives and feeds exclusively on the scalp, whereas the body louse feeds on the body but lives in clothing. This ecological differentiation probably arose when humans adopted frequent use of clothing, an important event in human evolution for which there is no direct archaeological evidence. We therefore used a molecular clock approach to date the origin of body lice, assuming that this should correspond with the frequent use of clothing. Sequences were obtained from two mtDNA and two nuclear DNA segments from a global sample of 40 head and body lice, and from a chimpanzee louse to use as an outgroup. The results indicate greater diversity in African than non-African lice, suggesting an African origin of human lice. A molecular clock analysis indicates that body lice originated not more than about 72,000 +/- 42,000 years ago; the mtDNA sequences also indicate a demographic expansion of body lice that correlates with the spread of modern humans out of Africa. These results suggest that clothing was a surprisingly recent innovation in human evolution.

  6. Integrating fossils with molecular phylogenies improves inference of trait evolution.

    PubMed

    Slater, Graham J; Harmon, Luke J; Alfaro, Michael E

    2012-12-01

    Comparative biologists often attempt to draw inferences about tempo and mode in evolution by comparing the fit of evolutionary models to phylogenetic comparative data consisting of a molecular phylogeny with branch lengths and trait measurements from extant taxa. These kinds of approaches ignore historical evidence for evolutionary pattern and process contained in the fossil record. In this article, we show through simulation that incorporation of fossil information dramatically improves our ability to distinguish among models of quantitative trait evolution using comparative data. We further suggest a novel Bayesian approach that allows fossil information to be integrated even when explicit phylogenetic hypotheses are lacking for extinct representatives of extant clades. By applying this approach to a comparative dataset comprising body sizes for caniform carnivorans, we show that incorporation of fossil information not only improves ancestral state estimates relative to those derived from extant taxa alone, but also results in preference of a model of evolution with trend toward large body size over alternative models such as Brownian motion or Ornstein-Uhlenbeck processes. Our approach highlights the importance of considering fossil information when making macroevolutionary inference, and provides a way to integrate the kind of sparse fossil information that is available to most evolutionary biologists.

  7. Statistical mechanics of quasispecies theories of molecular evolution

    NASA Astrophysics Data System (ADS)

    Munoz Tavera, Enrique

    This thesis presents a statistical mechanical analysis of different formulations of quasispecies theory of molecular evolution. These theories, characterized by two different families of models, the Crow-Kimura and the Eigen model, constitute a microscopie description of evolution. These models are most often used for RNA viruses, where a phase transition is predicted, in agreement with experiments, between an organized or quasispecies phase, and a disordered non-selective phase when the mutation rate exceeds a critical value. The methods of statistical mechanics, in particular field-theoretic methods, are employed to obtain analytic solutions to four problems relevant to biological interest. The first chapter presents the study of evolution under a multiple-peak fitness landscape, with biological applications in the study of the proliferation of viruses or cancer under the control of drugs or the immune system. The second chapter studies the effect of incorporating different forms of horizontal gene transfer and two-parent recombination to the classical formulation of quasispecies models. As an example, we study the effect of the sign of epistasis of the fitness landscape on the advantage or disadvantage of recombination for the mean fitness. The third chapter considers the relaxation of the purine/pyrimidine assumption in the classical formulation of the models, by formulating and solving the parallel and Eigen models in the context of a four-letter alphabet. The fourth and final chapter studies finite population effects, both in the presence and in the absence of horizontal gene transfer.

  8. Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

    PubMed Central

    Zhao, Huabin; Ru, Binghua; Teeling, Emma C.; Faulkes, Christopher G.; Zhang, Shuyi; Rossiter, Stephen J.

    2009-01-01

    The ecological radiation of mammals to inhabit a variety of light environments is largely attributed to adaptive changes in their visual systems. Visual capabilities are conferred by anatomical features of the eyes as well as the combination and properties of their constituent light sensitive pigments. To test whether evolutionary switches to different niches characterized by dim-light conditions coincided with molecular adaptation of the rod pigment rhodopsin, we sequenced the rhodopsin gene in twenty-two mammals including several bats and subterranean mole-rats. We compared these to thirty-seven published mammal rhodopsin sequences, from species with divergent visual ecologies, including nocturnal, diurnal and aquatic groups. All taxa possessed an intact functional rhodopsin; however, phylogenetic tree reconstruction recovered a gene tree in which rodents were not monophyletic, and also in which echolocating bats formed a monophyletic group. These conflicts with the species tree appear to stem from accelerated evolution in these groups, both of which inhabit low light environments. Selection tests confirmed divergent selection pressures in the clades of subterranean rodents and bats, as well as in marine mammals that live in turbid conditions. We also found evidence of divergent selection pressures among groups of bats with different sensory modalities based on vision and echolocation. Sliding window analyses suggest most changes occur in transmembrane domains, particularly obvious within the pinnipeds; however, we found no obvious pattern between photopic niche and predicted spectral sensitivity based on known critical amino acids. This study indicates that the independent evolution of rhodopsin vision in ecologically specialised groups of mammals has involved molecular evolution at the sequence level, though such changes might not mediate spectral sensitivity directly. PMID:20016835

  9. Selection by differential molecular survival: a possible mechanism of early chemical evolution.

    PubMed Central

    de Duve, C

    1987-01-01

    A model is proposed to account for selective chemical evolution, progressing from a relatively simple initial set of abiotic synthetic phenomena up to the elaborately sophisticated processes that are almost certainly required to produce the complex molecules, such as replicatable RNA-like oligonucleotides, needed for a Darwinian form of selection to start operating. The model makes the following assumptions: (i) that a small number of micromolecular substances were present at high concentration; (ii) that a random assembly mechanism combined these molecules into a variety of multimeric compounds comprising a wide repertoire of rudimentary catalytic activities; and (iii) that a lytic system capable of breaking down the assembled products existed. The model assumes further that catalysts supplied with substrates were significantly protected against breakdown. It is shown that, by granting these assumptions, an increasingly complex network of metabolic pathways would progressively be established. At the same time, the catalysts concerned would accumulate selectively to become choice substrates for elongation and other modifications that could enhance their efficiency, as well as their survival. Chemical evolution would thus proceed by a dual process of metabolic extension and catalytic innovation. Such a process should be largely deterministic and predictable from initial conditions. PMID:3479788

  10. Supernova feedback in molecular clouds: global evolution and dynamics

    NASA Astrophysics Data System (ADS)

    Körtgen, Bastian; Seifried, Daniel; Banerjee, Robi; Vázquez-Semadeni, Enrique; Zamora-Avilés, Manuel

    2016-07-01

    We use magnetohydrodynamical simulations of converging warm neutral medium flows to analyse the formation and global evolution of magnetized and turbulent molecular clouds subject to supernova feedback from massive stars. We show that supernova feedback alone fails to disrupt entire, gravitationally bound, molecular clouds, but is able to disperse small-sized (˜10 pc) regions on time-scales of less than 1 Myr. Efficient radiative cooling of the supernova remnant as well as strong compression of the surrounding gas result in non-persistent energy and momentum input from the supernovae. However, if the time between subsequent supernovae is short and they are clustered, large hot bubbles form that disperse larger regions of the parental cloud. On longer time-scales, supernova feedback increases the amount of gas with moderate temperatures (T ≈ 300-3000 K). Despite its inability to disrupt molecular clouds, supernova feedback leaves a strong imprint on the star formation process. We find an overall reduction of the star formation efficiency by a factor of 2 and of the star formation rate by roughly factors of 2-4.

  11. Hepatitis A virus: host interactions, molecular epidemiology and evolution.

    PubMed

    Vaughan, Gilberto; Goncalves Rossi, Livia Maria; Forbi, Joseph C; de Paula, Vanessa S; Purdy, Michael A; Xia, Guoliang; Khudyakov, Yury E

    2014-01-01

    Infection with hepatitis A virus (HAV) is the commonest viral cause of liver disease and presents an important public health problem worldwide. Several unique HAV properties and molecular mechanisms of its interaction with host were recently discovered and should aid in clarifying the pathogenesis of hepatitis A. Genetic characterization of HAV strains have resulted in the identification of different genotypes and subtypes, which exhibit a characteristic worldwide distribution. Shifts in HAV endemicity occurring in different parts of the world, introduction of genetically diverse strains from geographically distant regions, genotype displacement observed in some countries and population expansion detected in the last decades of the 20th century using phylogenetic analysis are important factors contributing to the complex dynamics of HAV infections worldwide. Strong selection pressures, some of which, like usage of deoptimized codons, are unique to HAV, limit genetic variability of the virus. Analysis of subgenomic regions has been proven useful for outbreak investigations. However, sharing short sequences among epidemiologically unrelated strains indicates that specific identification of HAV strains for molecular surveillance can be achieved only using whole-genome sequences. Here, we present up-to-date information on the HAV molecular epidemiology and evolution, and highlight the most relevant features of the HAV-host interactions.

  12. Endoreplication: a molecular trick during animal neuron evolution.

    PubMed

    Mandrioli, Mauro; Mola, Lucrezia; Cuoghi, Barbara; Sonetti, Dario

    2010-06-01

    The occurrence of endoreplication has been repeatedly reported in many organisms, including protists, plants, worms, arthropods, molluscs, fishes, and mammals. As a general rule, cells possessing endoreplicated genomes are large-sized and highly metabolically active. Endoreplication has not been frequently reported in neuronal cells that are typically considered to be fully differentiated and non-dividing, and which normally contain a diploid genome. Despite this general statement, various papers indicate that giant neurons in molluscs, as well as supramedullary and hypothalamic magnocellular neurons in fishes, contain DNA amounts larger than 2C. In order to study this issue in greater detail here, we review the available data about endoreplication in invertebrate and vertebrate neurons, and discuss its possible functional significance. As a whole, endoreplication seems to be a sort of molecular trick used by neurons in response to the high functional demands that they experience during evolution.

  13. The evolution of endothermy: role for membranes and molecular activity.

    PubMed

    Else, Paul L; Turner, N; Hulbert, A J

    2004-01-01

    On the basis of the comparative approach and three models of metabolism (endothermic and ectothermic vertebrates, body mass, and mammalian development), we suggest that a few common cellular processes, linked either directly or indirectly to membranes, consume the majority of energy used by most organisms; that membranes act as pacemakers of metabolism through changes in lipid composition, altering membrane characteristics and the working environment of membrane proteins--specifically, that changes in the membrane environment similarly affect the molecular activities (specific rates of activity) of membrane-bound proteins; and that polyunsaturation of membranes increases whereas monounsaturation decreases the activity of membrane proteins. Experiments designed to test this theory using the sodium pump support this supposition. Potential mechanisms considered include fluidity, electrical fields, and related surface area requirements of lipids. In considering the evolution of endothermy in mammals, for example, if the first mammals were small, possibly nocturnal and active organisms, all these factors would favour increased polyunsaturation of membranes. Such changes (from monounsaturated to polyunsaturated membranes) would allow membranes to set the pace of metabolism in the evolution of endothermy.

  14. Extraordinary molecular evolution in the PRDM9 fertility gene.

    PubMed

    Thomas, James H; Emerson, Ryan O; Shendure, Jay

    2009-12-30

    Recent work indicates that allelic incompatibility in the mouse PRDM9 (Meisetz) gene can cause hybrid male sterility, contributing to genetic isolation and potentially speciation. The only phenotype of mouse PRDM9 knockouts is a meiosis I block that causes sterility in both sexes. The PRDM9 gene encodes a protein with histone H3(K4) trimethyltransferase activity, a KRAB domain, and a DNA-binding domain consisting of multiple tandem C2H2 zinc finger (ZF) domains. We have analyzed human coding polymorphism and interspecies evolutionary changes in the PRDM9 gene. The ZF domains of PRDM9 are evolving very rapidly, with compelling evidence of positive selection in primates. Positively selected amino acids are predominantly those known to make nucleotide specific contacts in C2H2 zinc fingers. These results suggest that PRDM9 is subject to recurrent selection to change DNA-binding specificity. The human PRDM9 protein is highly polymorphic in its ZF domains and nearly all polymorphisms affect the same nucleotide contact residues that are subject to positive selection. ZF domain nucleotide sequences are strongly homogenized within species, indicating that interfinger recombination contributes to their evolution. PRDM9 has previously been assumed to be a transcription factor required to induce meiosis specific genes, a role that is inconsistent with its molecular evolution. We suggest instead that PRDM9 is involved in some aspect of centromere segregation conflict and that rapidly evolving centromeric DNA drives changes in PRDM9 DNA-binding domains.

  15. Molecular evolution of GPCRs: Kisspeptin/kisspeptin receptors.

    PubMed

    Pasquier, Jérémy; Kamech, Nédia; Lafont, Anne-Gaëlle; Vaudry, Hubert; Rousseau, Karine; Dufour, Sylvie

    2014-06-01

    Following the discovery of kisspeptin (Kiss) and its receptor (GPR54 or KissR) in mammals, phylogenetic studies revealed up to three Kiss and four KissR paralogous genes in other vertebrates. The multiplicity of Kiss and KissR types in vertebrates probably originated from the two rounds of whole-genome duplication (1R and 2R) that occurred in early vertebrates. This review examines compelling recent advances on molecular diversity and phylogenetic evolution of vertebrate Kiss and KissR. It also addresses, from an evolutionary point of view, the issues of the structure-activity relationships and interaction of Kiss with KissR and of their signaling pathways. Independent gene losses, during vertebrate evolution, have shaped the repertoire of Kiss and KissR in the extant vertebrate species. In particular, there is no conserved combination of a given Kiss type with a KissR type, across vertebrate evolution. The striking conservation of the biologically active ten-amino-acid C-terminal sequence of all vertebrate kisspeptins, probably allowed this evolutionary flexibility of Kiss/KissR pairs. KissR mutations, responsible for hypogonadotropic hypogonadism in humans, mostly occurred at highly conserved amino acid positions among vertebrate KissR. This further highlights the key role of these amino acids in KissR function. In contrast, less conserved KissR regions, notably in the intracellular C-terminal domain, may account for differential intracellular signaling pathways between vertebrate KissR. Cross talk between evolutionary and biomedical studies should contribute to further understanding of the Kiss/KissR structure-activity relationships and biological functions.

  16. Warfare, genocide, and ethnic conflict: a Darwinian approach

    PubMed Central

    2010-01-01

    As the 21st century dawns, I reflect on the history of humankind with growing concern about the need to understand the underlying biological and cultural roots of ethnic conflict and warfare. In the many studies of human conflict, innate biological predispositions have been neglected. This article is the third part of a series of seminars for medical residents at the University of Texas Southwestern Medical School at Dallas (see http://adarwinstudygroup.org/). The series starts with in-depth coverage of Darwinian natural and sexual selection, with examples from the domestication of animals and plants and the crisis of antibiotic resistance. The series strives to show how biology has been neglected in the study of the we-they orientation of human behavior, with its devastating consequences. The subject material is profoundly disturbing, as it looks at “human nature” and contrasts the “dark side” of human behavior with the opposite, profoundly caring and loving side. PMID:21240320

  17. Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution

    PubMed Central

    McDonald, Michael J.; Rice, Daniel P.; Desai, Michael M.

    2016-01-01

    Sex and recombination are pervasive throughout nature despite their substantial costs1. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology2,3. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation4. Theory has proposed a number of distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect)5,6 or by separating them from deleterious load (the ruby in the rubbish effect)7,8. Previous experiments confirm that sex can increase the rate of adaptation9–17, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here, we present the first comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations. PMID:26909573

  18. Karyotype evolution in the Pinaceae: implication with molecular phylogeny.

    PubMed

    Nkongolo, K K; Mehes-Smith, M

    2012-11-01

    The family Pinaceae is made up mostly of diploid species (2n = 24). Systematization of karyotype analysis was developed to make comparison of intra- and interspecific karyotypes among the Pinaceae more accurate and reliable. Considering all parameters, the genera Pseudotsuga and Pseudolarix have the "most derived" (or advanced) and asymmetric karyotypes in the Pinaceae, followed by Larix, Picea, Abies, and Cedrus. The genus Pinus was the "least derived" (or ancestral) of all the genera of the Pinaceae analyzed. Differences in karyotype formulae and asymmetry indices were found among species within the same genera, suggesting that structural changes may have contributed to the diversification of the genus. This review is a detailed analysis of comparative karyotyping based on similar parameters, including numeric data and cytogenetic information. Telomeric sequence repeats and rDNA distribution in the Pinaceae were surveyed. The role of transposition in rDNA chromosome distribution is analyzed. Cytogenetic implications of hybridization between related species are reported. Likewise, the relationships between molecular phylogenetic and karyotype evolution is discussed in light of several reports. Within many genera, chromosomal organization was conserved despite independent molecular divergence and adaptation through the evolutionary history of the species of the Pinaceae.

  19. Sex speeds adaptation by altering the dynamics of molecular evolution.

    PubMed

    McDonald, Michael J; Rice, Daniel P; Desai, Michael M

    2016-03-10

    Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.

  20. Linking the molecular evolution of avian beta (β) keratins to the evolution of feathers.

    PubMed

    Greenwold, Matthew J; Sawyer, Roger H

    2011-12-15

    Feathers of today's birds are constructed of beta (β)-keratins, structural proteins of the epidermis that are found solely in reptiles and birds. Discoveries of "feathered dinosaurs" continue to stimulate interest in the evolutionary origin of feathers, but few studies have attempted to link the molecular evolution of their major structural proteins (β-keratins) to the appearance of feathers in the fossil record. Using molecular dating methods, we show that before the appearance of Anchiornis (∼155 Million years ago (Ma)) the basal β-keratins of birds began diverging from their archosaurian ancestor ∼216 Ma. However, the subfamily of feather β-keratins, as found in living birds, did not begin diverging until ∼143 Ma. Thus, the pennaceous feathers on Anchiornis, while being constructed of avian β-keratins, most likely did not contain the feather β-keratins found in the feathers of modern birds. Our results demonstrate that the evolutionary origin of feathers does not coincide with the molecular evolution of the feather β-keratins found in modern birds. More likely, during the Late Jurassic, the epidermal structures that appeared on organisms in the lineage leading to birds, including early forms of feathers, were constructed of avian β-keratins other than those found in the feathers of modern birds. Recent biophysical studies of the β-keratins in feathers support the view that the appearance of the subfamily of feather β-keratins altered the biophysical nature of the feather establishing its role in powered flight.

  1. The First Molecular Phylogeny of Strepsiptera (Insecta) Reveals an Early Burst of Molecular Evolution Correlated with the Transition to Endoparasitism

    PubMed Central

    McMahon, Dino P.; Hayward, Alexander; Kathirithamby, Jeyaraney

    2011-01-01

    A comprehensive model of evolution requires an understanding of the relationship between selection at the molecular and phenotypic level. We investigate this in Strepsiptera, an order of endoparasitic insects whose evolutionary biology is poorly studied. We present the first molecular phylogeny of Strepsiptera, and use this as a framework to investigate the association between parasitism and molecular evolution. We find evidence of a significant burst in the rate of molecular evolution in the early history of Strepsiptera. The evolution of morphological traits linked to parasitism is significantly correlated with the pattern in molecular rate. The correlated burst in genotypic-phenotypic evolution precedes the main phase of strepsipteran diversification, which is characterised by the return to a low and even molecular rate, and a period of relative morphological stability. These findings suggest that the transition to endoparasitism led to relaxation of selective constraint in the strepsipteran genome. Our results indicate that a parasitic lifestyle can affect the rate of molecular evolution, although other causal life-history traits correlated with parasitism may also play an important role. PMID:21738621

  2. HIV Evolution and Escape.

    PubMed Central

    Richman, Douglas D.; Little, Susan J.; Smith, Davey M.; Wrin, Terri; Petropoulos, Christos; Wong, Joseph K.

    2004-01-01

    Human immunodeficiency virus (HIV) exemplifies the principles of Darwinian evolution with a telescoped chronology. Because of its high mutation rate and remarkably high rates of replication, evolution can be appreciated over periods of days in contrast to the durations conceived of by Darwin. Certain selective pressures that drive the evolution of HIV include chemotherapy, anatomic compartmentalization and the immune response. Examples of these selective forces on HIV evolution are described. Images Fig. 5 PMID:17060974

  3. Chemical evolution of giant molecular clouds in simulations of galaxies

    NASA Astrophysics Data System (ADS)

    Richings, Alexander J.; Schaye, Joop

    2016-08-01

    We present an analysis of giant molecular clouds (GMCs) within hydrodynamic simulations of isolated, low-mass (M* ˜ 109 M⊙) disc galaxies. We study the evolution of molecular abundances and the implications for CO emission and the XCO conversion factor in individual clouds. We define clouds either as regions above a density threshold n_{H, min} = 10 {cm}^{-3}, or using an observationally motivated CO intensity threshold of 0.25 {K} {km} {s}^{-1}. Our simulations include a non-equilibrium chemical model with 157 species, including 20 molecules. We also investigate the effects of resolution and pressure floors (i.e. Jeans limiters). We find cloud lifetimes up to ≈ 40 Myr, with a median of 13 Myr, in agreement with observations. At one-tenth solar metallicity, young clouds ( ≲ 10-15 Myr) are underabundant in H2 and CO compared to chemical equilibrium, by factors of ≈3 and one to two orders of magnitude, respectively. At solar metallicity, GMCs reach chemical equilibrium faster (within ≈ 1 Myr). We also compute CO emission from individual clouds. The mean CO intensity, ICO, is strongly suppressed at low dust extinction, Av, and possibly saturates towards high Av, in agreement with observations. The ICO-Av relation shifts towards higher Av for higher metallicities and, to a lesser extent, for stronger UV radiation. At one-tenth solar metallicity, CO emission is weaker in young clouds ( ≲ 10-15 Myr), consistent with the underabundance of CO. Consequently, XCO decreases by an order of magnitude from 0 to 15 Myr, albeit with a large scatter.

  4. Molecular phylogeny and evolution of the genus Neoerysiphe (Erysiphaceae, Ascomycota).

    PubMed

    Takamatsu, Susumu; Havrylenko, Maria; Wolcan, Silvia M; Matsuda, Sanae; Niinomi, Seiko

    2008-06-01

    The genus Neoerysiphe belongs to the tribe Golovinomyceteae of the Erysiphaceae together with the genera Arthrocladiella and Golovinomyces. This is a relatively small genus, comprising only six species, and having ca 300 species from six plant families as hosts. To investigate the molecular phylogeny and evolution of the genus, we determined the nucleotide sequences of the rDNA ITS regions and the divergent domains D1 and D2 of the 28S rDNA. The 30 ITS sequences from Neoerysiphe are divided into three monophyletic groups that are represented by their host families. Groups 1 and 3 consist of N. galeopsidis from Lamiaceae and N. galii from Rubiaceae, respectively, and the genetic diversity within each group is extremely low. Group 2 is represented by N. cumminsiana from Asteraceae. This group also includes Oidium baccharidis, O. maquii, and Oidium spp. from Galinsoga (Asteraceae) and Aloysia (Verbenaceae), and is further divided into four subgroups. N. galeopsidis is distributed worldwide, but is especially common in western Eurasia from Central Asia to Europe. N. galii is also common in western Eurasia. In contrast, the specimens of group 2 were all collected in the New World, except for one specimen that was collected in Japan; this may indicate a close relationship of group 2 with the New World. Molecular clock calibration demonstrated that Neoerysiphe split from other genera of the Erysiphaceae ca 35-45M years ago (Mya), and that the three groups of Neoerysiphe diverged between 10 and 15Mya, in the Miocene. Aloysia citriodora is a new host for the Erysiphaceae and the fungus on this plant is described as O. aloysiae sp. nov.

  5. Molecular evolution of the Sorghum Maturity Gene Ma3.

    PubMed

    Wang, Yan; Tan, Lubin; Fu, Yongcai; Zhu, Zuofeng; Liu, Fengxia; Sun, Chuanqing; Cai, Hongwei

    2015-01-01

    Time to maturity is a critical trait in sorghum (Sorghum bicolor) breeding, as it determines whether a variety can be grown in a particular cropping system or ecosystem. Understanding the nucleotide variation and the mechanisms of molecular evolution of the maturity genes would be helpful for breeding programs. In this study, we analyzed the nucleotide diversity of Ma3, an important maturity gene in sorghum, using 252 cultivated and wild sorghum materials from all over the world. The nucleotide variation and diversity were analyzed based both on race- and usage-based groups. We also sequenced 12 genes around the Ma3 gene in 185 of these materials to search for a selective sweep and found that purifying selection was the strongest force on Ma3, as low nucleotide diversity and low-frequency amino acid variants were observed. However, a very special mutation, described as ma3R, seemed to be under positive selection, as indicated by dramatically reduced nucleotide variation not only at the loci but also in the surrounding regions among individuals carrying the mutations. In addition, in an association study using the Ma3 nucleotide variations, we detected 3 significant SNPs for the heading date at a high-latitude environment (Beijing) and 17 at a low-latitude environment (Hainan). The results of this study increases our understanding of the evolutionary mechanisms of the maturity genes in sorghum and will be useful in sorghum breeding.

  6. Darwinian hydrology: can the methodology Charles Darwin pioneered help hydrologic science?

    NASA Astrophysics Data System (ADS)

    Harman, C.; Troch, P. A.

    2013-05-01

    There have been repeated calls for a Darwinian approach to hydrologic science or for a synthesis of Darwinian and Newtonian approaches, to deepen understanding the hydrologic system in the larger landscape context, and so develop a better basis for predictions now and in an uncertain future. But what exactly makes a Darwinian approach to hydrology "Darwinian"? While there have now been a number of discussions of Darwinian approaches, many referencing Harte (2002), the term is potentially a source of confusion while its connections to Darwin remain allusive rather than explicit. Here we discuss the methods that Charles Darwin pioneered to understand a variety of complex systems in terms of their historical processes of change. We suggest that the Darwinian approach to hydrology follows his lead by focusing attention on the patterns of variation in populations, seeking hypotheses that explain these patterns in terms of the mechanisms and conditions that determine their historical development, using deduction and modeling to derive consequent hypotheses that follow from a proposed explanation, and critically testing these hypotheses against new observations. It is not sufficient to catalogue the patterns or predict them statistically. Nor is it sufficient for the explanations to amount to a "just-so" story not subject to critical analysis. Darwin's theories linked present-day variation to mechanisms that operated over history, and could be independently test and falsified by comparing new observations to the predictions of corollary hypotheses they generated. With a Darwinian framework in mind it is easy to see that a great deal of hydrologic research has already been done that contributes to a Darwinian hydrology - whether deliberately or not. The various heuristic methods that Darwin used to develop explanatory theories - extrapolating mechanisms, space for time substitution, and looking for signatures of history - have direct application in hydrologic science. Some

  7. Built for speed, not for comfort. Darwinian theory and human culture.

    PubMed

    Richerson, P J; Boyd, R

    2001-01-01

    Darwin believed that his theory of evolution would stand or fall on its ability to account for human behavior. No species could be an exception to his theory without imperiling the whole edifice. The ideas in the Descent of Man were widely discussed by his contemporaries although they were far from being the only evolutionary theories current in the late nineteenth century. Darwin's specific evolutionary ideas and those of his main followers had very little impact on the social sciences as they emerged as separate disciplines in the early Twentieth Century. Not until the late twentieth century were concerted, sophisticated efforts made to apply Darwinian theory to human behavior. Why such a long delay? We argue that Darwin's theory was rather modern in respects that conflicted with Victorian sensibilities and that he and his few close followers failed to influence any of the social sciences. The late Twentieth Century work takes up almost exactly where James Baldwin left off at the turn of the century.

  8. Mars life: how Darwinian pressures might have shaped its form and function

    NASA Astrophysics Data System (ADS)

    Levin, Gilbert V.

    2005-09-01

    The possible existence of life on Mars is now gaining credence. Evidence consistent with or supporting the presence of extant microbial life, as reported by a life detection experiment on the Viking Mission in 1976, has been rapidly accumulating from spacecraft orbital and lander operations, and from terrestrial observations. Vast oceans of frozen water near the planet's surface are being discovered, with strong indications of recent or present liquid flows, and theory and laboratory experiment have demonstrated that liquid water should exist on the surface of Mars. The biosphere on Earth has been extended into extreme environments until recently thought inimical to life. Places void of life have become rare. No life requirement has been found lacking on Mars. It is possible that, by the time of this 50th Anniversary SPIE Meeting, the paradigm shift accepting life beyond the Earth may have been made. Mankind will then emerge from its ancient fear of loneliness into a new fear of anticipation of what that still unidentified life might portend. The author attempts to apply Darwinian principles of evolution to life on Mars under the selection pressures, opportunities and constraints that have been imposed by past and present Martian conditions. Starting with the type of cell believed to have begun the evolutionary process on Earth, he speculates on what the current life on Mars may be like in form and function, including what threat or promise it might hold for Earth life.

  9. Molecular evolution of SRP cycle components: functional implications.

    PubMed

    Althoff, S; Selinger, D; Wise, J A

    1994-06-11

    Signal recognition particle (SRP) is a cytoplasmic ribonucleoprotein that targets a subset of nascent presecretory proteins to the endoplasmic reticulum membrane. We have considered the SRP cycle from the perspective of molecular evolution, using recently determined sequences of genes or cDNAs encoding homologs of SRP (7SL) RNA, the Srp54 protein (Srp54p), and the alpha subunit of the SRP receptor (SR alpha) from a broad spectrum of organisms, together with the remaining five polypeptides of mammalian SRP. Our analysis provides insight into the significance of structural variation in SRP RNA and identifies novel conserved motifs in protein components of this pathway. The lack of congruence between an established phylogenetic tree and size variation in 7SL homologs implies the occurrence of several independent events that eliminated more than half the sequence content of this RNA during bacterial evolution. The apparently non-essential structures are domain I, a tRNA-like element that is constant in archaea, varies in size among eucaryotes, and is generally missing in bacteria, and domain III, a tightly base-paired hairpin that is present in all eucaryotic and archeal SRP RNAs but is invariably absent in bacteria. Based on both structural and functional considerations, we propose that the conserved core of SRP consists minimally of the 54 kDa signal sequence-binding protein complexed with the loosely base-paired domain IV helix of SRP RNA, and is also likely to contain a homolog of the Srp68 protein. Comparative sequence analysis of the methionine-rich M domains from a diverse array of Srp54p homologs reveals an extended region of amino acid identity that resembles a recently identified RNA recognition motif. Multiple sequence alignment of the G domains of Srp54p and SR alpha homologs indicates that these two polypeptides exhibit significant similarity even outside the four GTPase consensus motifs, including a block of nine contiguous amino acids in a location

  10. Non-Darwinian estimation: My ancestors, my genes' ancestors

    PubMed Central

    Weiss, Kenneth M.; Long, Jeffrey C.

    2009-01-01

    There is widespread interest in characterizing the organization of human genetic variation around the world from a population perspective. Related to this are attempts to describe the pattern of genetic variation in the human species generally, including “recreational” genomics, the genome-based estimation of the ancestry of individuals. These approaches rest on subtle concepts of variation, time, and ancestry that are perhaps not widely appreciated. They share the idea that there are, or were, discrete panmictic human populations such that every person is either a member of such a population or is an admixed descendant of them. Ancestry fraction estimation is biased by assumptions about past and present human population structure, as when we trace ancestry to hypothetical unmixed ancestral populations, or assign an individual's ancestry to continental populations that are indistinguishable from classical “races.” Attempts to identify even individuals' local subpopulations are less precise than most (geneticists included) expect, because that is usually based on a small portion of a person's ancestry, relative to the much larger pool of comparably related ancestors. It is easier to show that two people have some relationship than to show who or where the actual ancestor was. There is an important distinction between individuals' demographic ancestry and the ancestry of their genes. Despite superficial appearances, these interpretations of genetic data are often based on typological rather than Darwinian thinking, raising important issues about the questions that are actually being asked. PMID:19411595

  11. Molecular epidemiology, phylogeny and evolution of Candida albicans.

    PubMed

    McManus, Brenda A; Coleman, David C

    2014-01-01

    A small number of Candida species form part of the normal microbial flora of mucosal surfaces in humans and may give rise to opportunistic infections when host defences are impaired. Candida albicans is by far the most prevalent commensal and pathogenic Candida species. Several different molecular typing approaches including multilocus sequence typing, multilocus microsatellite typing and DNA fingerprinting using C. albicans-specific repetitive sequence-containing DNA probes have yielded a wealth of information regarding the epidemiology and population structure of this species. Such studies revealed that the C. albicans population structure consists of multiple major and minor clades, some of which exhibit geographical or phenotypic enrichment and that C. albicans reproduction is predominantly clonal. Despite this, losses of heterozygosity by recombination, the existence of a parasexual cycle, toleration of a wide range of aneuploidies and the recent description of viable haploid strains have all demonstrated the extensive plasticity of the C. albicans genome. Recombination and gross chromosomal rearrangements are more common under stressful environmental conditions, and have played a significant role in the evolution of this opportunistic pathogen. Surprisingly, Candida dubliniensis, the closest relative of C. albicans exhibits more karyotype variability than C. albicans, but is significantly less adaptable to unfavourable environments. This disparity most likely reflects the evolutionary processes that occurred during or soon after the divergence of both species from their common ancestor. Whilst C. dubliniensis underwent significant gene loss and pseudogenisation, C. albicans expanded gene families considered to be important in virulence. It is likely that technological developments in whole genome sequencing and data analysis in coming years will facilitate its routine use for population structure, epidemiological investigations, and phylogenetic analyses of

  12. Using experimental evolution to probe molecular mechanisms of protein function.

    PubMed

    Fischer, Marlies; Kang, Mandeep; Brindle, Nicholas Pj

    2016-02-01

    Directed evolution is a powerful tool for engineering protein function. The process of directed evolution involves iterative rounds of sequence diversification followed by assaying activity of variants and selection. The range of sequence variants and linked activities generated in the course of an evolution are a rich information source for investigating relationships between sequence and function. Key residue positions determining protein function, combinatorial contributors to activity and even potential functional mechanisms have been revealed in directed evolutions. The recent application of high throughput sequencing substantially increases the information that can be retrieved from directed evolution experiments. Combined with computational analysis this additional sequence information has allowed high-resolution analysis of individual residue contributions to activity. These developments promise to significantly enhance the depth of insight that experimental evolution provides into mechanisms of protein function.

  13. Bacterial flagella and Type III secretion: case studies in the evolution of complexity.

    PubMed

    Pallen, M J; Gophna, U

    2007-01-01

    Bacterial flagella at first sight appear uniquely sophisticated in structure, so much so that they have even been considered 'irreducibly complex' by the intelligent design movement. However, a more detailed analysis reveals that these remarkable pieces of molecular machinery are the product of processes that are fully compatible with Darwinian evolution. In this chapter we present evidence for such processes, based on a review of experimental studies, molecular phylogeny and microbial genomics. Several processes have played important roles in flagellar evolution: self-assembly of simple repeating subunits, gene duplication with subsequent divergence, recruitment of elements from other systems ('molecular bricolage'), and recombination. We also discuss additional tentative new assignments of homology (FliG with MgtE, FliO with YscJ). In conclusion, rather than providing evidence of intelligent design, flagellar and non-flagellar Type III secretion systems instead provide excellent case studies in the evolution of complex systems from simpler components.

  14. Stand and be counted: the neo-Darwinian synthesis and the ascension of bipedalism as an essential hominid synapomorphy.

    PubMed

    Gundling, Tom

    2012-01-01

    Since its inception in the early- to middle-nineteenth century, human origins studies have been informed by a variety of disciplines beyond physical anthropology and archaeology, most notably geology and biology. This study examines dramatic changes within human origins research that occurred in the mid-twentieth century largely as a consequence of the dissemination of the neo-Darwinian synthesis from biology (sensu lato) into the new" physical anthropology. This paradigm shift resulted in foregrounding evolution as a process affecting variable populations over exercises in typological classification. It led to the acknowledgement of bipedalism as the earliest hominidi adaptation, preceding other important changes in morphology (e.g., increased encephalization quotient) and behavior (e.g., stone tool manufacture and use). An important corollary of the recognition of a bipedal ape phase in our ancestry was the decoupling of the grade category "human" from the phylogenetic term "hominid".

  15. Patterns of molecular evolution of RNAi genes in social and socially parasitic bumblebees.

    PubMed

    Helbing, Sophie; Lattorff, H Michael G

    2016-08-01

    The high frequency of interactions amongst closely related individuals in social insect colonies enhances pathogen transmission. Group-mediated behavior supporting immune defenses tends to decrease selection acting on immune genes. Along with low effective population sizes this might result in relaxed constraint and rapid evolution of immune system genes. Here, we show that antiviral siRNA genes show high rates of molecular evolution with argonaute 2, armitage and maelstrom evolving faster in social bumblebees compared to their socially parasitic cuckoo bumblebees that lack a worker caste. RNAi genes show frequent positive selection at the codon level additionally supported by the occurrence of parallel evolution. Their evolutionary rate is linked to their pathway specific position with genes directly interacting with viruses showing the highest rates of molecular evolution. We suggest that higher pathogen load in social insects indeed drives the molecular evolution of immune genes including antiviral siRNA, if not compensated by behavior.

  16. An organismic critique of molecular darwinism.

    PubMed

    Wicken, J S

    1985-12-21

    The molecular darwinian approach to the emergence of life treats the competition between RNA sequences for nucleotide resources as the primordial selective process in prebiotic evolution, which prescribes possible pathways for the subsequent elaboration of organizational relationships. Since success in this competition is determined by the "phenotypic" properties of RNA strands in the absence of organizational context, the genesis of biotic organization is dependent upon the establishment of co-operative, hypercyclic interactions between competing RNA sequences. The thesis of this paper is that hypercycle theory is based on unwarranted assumptions about the conditions of prebiotic evolution, and that the implications of these assumptions run counter to both empirical evidence and to the rational by which natural selection operates in evolution generally. An organismic alternative to hypercycle theory is suggested, based on the catalytic microsphere and the thermodynamics of selection.

  17. A molecular description of the evolution of resistance

    NASA Technical Reports Server (NTRS)

    Ordoukhanian, P.; Joyce, G. F.

    1999-01-01

    BACKGROUND: In vitro evolution has been used to obtain nucleic acid molecules with interesting functional properties. The evolution process usually is carried out in a stepwise manner, involving successive rounds of selection, amplification and mutation. Recently, a continuous in vitro evolution system was devised for RNAs that catalyze the ligation of oligonucleotide substrates, allowing the evolution of catalytic function to be studied in real time. RESULTS: Continuous in vitro evolution of an RNA ligase ribozyme was carried out in the presence of a DNA enzyme that was capable of cleaving, and thereby inactivating, the ribozyme. The DNA concentration was increased steadily over 33.5 hours of evolution, reaching a final concentration that would have been sufficient to inactivate the starting population in one second. The evolved population of ribozymes developed resistance to the DNA enzyme, reducing their vulnerability to cleavage by 2000-fold but retaining their own catalytic function. Based on sequencing and kinetic analysis of the ribozymes, two mechanisms are proposed for this resistance. One involves three nucleotide substitutions, together with two compensatory mutations, that alter the site at which the DNA enzyme binds the ribozyme. The other involves enhancement of the ribozyme's ability to bind its own substrate in a way that protects it from cleavage by the DNA enzyme. CONCLUSIONS: The ability to direct the evolution of an enzyme's biochemical properties in response to the behavior of another macromolecule provides insight into the evolution of resistance and may be useful in developing enzymes with novel or enhanced function.

  18. Brassinosteroid action in flowering plants: a Darwinian perspective

    PubMed Central

    Kutschera, Ulrich; Wang, Zhi-Yong

    2012-01-01

    The year 2012 marks the 150th anniversary of the publication of Charles Darwin's first botanical book, on the fertilization of orchids (1862), wherein he described pollen grains and outlined his evolutionary principles with respect to plant research. Five decades later, the growth-promoting effect of extracts of Orchid pollen on coleoptile elongation was documented. These studies led to the discovery of a new class of phytohormones, the brassinosteroids (BRs) that were isolated from rapeseed (Brassica napus) pollen. These growth-promoting steroids, which regulate height, fertility, and seed-filling in crop plants such as rice (Oryza sativa), also induce stress- and disease resistance in green algae and angiosperms. The origin and current status of BR-research is described here, with reference to BR-action and -signal transduction, and it is shown that modern high-yield rice varieties with erect leaves are deficient in endogenous BRs. Since brassinosteroids induce pathogen resistance in rice plants and hence can suppress rice blast- and bacterial blight-diseases, genetic manipulation of BR-biosynthesis or -perception may be a means to increase crop production. Basic research on BR activity in plants, such as Arabidopsis and rice, has the potential to increase crop yields further as part of a 21th century ‘green biotech-revolution’ that can be traced back to Darwin's classical breeding experiments. It is concluded that ‘Nothing in brassinosteroid research makes sense except in the light of Darwinian evolution’ and the value of basic science is highlighted, with reference to the genetic engineering of better food crops that may become resistant to a variety of plant diseases. PMID:22547659

  19. Molecular Diversity and Functional Evolution of Scorpion Potassium Channel Toxins*

    PubMed Central

    Zhu, Shunyi; Peigneur, Steve; Gao, Bin; Luo, Lan; Jin, Di; Zhao, Yong; Tytgat, Jan

    2011-01-01

    Scorpion toxins affecting K+ channels (KTxs) represent important pharmacological tools and potential drug candidates. Here, we report molecular characterization of seven new KTxs in the scorpion Mesobuthus eupeus by cDNA cloning combined with biochemical approaches. Comparative modeling supports that all these KTxs share a conserved cysteine-stabilized α-helix/β-sheet structural motif despite the differences in protein sequence and size. We investigated functional diversification of two orthologous α-KTxs (MeuTXKα1 from M. eupeus and BmP01 from Mesobuthus martensii) by comparing their K+ channel-blocking activities. Pharmacologically, MeuTXKα1 selectively blocked Kv1.3 channel with nanomolar affinity (IC50, 2.36 ± 0.9 nm), whereas only 35% of Kv1.1 currents were inhibited at 3 μm concentration, showing more than 1271-fold selectivity for Kv1.3 over Kv1.1. This peptide displayed a weak effect on Drosophila Shaker channel and no activity on Kv1.2, Kv1.4, Kv1.5, Kv1.6, and human ether-a-go-go-related gene (hERG) K+ channels. Although BmB01 and MeuTXKα1 have a similar channel spectrum, their affinity and selectivity for these channels largely varies. In comparison with MeuTXKα1, BmP01 only exhibits a submicromolar affinity (IC50, 133.72 ± 10.98 nm) for Kv1.3, showing 57-fold less activity than MeuTXKα1. Moreover, it lacks the ability to distinguish between Kv1.1 and Kv1.3. We also found that MeuTXKα1 inhibited the proliferation of activated T cells induced by phorbol myristate acetate and ionomycin at micromolar concentrations. Our results demonstrate that accelerated evolution drives affinity variations of orthologous α-KTxs on Kv channels and indicate that MeuTXKα1 is a promising candidate to develop an immune modulation agent for human autoimmune diseases. PMID:20889474

  20. Contributions of experimental protobiogenesis to the theory of evolution

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1976-01-01

    Inferences from experiments in protobiogenesis are examined as a forward extension of the theory of evolutionary biology. A nondiscontinuous, intraconsistent theory of general evolution embracing both protobiology and biology is outlined. This overview emphasizes Darwinian selection in the later stages of evolution, and stereochemical molecular selection in some of its earlier stages. It incorporates the concept of limitation of the scope of evolution by internal constraints on variation, based on the argument that internally limiting constraints observed in experiments with molecules are operative in organisms, if chemical processes occur within biological processes and biological processes are assumed to be exponentializations of chemical processes. Major evolutionary events might have occurred by rapid self-assembly processes analogous to those observed in the formation of phase-separated microspheres from amorphous powder or supersaturated solutions.

  1. The Eyes Have It: A Problem-Based Learning Exercise in Molecular Evolution

    ERIC Educational Resources Information Center

    White, Harold B.

    2007-01-01

    Molecular evolution provides an interesting context in which to use problem-based learning because it integrates a variety of topics in biology, biochemistry, and molecular biology. This three-stage problem for advanced students deals with the structure, multiple functions, and properties of lactate dehydrogenase isozymes, and the related…

  2. Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) – Insights from transcriptome sequences

    PubMed Central

    Yu, Yan; Xiang, Qiuyun; Manos, Paul S.; Soltis, Douglas E.; Soltis, Pamela S.; Song, Bao-Hua; Cheng, Shifeng; Liu, Xin; Wong, Gane

    2017-01-01

    The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework. Here we compare ten de novo-assembled transcriptomes representing the major lineages of the angiosperm genus Cornus (dogwood) and relevant outgroups using a customized pipeline for analyses. Using three distinct approaches, molecular dating of orthologous genes, analyses of the distribution of synonymous substitutions between paralogous genes, and examination of substitution rates through time, we detected a shared WGD event in the late Cretaceous across all taxa sampled. The inferred doubling event coincides temporally with the paleoclimatic changes associated with the initial divergence of the genus into three major lineages. Analyses also showed an acceleration of rates of molecular evolution after WGD. The highest rates of molecular evolution were observed in the transcriptome of the herbaceous lineage, C. canadensis, a species commonly found at higher latitudes, including the Arctic. Our study demonstrates the value of transcriptome data for understanding genome evolution in closely related species. The results suggest dramatic increase in sea surface temperature in the late Cretaceous may have contributed to the evolution and diversification of flowering plants. PMID:28225773

  3. Evolution of photoelectron vibrational coupling with molecular complexity

    NASA Astrophysics Data System (ADS)

    Poliakoff, E. D.; Lucchese, R. R.

    2006-11-01

    We review how electronic and vibrational degrees of freedom become coupled in molecular photoionization, and describe effects that emerge as the molecular complexity increases. Molecular photoionization is frequently influenced by the temporary trapping of the continuum electron in the field of the target molecules, which is referred to as a shape resonance, as it depends on the shape of the potential experienced by the exiting photoelectron. Such resonances couple electronic and vibrational motion, and the nature of the coupling can vary widely for polyatomic molecules. We show how vibrationally resolved photoelectron spectra acquired as a function of energy can be used to elucidate such coupling. The experiments are analysed using physically realistic and computationally tractable Schwinger variational theory, and the systems studied to date can be well understood using an independent-particle, adiabatic nuclei framework. As a result, simple and intuitive pictures emerge, even when dealing with scattering phenomena involving complex molecular targets and potentials.

  4. On the Stability and Evolution of Isolated Molecular Clouds

    NASA Technical Reports Server (NTRS)

    Langer, W.; Nelson, R.

    1998-01-01

    We present the results of three dimensional hydrodynamic models of evolving, isolated, low mass, quiescent clouds and Bok gobules, where the interstellar radiation field plays an important role in the thermal and chemical evolution, and thermal pressure provides dominant support against gravitational collapse.

  5. "Eve" in Africa: Human Evolution Meets Molecular Biology.

    ERIC Educational Resources Information Center

    Seager, Robert D.

    1990-01-01

    Presented is a discussion of recent evidence on the evolution of human forms on earth gathered and evaluated using mitochondrial DNA techniques. Theories regarding the possibility that a common female ancestor existed in Africa about 200,000 years ago are discussed. A list of teaching aids is provided. (CW)

  6. Extracellular Matrix Molecular Remodeling in Human Liver Fibrosis Evolution

    PubMed Central

    Baiocchini, Andrea; Montaldo, Claudia; Conigliaro, Alice; Grimaldi, Alessio; Correani, Virginia; Mura, Francesco; Ciccosanti, Fabiola; Rotiroti, Nicolina; Brenna, Alessia; Montalbano, Marzia; D’Offizi, Gianpiero; Capobianchi, Maria Rosaria; Alessandro, Riccardo; Piacentini, Mauro; Schininà, Maria Eugenia; Maras, Bruno; Del Nonno, Franca; Tripodi, Marco; Mancone, Carmine

    2016-01-01

    Chronic liver damage leads to pathological accumulation of ECM proteins (liver fibrosis). Comprehensive characterization of the human ECM molecular composition is essential for gaining insights into the mechanisms of liver disease. To date, studies of ECM remodeling in human liver diseases have been hampered by the unavailability of purified ECM. Here, we developed a decellularization method to purify ECM scaffolds from human liver tissues. Histological and electron microscopy analyses demonstrated that the ECM scaffolds, devoid of plasma and cellular components, preserved the three-dimensional ECM structure and zonal distribution of ECM components. This method has been then applied on 57 liver biopsies of HCV-infected patients at different stages of liver fibrosis according to METAVIR classification. Label-free nLC-MS/MS proteomics and computation biology were performed to analyze the ECM molecular composition in liver fibrosis progression, thus unveiling protein expression signatures specific for the HCV-related liver fibrotic stages. In particular, the ECM molecular composition of liver fibrosis was found to involve dynamic changes in matrix stiffness, flexibility and density related to the dysregulation of predominant collagen, elastic fibers and minor components with both structural and signaling properties. This study contributes to the understanding of the molecular bases underlying ECM remodeling in liver fibrosis and suggests new molecular targets for fibrolytic strategies. PMID:26998606

  7. Structural limits for evolutive capacities in complex molecular systems.

    PubMed

    Bergareche, A M; Ostolaza, J F

    1990-01-01

    The possibilities of evolution for a system with and without a code of translation from nucleic acids into proteins are evaluated. Our interest is mainly centred on the enzymatic RNA case since this molecule has, at the same time, reproductive and functional properties. After scanning the evolutive capacities of the enzymatic RNAs, including the possibility to play the role of "synthetase" which would match nucleic acids with amino acids as a transition step towards a code, we will try to show that due to their own functional limitative factors, the matching system (code) is necessary. This would be the only way to transform the formal complexity--complexity which has not entered into action before the translation process--into functional information to drive the instructive self-reproductive process. Once this stage is reached, the system could evolve without a limit.

  8. Evolution and Molecular Control of Hybrid Incompatibility in Plants

    PubMed Central

    Chen, Chen; E, Zhiguo; Lin, Hong-Xuan

    2016-01-01

    Postzygotic reproductive isolation (RI) plays an important role in speciation. According to the stage at which it functions and the symptoms it displays, postzygotic RI can be called hybrid inviability, hybrid weakness or necrosis, hybrid sterility, or hybrid breakdown. In this review, we summarized new findings about hybrid incompatibilities in plants, most of which are from studies on Arabidopsis and rice. Recent progress suggests that hybrid incompatibility is a by-product of co-evolution either with “parasitic” selfish elements in the genome or with invasive microbes in the natural environment. We discuss the environmental influences on the expression of hybrid incompatibility and the possible effects of environment-dependent hybrid incompatibility on sympatric speciation. We also discuss the role of domestication on the evolution of hybrid incompatibilities. PMID:27563306

  9. Primer and interviews: molecular mechanisms of morphological evolution.

    PubMed

    Kiefer, Julie C

    2010-12-01

    The beauty of the developing embryo, and the awe that it inspires, lure many scientists into the field of developmental biology. What compels cells to divide, migrate, and morph into a being with a complex body plan? Evolutionary developmental biologists hold similar fascinations, with dynamics that take place on a grander timescale. How do phenotypic traits diverge over evolutionary time? This primer illustrates how a deep understanding of the basic principles that underlie developmental biology have changed how scientists think about the evolution of body form. The primer culminates in a conversation with David Stern, PhD, and Michael Shapiro, PhD, who discuss current topics in morphological evolution, why the field should be of interest to classic developmental biologists, and what lies ahead.

  10. Primer and interviews: Molecular mechanisms of morphological evolution

    PubMed Central

    Kiefer, Julie C

    2010-01-01

    The beauty of the developing embryo, and the awe that it inspires, lure many scientists into the field of developmental biology. What compels cells to divide, migrate, and morph into a being with a complex body plan? Evolutionary developmental biologists hold similar fascinations, with dynamics that take place on a grander timescale. How do phenotypic traits diverge over evolutionary time? This primer illustrates how a deep understanding of the basic principles that underlie developmental biology have changed how scientists think about the evolution of body form. The primer culminates in a conversation with David Stern, PhD, and Michael Shapiro, PhD, who discuss current topics in morphological evolution, why the field should be of interest to classic developmental biologists, and what lies ahead. Developmental Dynamics 239:3497–3505, 2010. © 2010 Wiley-Liss, Inc. PMID:21069831

  11. Abrupt deceleration of molecular evolution linked to the origin of arborescence in ferns.

    PubMed

    Korall, Petra; Schuettpelz, Eric; Pryer, Kathleen M

    2010-09-01

    Molecular rate heterogeneity, whereby rates of molecular evolution vary among groups of organisms, is a well-documented phenomenon. Nonetheless, its causes are poorly understood. For animals, generation time is frequently cited because longer-lived species tend to have slower rates of molecular evolution than their shorter-lived counterparts. Although a similar pattern has been uncovered in flowering plants, using proxies such as growth form, the underlying process has remained elusive. Here, we find a deceleration of molecular evolutionary rate to be coupled with the origin of arborescence in ferns. Phylogenetic branch lengths within the “tree fern” clade are considerably shorter than those of closely related lineages, and our analyses demonstrate that this is due to a significant difference in molecular evolutionary rate. Reconstructions reveal that an abrupt rate deceleration coincided with the evolution of the long-lived tree-like habit at the base of the tree fern clade. This suggests that a generation time effect may well be ubiquitous across the green tree of life, and that the search for a responsible mechanism must focus on characteristics shared by all vascular plants. Discriminating among the possibilities will require contributions from various biological disciplines,but will be necessary for a full appreciation of molecular evolution.

  12. Molecular evolution of communication signals in electric fish.

    PubMed

    Zakon, Harold H; Zwickl, Derrick J; Lu, Ying; Hillis, David M

    2008-06-01

    Animal communication systems are subject to natural selection so the imprint of selection must reside in the genome of each species. Electric fish generate electric organ discharges (EODs) from a muscle-derived electric organ (EO) and use these fields for electrolocation and communication. Weakly electric teleosts have evolved at least twice (mormyriforms, gymnotiforms) allowing a comparison of the workings of evolution in two independently evolved sensory/motor systems. We focused on the genes for two Na(+) channels, Nav1.4a and Nav1.4b, which are orthologs of the mammalian muscle-expressed Na(+) channel gene Nav1.4. Both genes are expressed in muscle in non-electric fish. Nav1.4b is expressed in muscle in electric fish, but Nav1.4a expression has been lost from muscle and gained in the evolutionarily novel EO in both groups. We hypothesized that Nav1.4a might be evolving to optimize the EOD for different sensory environments and the generation of species-specific communication signals. We obtained the sequence for Nav1.4a from non-electric, mormyriform and gymnotiform species, estimated a phylogenetic tree, and determined rates of evolution. We observed elevated rates of evolution in this gene in both groups coincident with the loss of Nav1.4a from muscle and its compartmentalization in EO. We found amino acid substitutions at sites known to be critical for channel inactivation; analyses suggest that these changes are likely to be the result of positive selection. We suggest that the diversity of EOD waveforms in both groups of electric fish is correlated with accelerations in the rate of evolution of the Nav1.4a Na(+) channel gene due to changes in selection pressure on the gene once it was solely expressed in the EO.

  13. Exaptation in human evolution: how to test adaptive vs exaptive evolutionary hypotheses.

    PubMed

    Pievani, Telmo; Serrelli, Emanuele

    2011-01-01

    Palaeontologists, Stephen J. Gould and Elisabeth Vrba, introduced the term "ex-aptation" with the aim of improving and enlarging the scientific language available to researchers studying the evolution of any useful character, instead of calling it an "adaptation" by default, coming up with what Gould named an "extended taxonomy of fitness". With the extension to functional co-optations from non-adaptive structures ("spandrels"), the notion of exaptation expanded and revised the neo-Darwinian concept of "pre-adaptation" (which was misleading, for Gould and Vrba, suggesting foreordination). Exaptation is neither a "saltationist" nor an "anti-Darwinian" concept and, since 1982, has been adopted by many researchers in evolutionary and molecular biology, and particularly in human evolution. Exaptation has also been contested. Objections include the "non-operationality objection".We analyze the possible operationalization of this concept in two recent studies, and identify six directions of empirical research, which are necessary to test "adaptive vs. exaptive" evolutionary hypotheses. We then comment on a comprehensive survey of literature (available online), and on the basis of this we make a quantitative and qualitative evaluation of the adoption of the term among scientists who study human evolution. We discuss the epistemic conditions that may have influenced the adoption and appropriate use of exaptation, and comment on the benefits of an "extended taxonomy of fitness" in present and future studies concerning human evolution.

  14. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    ERIC Educational Resources Information Center

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  15. Molecular evolution of monotreme and marsupial whey acidic protein genes.

    PubMed

    Sharp, Julie A; Lefèvre, Christophe; Nicholas, Kevin R

    2007-01-01

    Whey acidic protein (WAP), a major whey protein present in milk of a number of mammalian species has characteristic cysteine-rich domains known as four-disulfide cores (4-DSC). Eutherian WAP, expressed in the mammary gland throughout lactation, has two 4-DSC domains, (DI-DII) whereas marsupial WAP, expressed only during mid-late lactation, contains an additional 4-DSC (DIII), and has a DIII-D1-DII configuration. We report the expression and evolution of echidna (Tachyglossus aculeatus) and platypus (Onithorhynchus anatinus) WAP cDNAs. Predicted translation of monotreme cDNAs showed echidna WAP contains two 4-DSC domains corresponding to DIII-DII, whereas platypus WAP contains an additional domain at the C-terminus with homology to DII and has the configuration DIII-DII-DII. Both monotreme WAPs represent new WAP protein configurations. We propose models for evolution of the WAP gene in the mammalian lineage either through exon loss from an ancient ancestor or by rapid evolution via the process of exon shuffling. This evolutionary outcome may reflect differences in lactation strategy between marsupials, monotremes, and eutherians, and give insight to biological function of the gene products. WAP four-disulfide core domain 2 (WFDC2) proteins were also identified in echidna, platypus and tammar wallaby (Macropus eugenii) lactating mammary cells. WFDC2 proteins are secreted proteins not previously associated with lactation. Mammary gland expression of tammar WFDC2 during the course of lactation showed WFDC2 was elevated during pregnancy, reduced in early lactation and absent in mid-late lactation.

  16. Molecular evolution and genetics of postzygotic reproductive isolation in plants

    PubMed Central

    2012-01-01

    In just the last few years, plant geneticists have made tremendous progress in identifying the molecular genetic basis of postzygotic reproductive isolation. With more than a dozen genes now cloned, it is clear that plant hybrid incompatibilities usually evolve via two or more mutational steps, as is predicted by the Dobzhansky-Muller model. There is evidence that natural selection or random genetic drift can be responsible for these incompatibilities. PMID:23236340

  17. Molecular phylogeny, biogeography, and habitat preference evolution of marsupials.

    PubMed

    Mitchell, Kieren J; Pratt, Renae C; Watson, Laura N; Gibb, Gillian C; Llamas, Bastien; Kasper, Marta; Edson, Janette; Hopwood, Blair; Male, Dean; Armstrong, Kyle N; Meyer, Matthias; Hofreiter, Michael; Austin, Jeremy; Donnellan, Stephen C; Lee, Michael S Y; Phillips, Matthew J; Cooper, Alan

    2014-09-01

    Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.

  18. Emerging of Stochastic Dynamical Equalities and Steady State Thermodynamics from Darwinian Dynamics.

    PubMed

    Ao, P

    2008-05-15

    The evolutionary dynamics first conceived by Darwin and Wallace, referring to as Darwinian dynamics in the present paper, has been found to be universally valid in biology. The statistical mechanics and thermodynamics, while enormous successful in physics, have been in an awkward situation of wanting a consistent dynamical understanding. Here we present from a formal point of view an exploration of the connection between thermodynamics and Darwinian dynamics and a few related topics. We first show that the stochasticity in Darwinian dynamics implies the existence temperature, hence the canonical distribution of Boltzmann-Gibbs type. In term of relative entropy the Second Law of thermodynamics is dynamically demonstrated without detailed balance condition, and is valid regardless of size of the system. In particular, the dynamical component responsible for breaking detailed balance condition does not contribute to the change of the relative entropy. Two types of stochastic dynamical equalities of current interest are explicitly discussed in the present approach: One is based on Feynman-Kac formula and another is a generalization of Einstein relation. Both are directly accessible to experimental tests. Our demonstration indicates that Darwinian dynamics represents logically a simple and straightforward starting point for statistical mechanics and thermodynamics and is complementary to and consistent with conservative dynamics that dominates the physical sciences. Present exploration suggests the existence of a unified stochastic dynamical framework both near and far from equilibrium.

  19. Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins.

    PubMed

    Remington, David L

    2015-12-01

    Perspectives on the role of large-effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular-based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular-based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome-wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology.

  20. Gibberellin Receptor GID1: Gibberellin Recognition and Molecular Evolution

    NASA Astrophysics Data System (ADS)

    Kato, Hiroaki; Sato, Tomomi; Ueguchi-Tanaka, Miyako

    Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. We analyzed the crystal structure of a nuclear GA receptor, GIBBERELLIN INSENSITIVE DWARF 1 (GID1) from Oryza sativa. As it was proposed from the sequence similarity, the overall structure of GID1 shows an α/β-hydrolase fold similar to that of the hormone-sensitive lipases (HSLs) except for an amino-terminal lid. The GA-binding site corresponds to the substrate-binding site of HSLs. Almost residues assigned for GA binding showed very little or no activity when they were replaced with Ala. The substitution of the residues corresponding to those of the lycophyte GID1s caused an increase in the binding affinity for GA34, a 2β-hydroxylated GA4. These findings indicate that GID1 originated from HSL and was tinkered to have the specificity for bioactive GAs in the course of plant evolution.

  1. Molecular Imaging and Contrast Agent Database (MICAD): evolution and progress.

    PubMed

    Chopra, Arvind; Shan, Liang; Eckelman, W C; Leung, Kam; Latterner, Martin; Bryant, Stephen H; Menkens, Anne

    2012-02-01

    The purpose of writing this review is to showcase the Molecular Imaging and Contrast Agent Database (MICAD; www.micad.nlm.nih.gov ) to students, researchers, and clinical investigators interested in the different aspects of molecular imaging. This database provides freely accessible, current, online scientific information regarding molecular imaging (MI) probes and contrast agents (CA) used for positron emission tomography, single-photon emission computed tomography, magnetic resonance imaging, X-ray/computed tomography, optical imaging and ultrasound imaging. Detailed information on >1,000 agents in MICAD is provided in a chapter format and can be accessed through PubMed. Lists containing >4,250 unique MI probes and CAs published in peer-reviewed journals and agents approved by the United States Food and Drug Administration as well as a comma separated values file summarizing all chapters in the database can be downloaded from the MICAD homepage. Users can search for agents in MICAD on the basis of imaging modality, source of signal/contrast, agent or target category, pre-clinical or clinical studies, and text words. Chapters in MICAD describe the chemical characteristics (structures linked to PubChem), the in vitro and in vivo activities, and other relevant information regarding an imaging agent. All references in the chapters have links to PubMed. A Supplemental Information Section in each chapter is available to share unpublished information regarding an agent. A Guest Author Program is available to facilitate rapid expansion of the database. Members of the imaging community registered with MICAD periodically receive an e-mail announcement (eAnnouncement) that lists new chapters uploaded to the database. Users of MICAD are encouraged to provide feedback, comments, or suggestions for further improvement of the database by writing to the editors at micad@nlm.nih.gov.

  2. Molecular tools in understanding the evolution of Vibrio cholerae

    PubMed Central

    Rahaman, Md. Habibur; Islam, Tarequl; Colwell, Rita R.; Alam, Munirul

    2015-01-01

    Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies. PMID:26500613

  3. The molecular evolution of the vertebrate behavioural repertoire

    PubMed Central

    2016-01-01

    How the sophisticated vertebrate behavioural repertoire evolved remains a major question in biology. The behavioural repertoire encompasses the set of individual behavioural components that an organism uses when adapting and responding to changes in its external world. Although unicellular organisms, invertebrates and vertebrates share simple reflex responses, the fundamental mechanisms that resulted in the complexity and sophistication that is characteristic of vertebrate behaviours have only recently been examined. A series of behavioural genetic experiments in mice and humans support a theory that posited the importance of synapse proteome expansion in generating complexity in the behavioural repertoire. Genome duplication events, approximately 550 Ma, produced expansion in the synapse proteome that resulted in increased complexity in synapse signalling mechanisms that regulate components of the behavioural repertoire. The experiments demonstrate the importance to behaviour of the gene duplication events, the diversification of paralogues and sequence constraint. They also confirm the significance of comparative proteomic and genomic studies that identified the molecular origins of synapses in unicellular eukaryotes and the vertebrate expansion in proteome complexity. These molecular mechanisms have general importance for understanding the repertoire of behaviours in different species and for human behavioural disorders arising from synapse gene mutations. PMID:26598730

  4. Structure, molecular evolution, and hydrolytic specificities of largemouth bass pepsins.

    PubMed

    Miura, Yoko; Suzuki-Matsubara, Mieko; Kageyama, Takashi; Moriyama, Akihiko

    2016-02-01

    The nucleotide sequences of largemouth bass pepsinogens (PG1, 2 and 3) were determined after molecular cloning of the respective cDNAs. Encoded PG1, 2 and 3 were classified as fish pepsinogens A1, A2 and C, respectively. Molecular evolutionary analyses show that vertebrate pepsinogens are classified into seven monophyletic groups, i.e. pepsinogens A, F, Y (prochymosins), C, B, and fish pepsinogens A and C. Regarding the primary structures, extensive deletion was obvious in S'1 loop residues in fish pepsin A as well as tetrapod pepsin Y. This deletion resulted in a decrease in hydrophobic residues in the S'1 site. Hydrolytic specificities of bass pepsins A1 and A2 were investigated with a pepsin substrate and its variants. Bass pepsins preferred both hydrophobic/aromatic residues and charged residues at the P'1 sites of substrates, showing the dual character of S'1 sites. Thermodynamic analyses of bass pepsin A2 showed that its activation Gibbs energy change (∆G(‡)) was lower than that of porcine pepsin A. Several sites of bass pepsin A2 moiety were found to be under positive selection, and most of them are located on the surface of the molecule, where they are involved in conformational flexibility. The broad S'1 specificity and flexible structure of bass pepsin A2 are thought to cause its high proteolytic activity.

  5. Molecular tools in understanding the evolution of Vibrio cholerae.

    PubMed

    Rahaman, Md Habibur; Islam, Tarequl; Colwell, Rita R; Alam, Munirul

    2015-01-01

    Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies.

  6. The modern theory of biological evolution: an expanded synthesis.

    PubMed

    Kutschera, Ulrich; Niklas, Karl J

    2004-06-01

    In 1858, two naturalists, Charles Darwin and Alfred Russel Wallace, independently proposed natural selection as the basic mechanism responsible for the origin of new phenotypic variants and, ultimately, new species. A large body of evidence for this hypothesis was published in Darwin's Origin of Species one year later, the appearance of which provoked other leading scientists like August Weismann to adopt and amplify Darwin's perspective. Weismann's neo-Darwinian theory of evolution was further elaborated, most notably in a series of books by Theodosius Dobzhansky, Ernst Mayr, Julian Huxley and others. In this article we first summarize the history of life on Earth and provide recent evidence demonstrating that Darwin's dilemma (the apparent missing Precambrian record of life) has been resolved. Next, the historical development and structure of the "modern synthesis" is described within the context of the following topics: paleobiology and rates of evolution, mass extinctions and species selection, macroevolution and punctuated equilibrium, sexual reproduction and recombination, sexual selection and altruism, endosymbiosis and eukaryotic cell evolution, evolutionary developmental biology, phenotypic plasticity, epigenetic inheritance and molecular evolution, experimental bacterial evolution, and computer simulations (in silico evolution of digital organisms). In addition, we discuss the expansion of the modern synthesis, embracing all branches of scientific disciplines. It is concluded that the basic tenets of the synthetic theory have survived, but in modified form. These sub-theories require continued elaboration, particularly in light of molecular biology, to answer open-ended questions concerning the mechanisms of evolution in all five kingdoms of life.

  7. The modern theory of biological evolution: an expanded synthesis

    NASA Astrophysics Data System (ADS)

    Kutschera, Ulrich; Niklas, Karl J.

    In 1858, two naturalists, Charles Darwin and Alfred Russel Wallace, independently proposed natural selection as the basic mechanism responsible for the origin of new phenotypic variants and, ultimately, new species. A large body of evidence for this hypothesis was published in Darwin's Origin of Species one year later, the appearance of which provoked other leading scientists like August Weismann to adopt and amplify Darwin's perspective. Weismann's neo-Darwinian theory of evolution was further elaborated, most notably in a series of books by Theodosius Dobzhansky, Ernst Mayr, Julian Huxley and others. In this article we first summarize the history of life on Earth and provide recent evidence demonstrating that Darwin's dilemma (the apparent missing Precambrian record of life) has been resolved. Next, the historical development and structure of the ``modern synthesis'' is described within the context of the following topics: paleobiology and rates of evolution, mass extinctions and species selection, macroevolution and punctuated equilibrium, sexual reproduction and recombination, sexual selection and altruism, endosymbiosis and eukaryotic cell evolution, evolutionary developmental biology, phenotypic plasticity, epigenetic inheritance and molecular evolution, experimental bacterial evolution, and computer simulations (in silico evolution of digital organisms). In addition, we discuss the expansion of the modern synthesis, embracing all branches of scientific disciplines. It is concluded that the basic tenets of the synthetic theory have survived, but in modified form. These sub-theories require continued elaboration, particularly in light of molecular biology, to answer open-ended questions concerning the mechanisms of evolution in all five kingdoms of life.

  8. Molecular Evolution of Insect Sociality: An Eco-Evo-Devo Perspective.

    PubMed

    Toth, Amy L; Rehan, Sandra M

    2017-01-31

    The evolution of eusociality is a perennial issue in evolutionary biology, and genomic advances have fueled steadily growing interest in the genetic changes underlying social evolution. Along with a recent flurry of research on comparative and evolutionary genomics in different eusocial insect groups (bees, ants, wasps, and termites), several mechanistic explanations have emerged to describe the molecular evolution of eusociality from solitary behavior. These include solitary physiological ground plans, genetic toolkits of deeply conserved genes, evolutionary changes in protein-coding genes, cis regulation, and the structure of gene networks, epigenetics, and novel genes. Despite this proliferation of ideas, there has been little synthesis, even though these ideas are not mutually exclusive and may in fact be complementary. We review available data on molecular evolution of insect sociality and highlight key biotic and abiotic factors influencing social insect genomes. We then suggest both phylogenetic and ecological evolutionary developmental biology (eco-evo-devo) perspectives for a more synthetic view of molecular evolution in insect societies.

  9. Molecular Evolution of the Oxygen-Binding Hemerythrin Domain

    PubMed Central

    Alvarez-Carreño, Claudia; Becerra, Arturo; Lazcano, Antonio

    2016-01-01

    Background The evolution of oxygenic photosynthesis during Precambrian times entailed the diversification of strategies minimizing reactive oxygen species-associated damage. Four families of oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of arthropodan and molluscan hemocyanins) are known to have evolved independently the capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolutionary pressure of oxygen accumulation. Oxygen-binding hemerythrin was first studied in marine invertebrates but further research has made it clear that it is present in the three domains of life, strongly suggesting that its origin predated the emergence of eukaryotes. Results Oxygen-binding hemerythrins are a monophyletic sub-group of the hemerythrin/HHE (histidine, histidine, glutamic acid) cation-binding domain. Oxygen-binding hemerythrin homologs were unambiguously identified in 367/2236 bacterial, 21/150 archaeal and 4/135 eukaryotic genomes. Overall, oxygen-binding hemerythrin homologues were found in the same proportion as single-domain and as long protein sequences. The associated functions of protein domains in long hemerythrin sequences can be classified in three major groups: signal transduction, phosphorelay response regulation, and protein binding. This suggests that in many organisms the reversible oxygen-binding capacity was incorporated in signaling pathways. A maximum-likelihood tree of oxygen-binding hemerythrin homologues revealed a complex evolutionary history in which lateral gene transfer, duplications and gene losses appear to have played an important role. Conclusions Hemerythrin is an ancient protein domain with a complex evolutionary history. The distinctive iron-binding coordination site of oxygen-binding hemerythrins evolved first in prokaryotes, very likely prior to the divergence of Firmicutes and Proteobacteria, and spread into many bacterial, archaeal and eukaryotic species. The later

  10. Molecular evolution of urea amidolyase and urea carboxylase in fungi

    PubMed Central

    2011-01-01

    Background Urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. Urea amidolyase has been found only in some fungal species among eukaryotes. It contains two major domains: the amidase and urea carboxylase domains. A shorter form of urea amidolyase is known as urea carboxylase and has no amidase domain. Eukaryotic urea carboxylase has been found only in several fungal species and green algae. In order to elucidate the evolutionary origin of urea amidolyase and urea carboxylase, we studied the distribution of urea amidolyase, urea carboxylase, as well as other proteins including urease, across kingdoms. Results Among the 64 fungal species we examined, only those in two Ascomycota classes (Sordariomycetes and Saccharomycetes) had the urea amidolyase sequences. Urea carboxylase was found in many but not all of the species in the phylum Basidiomycota and in the subphylum Pezizomycotina (phylum Ascomycota). It was completely absent from the class Saccharomycetes (phylum Ascomycota; subphylum Saccharomycotina). Four Sordariomycetes species we examined had both the urea carboxylase and the urea amidolyase sequences. Phylogenetic analysis showed that these two enzymes appeared to have gone through independent evolution since their bacterial origin. The amidase domain and the urea carboxylase domain sequences from fungal urea amidolyases clustered strongly together with the amidase and urea carboxylase sequences, respectively, from a small number of beta- and gammaproteobacteria. On the other hand, fungal urea carboxylase proteins clustered together with another copy of urea carboxylases distributed broadly among bacteria. The urease proteins were found in all the fungal species examined except for those of the subphylum Saccharomycotina. Conclusions We conclude that the urea amidolyase genes currently found only in fungi are the results of a horizontal gene transfer event from

  11. Vibration-mediated Kondo transport in molecular junctions: conductance evolution during mechanical stretching

    PubMed Central

    Rakhmilevitch, David

    2015-01-01

    Summary The vibration-mediated Kondo effect attracted considerable theoretical interest during the last decade. However, due to lack of extensive experimental demonstrations, the fine details of the phenomenon were not addressed. Here, we analyze the evolution of vibration-mediated Kondo effect in molecular junctions during mechanical stretching. The described analysis reveals the different contributions of Kondo and inelastic transport. PMID:26734532

  12. Molecular phylogenetic study on the origin and evolution of Mustelidae.

    PubMed

    Yonezawa, Takahiro; Nikaido, Masato; Kohno, Naoki; Fukumoto, Yukio; Okada, Norihiro; Hasegawa, Masami

    2007-07-01

    The family Mustelidae, which consists of Mustelinae, Lutrinae, Melinae, and Taxidiinae, is the largest family among Carnivora and is a highly diverse group. Recent molecular phylogenetic studies have clarified the phylogenetic relations among Mustelidae, but there remain several unresolved problems, particularly concerning the deep branchings. Whereas many studies support the monophyly of Mustelidae+Procyonidae among Musteloidea, the relations between Mustelidae+Procyonidae, Ailuridae, and Miphitidae are still unclear. To address these problems, we inferred a tree on the basis of the sequences of mitochondrial genomes and of multiple nuclear genes using the maximum likelihood method. Our results strongly support the hypothesis that the Taxidiinae branched at first, followed by the branching of the Melinae. After that, Mustelinae diversified, and Lutrinae evolved within Mustelinae. With respect to the deep branchings in Musteloidea, the Ailuridae/Mephitidae monophyly tree and the Mephitidae-basal tree are indistinguishable in log-likelihood score, and this problem remains unresolved.

  13. Molecular evolution of toxin genes in Elapidae snakes.

    PubMed

    Tamiya, Toru; Fujimi, Takahiko J

    2006-11-01

    The venom of the sea krait, Laticauda semifasciata, consists primarily of two toxic proteins, phospholipase A(2) (PLA(2)) and a three-finger-structure toxin. We have cloned both toxic protein genes, including the upstream region. PLA(2) genes contain three types of inserted sequences: an AG-rich region, a chicken repeat 1-like long interspersed nucleotide element sequence and an intron II 3' side repeat sequence. The molecular divergence of L. semifasciata PLA(2) genes was defined on the basis of the inserted sequences and their sequence homology. The length of intron I in the three-finger-structure toxin genes differs from species to species. The alignment analysis of intron I of the three-finger-structure toxin genes revealed that the intron I sequence of the ancestral gene comprised ten genetic regions. A hypothetical evolutionary process for the three-finger-structure toxin genes has also been developed.

  14. Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations.

    PubMed

    López-Canut, Violeta; Roca, Maite; Bertrán, Juan; Moliner, Vicent; Tuñón, Iñaki

    2011-08-10

    We here present a theoretical study of the alkaline hydrolysis of a phosphodiester (methyl p-nitrophenyl phosphate or MpNPP) in the active site of Escherichia coli alkaline phosphatase (AP), a monoesterase that also presents promiscuous activity as a diesterase. The analysis of our simulations, carried out by means of molecular dynamics (MD) simulations with hybrid quantum mechanics/molecular mechanics (QM/MM) potentials, shows that the reaction takes place through a D(N)A(N) or dissociative mechanism, the same mechanism employed by AP in the hydrolysis of monoesters. The promiscuous activity observed in this superfamily can be then explained on the basis of a conserved reaction mechanism. According to our simulations the specialization in the hydrolysis of phosphomonoesters or phosphodiesters, developed in different members of the superfamily, is a consequence of the interactions established between the protein and the oxygen atoms of the phosphate group and, in particular, with the oxygen atom that bears the additional alkyl group when the substrate is a diester. A water molecule, belonging to the coordination shell of the Mg(2+) ion, and residue Lys328 seem to play decisive roles stabilizing a phosphomonoester substrate, but the latter contributes to increase the energy barrier for the hydrolysis of phosphodiesters. Then, mutations affecting the nature or positioning of Lys328 lead to an increased diesterase activity in AP. Finally, the capacity of this enzymatic family to catalyze the reaction of phosphoesters having different leaving groups, or substrate promiscuity, is explained by the ability of the enzyme to stabilize different charge distributions in the leaving group using different interactions involving either one of the zinc centers or residues placed on the outer side of the catalytic site.

  15. A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock.

    PubMed

    Pereira, Sergio L; Baker, Allan J

    2006-09-01

    Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather

  16. Low-molecular-weight carbon nitrides for solar hydrogen evolution.

    PubMed

    Lau, Vincent Wing-hei; Mesch, Maria B; Duppel, Viola; Blum, Volker; Senker, Jürgen; Lotsch, Bettina V

    2015-01-28

    This work focuses on the control of the polymerization process for melon ("graphitic carbon nitride"), with the aim of improving its photocatalytic activity intrinsically. We demonstrate here that reduction of the synthesis temperature leads to a mixture of the monomer melem and its higher condensates. We show that this mixture can be separated and provide evidence that the higher condensates are isolated oligomers of melem. On evaluating their photocatalytic activity for hydrogen evolution, the oligomers were found to be the most active species, having up to twice the activity of the monomer/oligomer mixture of the as-synthesized material, which in turn has 3 times the activity of the polymer melon, the literature benchmark. These results highlight the role of "defects", i.e., chain terminations, in increasing the catalytic activity of carbon nitrides and at the same time point to the ample potential of intrinsically improving the photocatalytic activity of "carbon nitride", especially through the selective synthesis of the active phase.

  17. Origin of noncoding DNA sequences: molecular fossils of genome evolution.

    PubMed

    Naora, H; Miyahara, K; Curnow, R N

    1987-09-01

    The total amount of noncoding sequences on chromosomes of contemporary organisms varies significantly from species to species. We propose a hypothesis for the origin of these noncoding sequences that assumes that (i) an approximately equal to 0.55-kilobase (kb)-long reading frame composed the primordial gene and (ii) a 20-kb-long single-stranded polynucleotide is the longest molecule (as a genome) that was polymerized at random and without a specific template in the primordial soup/cell. The statistical distribution of stop codons allows examination of the probability of generating reading frames of approximately equal to 0.55 kb in this primordial polynucleotide. This analysis reveals that with three stop codons, a run of at least 0.55-kb equivalent length of nonstop codons would occur in 4.6% of 20-kb-long polynucleotide molecules. We attempt to estimate the total amount of noncoding sequences that would be present on the chromosomes of contemporary species assuming that present-day chromosomes retain the prototype primordial genome structure. Theoretical estimates thus obtained for most eukaryotes do not differ significantly from those reported for these specific organisms, with only a few exceptions. Furthermore, analysis of possible stop-codon distributions suggests that life on earth would not exist, at least in its present form, had two or four stop codons been selected early in evolution.

  18. Phylogeography and molecular evolution of potato virus Y.

    PubMed

    Cuevas, José M; Delaunay, Agnès; Visser, Johan C; Bellstedt, Dirk U; Jacquot, Emmanuel; Elena, Santiago F

    2012-01-01

    Potato virus Y (PVY) is an important plant pathogen, whose host range includes economically important crops such as potato, tobacco, tomato, and pepper. PVY presents three main strains (PVY(O), PVY(N) and PVY(C)) and several recombinant forms. PVY has a worldwide distribution, yet the mechanisms that promote and maintain its population structure and genetic diversity are still unclear. In this study, we used a pool of 77 complete PVY genomes from isolates collected worldwide. After removing the effect of recombination in our data set, we used bayesian techniques to study the influence of geography and host species in both PVY population structure and dynamics. We have also performed selection and covariation analyses to identify evolutionarily relevant amino acid residues. Our results show that both geographic and host-driven adaptations explain PVY diversification. Furthermore, purifying selection is the main force driving PVY evolution, although some indications of positive selection accounted for the diversification of the different strains. Interestingly, the analysis of P3N-PIPO, a recently described gene in potyviruses, seems to show a variable length among the isolates analyzed, and this variability is explained, in part, by host-driven adaptation.

  19. Molecular evolution of GPCRs: GLP1/GLP1 receptors.

    PubMed

    Hwang, Jong-Ik; Yun, Seongsik; Moon, Mi Jin; Park, Cho Rong; Seong, Jae Young

    2014-06-01

    Glucagon-like peptide 1 (GLP1) is an intestinal incretin that regulates glucose homeostasis through stimulation of insulin secretion from pancreatic β-cells and inhibits appetite by acting on the brain. Thus, it is a promising therapeutic agent for the treatment of type 2 diabetes mellitus and obesity. Studies using synteny and reconstructed ancestral chromosomes suggest that families for GLP1 and its receptor (GLP1R) have emerged through two rounds (2R) of whole genome duplication and local gene duplications before and after 2R. Exon duplications have also contributed to the expansion of the peptide family members. Specific changes in the amino acid sequence following exon/gene/genome duplications have established distinct yet related peptide and receptor families. These specific changes also confer selective interactions between GLP1 and GLP1R. In this review, we present a possible macro (genome level)- and micro (gene/exon level)-evolution mechanisms of GLP1 and GLP1R, which allows them to acquire selective interactions between this ligand-receptor pair. This information may provide critical insight for the development of potent therapeutic agents targeting GLP1R.

  20. Molecular genetics and evolution of melanism in the cat family.

    PubMed

    Eizirik, Eduardo; Yuhki, Naoya; Johnson, Warren E; Menotti-Raymond, Marilyn; Hannah, Steven S; O'Brien, Stephen J

    2003-03-04

    Melanistic coat coloration occurs as a common polymorphism in 11 of 37 felid species and reaches high population frequency in some cases but never achieves complete fixation. To investigate the genetic basis, adaptive significance, and evolutionary history of melanistic variants in the Felidae, we mapped, cloned, and sequenced the cat homologs of two putative candidate genes for melanism (ASIP [agouti] and MC1R) and identified three independent deletions associated with dark coloration in three different felid species. Association and transmission analyses revealed that a 2 bp deletion in the ASIP gene specifies black coloration in domestic cats, and two different "in-frame" deletions in the MC1R gene are implicated in melanism in jaguars and jaguarundis. Melanistic individuals from five other felid species did not carry any of these mutations, implying that there are at least four independent genetic origins for melanism in the cat family. The inferred multiple origins and independent historical elevation in population frequency of felid melanistic mutations suggest the occurrence of adaptive evolution of this visible phenotype in a group of related free-ranging species.

  1. Molecular phylogeny and evolution of the extinct bovid Myotragus balearicus.

    PubMed

    Lalueza-Fox, Carles; Shapiro, Beth; Bover, Pere; Alcover, Josep Antoni; Bertranpetit, Jaume

    2002-12-01

    Myotragus balearicus was a dwarf artiodactyl endemic to the Eastern Balearic Islands, where it evolved in isolation for more than 5 million years before becoming extinct between 3640 and 2135 cal BC (calibrated years BC). Numerous unusual apomorphies obscure the relationship between Myotragus and the extant Caprinae. Therefore, genetic data for this species would significantly contribute to the clarification of its taxonomic position. In this study, we amplify, sequence, and clone a 338-base pair (bp) segment of the mitochondrial cytochrome b (cyt b) gene from a >9Kyr Myotragus subfossil from la Cova des Gorgs (Mallorca). Our results confirm the phylogenetic affinity of Myotragus with the sheep (Ovis) and the takin (Budorcas). In each tree, the Myotragus branch is long in comparison with the other taxa, which may be evidence of a local change in the rate of evolution in cyt b. This rate change may be due to in part to an early age of first reproduction and short generation time in Myotragus, factors that are potentially related to the extreme reduction in size of the adult Myotragus as compared to the other Caprinae.

  2. [Modern evolutional developmental biology: mechanical and molecular genetic or phenotypic approaches?].

    PubMed

    Vorob'eva, É I

    2010-01-01

    Heightened interest in the evolutionary problems of developmental biology in the 1980s was due to the success of molecular genetics and disappointment in the synthetic theory of evolution, where the chapters of embryology and developmental biology seem to have been left out. Modern evo-devo, which turned out to be antipodean to the methodology of the synthetic theory of evolution, propagandized in the development of evolutionary problems only the mechanical and molecular genetic approach to the evolution of ontogenesis, based on cellular and intercellular interactions. The phonotypical approach to the evaluation of evolutionary occurrences in ontogenesis, which aids in the joining of the genetic and epigenetic levels of research, the theory of natural selection, the nomogenetic conception, and the problem of the wholeness of the organism in onto- and phylogenesis may be against this. The phenotypic approach to ontogenesis is methodologically the most perspective for evolutionary developmental biology.

  3. Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny.

    PubMed

    Shibusawa, M; Nishibori, M; Nishida-Umehara, C; Tsudzuki, M; Masabanda, J; Griffin, D K; Matsuda, Y

    2004-01-01

    To define the process of karyotypic evolution in the Galliformes on a molecular basis, we conducted genome-wide comparative chromosome painting for eight species, i.e. silver pheasant (Lophura nycthemera), Lady Amherst's pheasant (Chrysolophus amherstiae), ring-necked pheasant (Phasianus colchicus), turkey (Meleagris gallopavo), Western capercaillie (Tetrao urogallus), Chinese bamboo-partridge (Bambusicola thoracica) and common peafowl (Pavo cristatus) of the Phasianidae, and plain chachalaca (Ortalis vetula) of the Cracidae, with chicken DNA probes of chromosomes 1-9 and Z. Including our previous data from five other species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and blue-breasted quail (Coturnix chinensis) of the Phasianidae, guinea fowl (Numida meleagris) of the Numididae and California quail (Callipepla californica) of the Odontophoridae, we represented the evolutionary changes of karyotypes in the 13 species of the Galliformes. In addition, we compared the cytogenetic data with the molecular phylogeny of the 13 species constructed with the nucleotide sequences of the mitochondrial cytochrome b gene, and discussed the process of karyotypic evolution in the Galliformes. Comparative chromosome painting confirmed the previous data on chromosome rearrangements obtained by G-banding analysis, and identified several novel chromosome rearrangements. The process of the evolutionary changes of macrochromosomes in the 13 species was in good accordance with the molecular phylogeny, and the ancestral karyotype of the Galliformes is represented.

  4. Are Molecular Alphabets Universal Enabling Factors for the Evolution of Complex Life?

    NASA Astrophysics Data System (ADS)

    Dunn, Ian S.

    2013-12-01

    Terrestrial biosystems depend on macromolecules, and this feature is often considered as a likely universal aspect of life. While opinions differ regarding the importance of small-molecule systems in abiogenesis, escalating biological functional demands are linked with increasing complexity in key molecules participating in biosystem operations, and many such requirements cannot be efficiently mediated by relatively small compounds. It has long been recognized that known life is associated with the evolution of two distinct molecular alphabets (nucleic acid and protein), specific sequence combinations of which serve as informational and functional polymers. In contrast, much less detailed focus has been directed towards the potential universal need for molecular alphabets in constituting complex chemically-based life, and the implications of such a requirement. To analyze this, emphasis here is placed on the generalizable replicative and functional characteristics of molecular alphabets and their concatenates. A primary replicative alphabet based on the simplest possible molecular complementarity can potentially enable evolutionary processes to occur, including the encoding of secondarily functional alphabets. Very large uniquely specified (`non-alphabetic') molecules cannot feasibly underlie systems capable of the replicative and evolutionary properties which characterize complex biosystems. Transitions in the molecular evolution of alphabets can be related to progressive bridging of barriers which enable higher levels of biosystem organization. It is thus highly probable that molecular alphabets are an obligatory requirement for complex chemically-based life anywhere in the universe. In turn, reference to molecular alphabets should be usefully applied in current definitions of life.

  5. Advances on molecular mechanism of the adaptive evolution of Chiroptera (bats).

    PubMed

    Yunpeng, Liang; Li, Yu

    2015-01-01

    As the second biggest animal group in mammals, Chiroptera (bats) demonstrates many unique adaptive features in terms of flight, echolocation, auditory acuity, feeding habit, hibernation and immune defense, providing an excellent system for understanding the molecular basis of how organisms adapt to the living environments encountered. In this review, we summarize the researches on the molecular mechanism of the adaptive evolution of Chiroptera, especially the recent researches at the genome levels, suggesting a far more complex evolutionary pattern and functional diversity than previously thought. In the future, along with the increasing numbers of Chiroptera species genomes available, new evolutionary patterns and functional divergence will be revealed, which can promote the further understanding of this animal group and the molecular mechanism of adaptive evolution.

  6. Molecular evolution of the mammalian ribosomal protein gene, RPS14.

    PubMed

    Rhoads, D D; Roufa, D J

    1991-07-01

    Ribosomal protein S14 genes (RPS14) in eukaryotic species from protozoa to primates exhibit dramatically different intron-exon structures yet share homologous polypeptide-coding sequences. To recognize common features of RPS14 gene architectures in closely related mammalian species and to evaluate similarities in their noncoding DNA sequences, we isolated the intron-containing S14 locus from Chinese hamster ovary (CHO) cell DNA by using a PCR strategy and compared it with human RPS14. We found that rodent and primate S14 genes are composed of identical protein-coding exons interrupted by introns at four conserved DNA sites. However, the structures of corresponding CHO and human RPS14 introns differ significantly. Nonetheless, individual intron splice donor, splice acceptor, and upstream flanking motifs have been conserved within mammalian S14 homologues as well as within RPS14 gene fragments PCR amplified from other vertebrate genera (birds and bony fish). Our data indicate that noncoding, intronic DNA sequences within highly conserved, single-copy ribosomal protein genes are useful molecular landmarks for phylogenetic analysis of closely related vertebrate species.

  7. Mesoamerican tree squirrels evolution (Rodentia: Sciuridae): a molecular phylogenetic analysis.

    PubMed

    Villalobos, Federico; Gutierrez-Espeleta, Gustavo

    2014-06-01

    The tribe Sciurini comprehends the genera Sciurus, Syntheosiurus, Microsciurus, Tamiasciurus and Rheinthrosciurus. The phylogenetic relationships within Sciurus have been only partially done, and the relationship between Mesoamerican species remains unsolved. The phylogenetic relationships of the Mesoamerican tree squirrels were examined using molecular data. Sequence data publicly available (12S, 16S, CYTB mitochondrial genes and IRBP nuclear gene) and cytochrome B gene sequences of four previously not sampled Mesoamerican Sciurus species were analyzed under a Bayesian multispecies coalescence model. Phylogenetic analysis of the multilocus data set showed the neotropical tree squirrels as a monophyletic clade. The genus Sciurus was paraphyletic due to the inclusion of Microsciurus species (M. alfari and M. flaviventer). The South American species S. aestuans and S. stramineus showed a sister taxa relationship. Single locus analysis based on the most compact and complete data set (i.e. CYTB gene sequences), supported the monophyly of the South American species and recovered a Mesoamerican clade including S. aureogaster, S. granatensis and S. variegatoides. These results corroborated previous findings based on cladistic analysis of cranial and post-cranial characters. Our data support a close relationship between Mesoamerican Sciurus species and a sister relationship with South American species, and corroborates previous findings in relation to the polyphyly of Microsciurus and Syntheosciurus paraphyly.

  8. Two Types of Molecular Evolution. Evidence from Studies of Interspecific Hybridization

    PubMed Central

    Wilson, A. C.; Maxson, L. R.; Sarich, V. M.

    1974-01-01

    To assess the significance of macromolecular sequence differences among species, we compared the serum albumins of 81 pairs of vertebrate species capable of producing viable hybrids. Micro-complement fixation experiments showed that the average difference between the albumins within such pairs was only 3 immunological distance units for placental mammals (31 pairs), but 36 units for frogs (50 pairs). Albumin immunological distance is strongly correlated with other measures of genetic distance, including those made with DNA annealing techniques. It therefore seems likely that mammalian species pairs capable of hybridization are far more similar at the macromolecular sequence level than is the case for most hybridizable frogs. We think the most likely explanation for the marked molecular restriction on hybridization among mammals is that the ratio of regulatory evolution to protein evolution is higher for mammals than for frogs. Mammals may have experienced unusually rapid regulatory evolution; indeed, this could be the factor responsible for their unusually rapid anatomical evolution. Images PMID:4212492

  9. Parasitic plants have increased rates of molecular evolution across all three genomes

    PubMed Central

    2013-01-01

    Background Theoretical models and experimental evidence suggest that rates of molecular evolution could be raised in parasitic organisms compared to non-parasitic taxa. Parasitic plants provide an ideal test for these predictions, as there are at least a dozen independent origins of the parasitic lifestyle in angiosperms. Studies of a number of parasitic plant lineages have suggested faster rates of molecular evolution, but the results of some studies have been mixed. Comparative analysis of all parasitic plant lineages, including sequences from all three genomes, is needed to examine the generality of the relationship between rates of molecular evolution and parasitism in plants. Results We analysed DNA sequence data from the mitochondrial, nuclear and chloroplast genomes for 12 independent evolutionary origins of parasitism in angiosperms. We demonstrated that parasitic lineages have a faster rate of molecular evolution than their non-parasitic relatives in sequences for all three genomes, for both synonymous and nonsynonymous substitutions. Conclusions Our results prove that raised rates of molecular evolution are a general feature of parasitic plants, not confined to a few taxa or specific genes. We discuss possible causes for this relationship, including increased positive selection associated with host-parasite arms races, relaxed selection, reduced population size or repeated bottlenecks, increased mutation rates, and indirect causal links with generation time and body size. We find no evidence that faster rates are due to smaller effective populations sizes or changes in selection pressure. Instead, our results suggest that parasitic plants have a higher mutation rate than their close non-parasitic relatives. This may be due to a direct connection, where some aspect of the parasitic lifestyle drives the evolution of raised mutation rates. Alternatively, this pattern may be driven by an indirect connection between rates and parasitism: for example, parasitic

  10. Reconstructing web evolution and spider diversification in the molecular era.

    PubMed

    Blackledge, Todd A; Scharff, Nikolaj; Coddington, Jonathan A; Szüts, Tamas; Wenzel, John W; Hayashi, Cheryl Y; Agnarsson, Ingi

    2009-03-31

    The evolutionary diversification of spiders is attributed to spectacular innovations in silk. Spiders are unique in synthesizing many different kinds of silk, and using silk for a variety of ecological functions throughout their lives, particularly to make prey-catching webs. Here, we construct a broad higher-level phylogeny of spiders combining molecular data with traditional morphological and behavioral characters. We use this phylogeny to test the hypothesis that the spider orb web evolved only once. We then examine spider diversification in relation to different web architectures and silk use. We find strong support for a single origin of orb webs, implying a major shift in the spinning of capture silk and repeated loss or transformation of orb webs. We show that abandonment of costly cribellate capture silk correlates with the 2 major diversification events in spiders (1). Replacement of cribellate silk by aqueous silk glue may explain the greater diversity of modern orb-weaving spiders (Araneoidea) compared with cribellate orb-weaving spiders (Deinopoidea) (2). Within the "RTA clade," which is the sister group to orb-weaving spiders and contains half of all spider diversity, >90% of species richness is associated with repeated loss of cribellate silk and abandonment of prey capture webs. Accompanying cribellum loss in both groups is a release from substrate-constrained webs, whether by aerially suspended webs, or by abandoning webs altogether. These behavioral shifts in silk and web production by spiders thus likely played a key role in the dramatic evolutionary success and ecological dominance of spiders as predators of insects.

  11. Molecular systematics and evolution of the Cyanocorax jays.

    PubMed

    Bonaccorso, Elisa; Peterson, A Townsend; Navarro-Sigüenza, Adolfo G; Fleischer, Robert C

    2010-03-01

    Phylogenetic relationships were studied in the genus Cyanocorax (Aves: Corvidae) and related genera, Psilorhinus and Calocitta, a diverse group of New World jays distributed from the southern United States south to Argentina. Although the ecology and behavior of some species in the group have been studied extensively, lack of a molecular phylogeny has precluded rigorous interpretations in an evolutionary framework. Given the diverse combinations of plumage coloration, size, and morphology, the taxonomy of the group has been inconsistent and understanding of biogeographic patterns problematic. Moreover, plumage similarity between two geographically disjuct species, the Tufted jay (Cyanocorax dickeyi) from western Mexico and the White-tailed jay (C. mystacalis) from western Ecuador and Peru, has puzzled ornithologists for decades. Here, a phylogeny of all species in the three genera is presented, based on study of two mitochondrial and three nuclear genes. Phylogenetic trees revealed the non-monophyly of Cyanocorax, and the division of the whole assemblage in two groups: "Clade A" containing Psilorhinus morio, both species in Calocitta,Cyanocorax violaceus, C. caeruleus, C. cristatellus, and C. cyanomelas, and "Clade B" consisting of the remaining species in Cyanocorax. Relationships among species in Clade A were ambiguous and, in general, not well resolved. Within Clade B, analyses revealed the monophyly of the "Cissilopha" jays and showed no evidence for a sister relationship between C. mystacalis and C. dickeyi. The phylogenetic complexity of lineages in the group suggests several complications for the understanding biogeographic patterns, as well as for proposing a taxonomy that is consistent with morphological variation. Although multiple taxonomic arrangements are possible, recommendations are for recognizing only one genus, Cyanocorax, with Psilorhinus and Calocitta as synonyms.

  12. DNA Re-EvolutioN: a game for learning molecular genetics and evolution.

    PubMed

    Miralles, Laura; Moran, Paloma; Dopico, Eduardo; Garcia-Vazquez, Eva

    2013-01-01

    Evolution is a main concept in biology, but not many students understand how it works. In this article we introduce the game DNA Re-EvolutioN as an active learning tool that uses genetic concepts (DNA structure, transcription and translation, mutations, natural selection, etc.) as playing rules. Students will learn about molecular evolution while playing a game that mixes up theory and entertainment. The game can be easily adapted to different educational levels. The main goal of this play is to arrive at the end of the game with the longest protein. Students play with pawns and dices, a board containing hypothetical events (mutations, selection) that happen to molecules, "Evolution cards" with indications for DNA mutations, prototypes of a DNA and a mRNA chain with colored "nucleotides" (plasticine balls), and small pieces simulating t-RNA with aminoacids that will serve to construct a "protein" based on the DNA chain. Students will understand how changes in DNA affect the final protein product and may be subjected to positive or negative selection, using a didactic tool funnier than classical theory lectures and easier than molecular laboratory experiments: a flexible and feasible game to learn and enjoy molecular evolution at no-cost. The game was tested by majors and non-majors in genetics from 13 different countries and evaluated with pre- and post-tests obtaining very positive results.

  13. Modelling the chemical evolution of molecular clouds as a function of metallicity

    NASA Astrophysics Data System (ADS)

    Penteado, E. M.; Cuppen, H. M.; Rocha-Pinto, H. J.

    2014-04-01

    The Galaxy is in continuous elemental evolution. Since new elements produced by dying stars are delivered to the interstellar medium, the formation of new generations of stars and planetary systems is influenced by this metal enrichment. We aim to study the role of the metallicity on the gas phase chemistry of the interstellar medium. Using a system of coupled ordinary differential equations to model the chemical reactions, we simulate the evolution of the abundance of molecules in the gas phase for different initial interstellar elemental compositions. These varying initial elemental compositions consider the change in the `elemental abundances' predicted by a self-consistent model of the elemental evolution of the Galaxy. As far as we are aware, this is the first attempt to combine elemental evolution of the Galaxy and chemical evolution of molecular clouds. The metallicity was found to have a strong effect on the overall gas phase composition. With decreasing metallicity, the number of long carbon chains was found to increase, the time-scale on which small molecular species are increases, and the main form of oxygen changed from O and CO to O2. These effects were found to be mainly due to the change in electron, H_3^+, and atomic oxygen abundance.

  14. Diet and our genetic legacy in the recent anthropocene: a Darwinian perspective to nutritional health.

    PubMed

    Lucock, Mark D; Martin, Charlotte E; Yates, Zoe R; Veysey, Martin

    2014-01-01

    Nutrient-gene research tends to focus on human disease, although such interactions are often a by-product of our evolutionary heritage. This review explores health in this context, reframing genetic variation/epigenetic phenomena linked to diet in the framework of our recent evolutionary past. This "Darwinian/evolutionary medicine" approach examines how diet helped us evolve among primates and to adapt (or fail to adapt) our metabolome to specific environmental conditions leading to major diseases of civilization. This review presents updated evidence from a diet-gene perspective, portraying discord that exists with respect to health and our overall nutritional, cultural, and activity patterns. While Darwinian theory goes beyond nutritional considerations, a significant component within this concept does relate to nutrition and the mismatch between genes, modern diet, obesogenic lifestyle, and health outcomes. The review argues that nutritional sciences should expand knowledge on the evolutionary connection between food and disease, assimilating it into clinical training with greater prominence.

  15. Darwinian fitness and the intensity of natural selection: studies in sensitivity analysis.

    PubMed

    Demetrius, Lloyd; Matthias Gundlach, Volker; Ziehe, Martin

    2007-12-21

    Darwinian fitness, the capacity of a variant type to establish itself in competition with the resident population, is determined by evolutionary entropy, a measure of the uncertainty in age of the mother of a randomly chosen newborn. This article shows that the intensity of natural selection, as measured by the sensitivity of entropy with respect to changes in the age-specific fecundity and mortality variables, is a convex function of age, decreasing at early and increasing at later ages. We exploit this result to provide quantitative evolutionary explanations of the large variation in survivorship curves observed in natural populations. Previous studies to explain variation in survivorship curves have been based on the proposition that Darwinian fitness is determined by the Malthusian parameter. Hence the intensity of natural selection will be determined by the sensitivity of the Malthusian parameter with respect to changes in the age-specific fecundity and mortality variables. This measure of the selection gradient is known to be a decreasing function of age, with implications which are inconsistent with empirical observations of survivorship curves in human and animal populations. The analysis described in this paper point to the mitigated import of sensitivity studies based on the Malthusian parameter. Our analysis provides theoretical and empirical support for the ecological and evolutionary significance of sensitivity analysis based on entropy, which is the appropriate measure of Darwinian fitness.

  16. The pattern of mammalian evolution and the relative rate of molecular evolution

    SciTech Connect

    Easteal, S. )

    1990-01-01

    The rates of nucleotide substitution at four genes in four orders of eutherian mammals are compared in relative rate tests using marsupial orthologs for reference. There is no evidence of systematic variation in evolutionary rate among the orders. The sequences are used to reconstruct the phylogeny of the orders using maximum likelihood, parsimony and compatibility methods. A branching order of rodent then ungulate then primate and lagomorph is overwhelmingly indicated. The nodes of the nucleotide based cladograms are widely separated in relation to the total lengths of the branches. The assumption of a star phylogeny that underlies Kimura's test for molecular evolutionary rate variation is shown to be invalid for eutherian mammals. Excess variance in nucleotide or amino acid differences between mammalian orders, above that predicted by neutral theory is explained better by variation in divergence time than by variation in evolutionary rate.

  17. The Molecular Basis of Evolution and Disease: A Cold War Alliance.

    PubMed

    Suárez-Díaz, Edna

    2017-03-28

    This paper extends previous arguments against the assumption that the study of variation at the molecular level was instigated with a view to solving an internal conflict between the balance and classical schools of population genetics. It does so by focusing on the intersection of basic research in protein chemistry and the molecular approach to disease with the enactment of global health campaigns during the Cold War period. The paper connects advances in research on protein structure and function as reflected in Christian Anfinsen´s The molecular basis of evolution, with a political reading of Emilé Zuckerkandl and Linus Pauling's identification of molecular disease and evolution. Beyond atomic fallout, these advances constituted a rationale for the promotion of genetic surveys of human populations in the Third World, in connection with international health programs. Light is shed not only on the experimental roots of the molecular challenge but on the broader geopolitical context where the rising role of biomedicine and public health (particularly the malaria eradication campaigns) had an impact on evolutionary biology.

  18. Morphological and Molecular Evolution Are Not Linked in Lamellodiscus (Plathyhelminthes, Monogenea)

    PubMed Central

    Poisot, Timothée; Verneau, Olivier; Desdevises, Yves

    2011-01-01

    Lamellodiscus Johnston & Tiegs 1922 (Monogenea, Diplectanidae) is a genus of common parasites on the gills of sparid fishes. Here we show that this genus is probably undergoing a fast molecular diversification, as reflected by the important genetic variability observed within three molecular markers (partial nuclear 18S rDNA, Internal Transcribed Spacer 1, and mitonchondrial Cytochrome Oxidase I). Using an updated phylogeny of this genus, we show that molecular and morphological evolution are weakly correlated, and that most of the morphologically defined taxonomical units are not consistent with the molecular data. We suggest that Lamellodiscus morphology is probably constrained by strong environmental (host-induced) pressure, and discuss why this result can apply to other taxa. Genetic variability within nuclear 18S and mitochondrial COI genes are compared for several monogenean genera, as this measure may reflect the level of diversification within a genus. Overall our results suggest that cryptic speciation events may occur within Lamellodiscus, and discuss the links between morphological and molecular evolution. PMID:22022582

  19. Evolution of molecular clouds in the starburst galaxy NGC 1808 revealed with ALMA

    NASA Astrophysics Data System (ADS)

    Salak, D.; Nakai, N.; Miyamoto, Y.

    2015-05-01

    We present large-field CO(1-0) observations of the starburst galaxy NGC 1808 conducted with ALMA. High-resolution (˜100 pc) images reveal a high concentration of molecular gas in the nucleus, 500-pc ring, gas-rich bar, and spiral arms. We derived the bar pattern speed and found an offset between CO and Hα emission peaks in the offset ridges along the bar. The results indicate that the evolution of molecular clouds on the galactic scale is driven by bar dynamics.

  20. Development of a Dinitrosyl Iron Complex Molecular Catalyst into a Hydrogen Evolution Cathode.

    PubMed

    Chiou, Tzung-Wen; Lu, Tsai-Te; Wu, Ying-Hao; Yu, Yi-Ju; Chu, Li-Kang; Liaw, Wen-Feng

    2015-12-01

    Despite extensive efforts, the electrocatalytic reduction of water using homogeneous/heterogeneous Fe, Co, Ni, Cu, W, and Mo complexes remains challenging because of issues involving the development of efficient, recyclable, stable, and aqueous-compatible catalysts. In this study, evolution of the de novo designed dinitrosyl iron complex DNIC-PMDTA from a molecular catalyst into a solid-state hydrogen evolution cathode, considering all the parameters to fulfill the electronic and structural requirements of each step of the catalytic cycle, is demonstrated. DNIC-PMDTA reveals electrocatalytic reduction of water at neutral and basic media, whereas its deposit on electrode preserves exceptional longevity, 139 h. This discovery will initiate a systematic study on the assembly of [Fe(NO)2] motif into current collector for mass production of H2, whereas the efficiency remains tailored by its molecular precursor [(L)Fe(NO)2].

  1. Evolution of land plants: insights from molecular studies on basal lineages.

    PubMed

    Ishizaki, Kimitsune

    2017-01-01

    The invasion of the land by plants, or terrestrialization, was one of the most critical events in the history of the Earth. The evolution of land plants included significant transformations in body plans: the emergence of a multicellular diploid sporophyte, transition from gametophyte-dominant to sporophyte-dominant life histories, and development of many specialized tissues and organs, such as stomata, vascular tissues, roots, leaves, seeds, and flowers. Recent advances in molecular genetics in two model basal plants, bryophytes Physcomitrella patens and Marchantia polymorpha, have begun to provide answers to several key questions regarding land plant evolution. This paper discusses the evolution of the genes and regulatory mechanisms that helped drive such significant morphological innovations among land-based plants.

  2. Darwinian sex roles confirmed across the animal kingdom

    PubMed Central

    Janicke, Tim; Häderer, Ines K.; Lajeunesse, Marc J.; Anthes, Nils

    2016-01-01

    Since Darwin’s conception of sexual selection theory, scientists have struggled to identify the evolutionary forces underlying the pervasive differences between male and female behavior, morphology, and physiology. The Darwin-Bateman paradigm predicts that anisogamy imposes stronger sexual selection on males, which, in turn, drives the evolution of conventional sex roles in terms of female-biased parental care and male-biased sexual dimorphism. Although this paradigm forms the cornerstone of modern sexual selection theory, it still remains untested across the animal tree of life. This lack of evidence has promoted the rise of alternative hypotheses arguing that sex differences are entirely driven by environmental factors or chance. We demonstrate that, across the animal kingdom, sexual selection, as captured by standard Bateman metrics, is indeed stronger in males than in females and that it is evolutionarily tied to sex biases in parental care and sexual dimorphism. Our findings provide the first comprehensive evidence that Darwin’s concept of conventional sex roles is accurate and refute recent criticism of sexual selection theory. PMID:26933680

  3. Darwinian sex roles confirmed across the animal kingdom.

    PubMed

    Janicke, Tim; Häderer, Ines K; Lajeunesse, Marc J; Anthes, Nils

    2016-02-01

    Since Darwin's conception of sexual selection theory, scientists have struggled to identify the evolutionary forces underlying the pervasive differences between male and female behavior, morphology, and physiology. The Darwin-Bateman paradigm predicts that anisogamy imposes stronger sexual selection on males, which, in turn, drives the evolution of conventional sex roles in terms of female-biased parental care and male-biased sexual dimorphism. Although this paradigm forms the cornerstone of modern sexual selection theory, it still remains untested across the animal tree of life. This lack of evidence has promoted the rise of alternative hypotheses arguing that sex differences are entirely driven by environmental factors or chance. We demonstrate that, across the animal kingdom, sexual selection, as captured by standard Bateman metrics, is indeed stronger in males than in females and that it is evolutionarily tied to sex biases in parental care and sexual dimorphism. Our findings provide the first comprehensive evidence that Darwin's concept of conventional sex roles is accurate and refute recent criticism of sexual selection theory.

  4. Ecological and Lineage-Specific Factors Drive the Molecular Evolution of Rhodopsin in Cichlid Fishes.

    PubMed

    Torres-Dowdall, Julián; Henning, Frederico; Elmer, Kathryn R; Meyer, Axel

    2015-11-01

    The visual system in the colorful cichlid fishes from the African great lakes is believed to be important for their adaptive radiations. However, few studies have attempted to compare the visual system of radiating cichlid lineages with that of cichlids that have not undergone recent radiations. One such study published in this journal (Schott RK, Refvik SP, Hauser FE, López-Fernández H, Chang BSW. 2014. Divergent positive selection in rhodopsin from lake and riverine cichlid fishes. Mol Biol Evol. 31:1149-1165) found divergent selection on rhodopsin between African lacustrine and riverine cichlid species and riverine Neotropical cichlids, concluding that ecology drives the molecular evolution of this opsin. Here, we expand this analysis by incorporating rhodopsin sequences from Neotropical lacustrine cichlids and show that both ecology and phylogeny are important drivers of the molecular evolution of rhodopsin in cichlids. We found little overlap of sites under selection between African and Neotropical lineages and a faster rate of molecular evolution in African compared with Neotropical cichlids. These results support the notion that genetic or population genetic features particular to African cichlids contributed to their radiations.

  5. Five molecular markers reveal extensive morphological homoplasy and reticulate evolution in the Malva alliance (Malvaceae).

    PubMed

    Escobar García, Pedro; Schönswetter, Peter; Fuertes Aguilar, Javier; Nieto Feliner, Gonzalo; Schneeweiss, Gerald M

    2009-02-01

    The Malva alliance is a well-defined group with extensive morphological homoplasy. As a result, the relationships among the taxa as well as the evolution of morphological traits have remained elusive and the traditional classifications are highly artificial. Using five molecular markers (nuclear ITS, plastid matK plus trnK, ndhF, trnL-trnF, psbA-trnH), we arrived at a phylogenetic hypothesis of this group, the genera Alcea, Althaea and Malvalthaea being studied here for the first time with molecular data. Althaea and, in particular, Lavatera and Malva are highly polyphyletic as currently circumscribed, because their diagnostic characters, the number and degree of fusion of the epicalyx bracts, evolve in a highly homoplasious manner. In contrast, fruit morphology largely agrees with the molecularly delimited groups. Hybrid origins confirmed for the genus Malvalthaea and for Lavatera mauritanica and hybridization in the group of ruderal small-flowered mallows underline the importance of reticulate evolution in shaping the history of this group and complicating the interpretation of morphological evolution.

  6. A new model for biological effects of radiation and the driven force of molecular evolution

    NASA Astrophysics Data System (ADS)

    Wada, Takahiro; Manabe, Yuichiro; Nakajima, Hiroo; Tsunoyama, Yuichi; Bando, Masako

    We proposed a new mathematical model to estimate biological effects of radiation, which we call Whack-A-Mole (WAM) model. A special feature of WAM model is that it involves the dose rate of radiation as a key ingredient. We succeeded to reproduce the experimental data of various species concerning the radiation induced mutation frequencies. From the analysis of the mega-mouse experiments, we obtained the mutation rate per base-pair per year for mice which is consistent with the so-called molecular clock in evolution genetics, 10-9 mutation/base-pair/year. Another important quantity is the equivalent dose rate for the whole spontaneous mutation, deff. The value of deff for mice is 1.1*10-3 Gy/hour which is much larger than the dose rate of natural radiation (10- (6 - 7) Gy/hour) by several orders of magnitude. We also analyzed Drosophila data and obtained essentially the same numbers. This clearly indicates that the natural radiation is not the dominant driving force of the molecular evolution, but we should look for other factors, such as miscopy of DNA in duplication process. We believe this is the first quantitative proof of the small contribution of the natural radiation in the molecular evolution.

  7. Sodium channel genes and the evolution of diversity in communication signals of electric fishes: convergent molecular evolution.

    PubMed

    Zakon, Harold H; Lu, Ying; Zwickl, Derrick J; Hillis, David M

    2006-03-07

    We investigated whether the evolution of electric organs and electric signal diversity in two independently evolved lineages of electric fishes was accompanied by convergent changes on the molecular level. We found that a sodium channel gene (Na(v)1.4a) that is expressed in muscle in nonelectric fishes has lost its expression in muscle and is expressed instead in the evolutionarily novel electric organ in both lineages of electric fishes. This gene appears to be evolving under positive selection in both lineages, facilitated by its restricted expression in the electric organ. This view is reinforced by the lack of evidence for selection on this gene in one electric species in which expression of this gene is retained in muscle. Amino acid replacements occur convergently in domains that influence channel inactivation, a key trait for shaping electric communication signals. Some amino acid replacements occur at or adjacent to sites at which disease-causing mutations have been mapped in human sodium channel genes, emphasizing that these replacements occur in functionally important domains. Selection appears to have acted on the final step in channel inactivation, but complementarily on the inactivation "ball" in one lineage, and its receptor site in the other lineage. Thus, changes in the expression and sequence of the same gene are associated with the independent evolution of signal complexity.

  8. Influence of shear motion on evolution of molecular clouds in the spiral galaxy M 51

    NASA Astrophysics Data System (ADS)

    Miyamoto, Yusuke; Nakai, Naomasa; Kuno, Nario

    2014-04-01

    We have investigated the dynamics of the molecular gas and the evolution of giant molecular associations (GMAs) in the spiral galaxy M 51 with the Nobeyama Radio Observatory 45-m telescope. The velocity components of the molecular gas perpendicular and parallel to the spiral arms are derived at each spiral phase from the distribution of the line-of-sight velocity of the CO gas. In addition, the shear motion in the galactic disk is determined from the velocity vectors at each spiral phase. It is revealed that the distributions of the shear strength and of GMAs are anti-correlated. GMAs exist only in the area of the weak shear strength and further on the upstream side of the high shear strength. GMAs and most giant molecular clouds (GMCs) exist in the regions where the shear critical surface density is smaller than the gravitational critical surface density, indicating that they can stably grow by self-gravity and the collisional agglomeration of small clouds without being destroyed by shear motion. These factors indicate that the shear motion is an important factor in evolution of GMCs and GMAs.

  9. Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity.

    PubMed

    Bartlett, Madelaine E; Whipple, Clinton J

    2013-10-10

    Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism's phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection's source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; altered protein-protein interactions; altered domain content; altered activity as an activator or repressor; altered protein stability; and hypomorphic and hypermorphic alleles. There was also variability in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution.

  10. Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity

    PubMed Central

    Bartlett, Madelaine E.; Whipple, Clinton J.

    2013-01-01

    Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism’s phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection’s source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; altered protein–protein interactions; altered domain content; altered activity as an activator or repressor; altered protein stability; and hypomorphic and hypermorphic alleles. There was also variability in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution. PMID:24124420

  11. Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata

    PubMed Central

    Maurer-Alcalá, Xyrus X.; Katz, Laura A.

    2016-01-01

    The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a “heteromeric” macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into “gene-sized” chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata, we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a “gene bank” that facilitates rapid changes in expression of genes required only in specific life history stages. By using “nonmodel” organisms like C. uncinata, we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features. PMID:27189988

  12. From the ultrasonic to the infrared: molecular evolution and the sensory biology of bats

    PubMed Central

    Jones, Gareth; Teeling, Emma C.; Rossiter, Stephen J.

    2013-01-01

    Great advances have been made recently in understanding the genetic basis of the sensory biology of bats. Research has focused on the molecular evolution of candidate sensory genes, genes with known functions [e.g., olfactory receptor (OR) genes] and genes identified from mutations associated with sensory deficits (e.g., blindness and deafness). For example, the FoxP2 gene, underpinning vocal behavior and sensorimotor coordination, has undergone diversification in bats, while several genes associated with audition show parallel amino acid substitutions in unrelated lineages of echolocating bats and, in some cases, in echolocating dolphins, representing a classic case of convergent molecular evolution. Vision genes encoding the photopigments rhodopsin and the long-wave sensitive opsin are functional in bats, while that encoding the short-wave sensitive opsin has lost functionality in rhinolophoid bats using high-duty cycle laryngeal echolocation, suggesting a sensory trade-off between investment in vision and echolocation. In terms of olfaction, bats appear to have a distinctive OR repertoire compared with other mammals, and a gene involved in signal transduction in the vomeronasal system has become non-functional in most bat species. Bitter taste receptors appear to have undergone a “birth-and death” evolution involving extensive gene duplication and loss, unlike genes coding for sweet and umami tastes that show conservation across most lineages but loss in vampire bats. Common vampire bats have also undergone adaptations for thermoperception, via alternative splicing resulting in the evolution of a novel heat-sensitive channel. The future for understanding the molecular basis of sensory biology is promising, with great potential for comparative genomic analyses, studies on gene regulation and expression, exploration of the role of alternative splicing in the generation of proteomic diversity, and linking genetic mechanisms to behavioral consequences. PMID

  13. From the ultrasonic to the infrared: molecular evolution and the sensory biology of bats.

    PubMed

    Jones, Gareth; Teeling, Emma C; Rossiter, Stephen J

    2013-01-01

    Great advances have been made recently in understanding the genetic basis of the sensory biology of bats. Research has focused on the molecular evolution of candidate sensory genes, genes with known functions [e.g., olfactory receptor (OR) genes] and genes identified from mutations associated with sensory deficits (e.g., blindness and deafness). For example, the FoxP2 gene, underpinning vocal behavior and sensorimotor coordination, has undergone diversification in bats, while several genes associated with audition show parallel amino acid substitutions in unrelated lineages of echolocating bats and, in some cases, in echolocating dolphins, representing a classic case of convergent molecular evolution. Vision genes encoding the photopigments rhodopsin and the long-wave sensitive opsin are functional in bats, while that encoding the short-wave sensitive opsin has lost functionality in rhinolophoid bats using high-duty cycle laryngeal echolocation, suggesting a sensory trade-off between investment in vision and echolocation. In terms of olfaction, bats appear to have a distinctive OR repertoire compared with other mammals, and a gene involved in signal transduction in the vomeronasal system has become non-functional in most bat species. Bitter taste receptors appear to have undergone a "birth-and death" evolution involving extensive gene duplication and loss, unlike genes coding for sweet and umami tastes that show conservation across most lineages but loss in vampire bats. Common vampire bats have also undergone adaptations for thermoperception, via alternative splicing resulting in the evolution of a novel heat-sensitive channel. The future for understanding the molecular basis of sensory biology is promising, with great potential for comparative genomic analyses, studies on gene regulation and expression, exploration of the role of alternative splicing in the generation of proteomic diversity, and linking genetic mechanisms to behavioral consequences.

  14. Eventful evolution of giant molecular clouds in dynamically evolving spiral arms

    NASA Astrophysics Data System (ADS)

    Baba, Junichi; Morokuma-Matsui, Kana; Saitoh, Takayuki R.

    2017-01-01

    The formation and evolution of giant molecular clouds (GMCs) in spiral galaxies have been investigated in the traditional framework of the combined quasi-stationary density wave and galactic shock model. In this study, we investigate the structure and evolution of GMCs in a dynamically evolving spiral arm using a three-dimensional N-body/hydrodynamic simulation of a barred spiral galaxy at parsec-scale resolution. This simulation incorporated self-gravity, molecular hydrogen formation, radiative cooling, heating due to interstellar far-ultraviolet radiation, and stellar feedback by both H II regions and Type II supernovae. In contrast to a simple expectation based on the traditional spiral model, the GMCs exhibited no systematic evolutionary sequence across the spiral arm. Our simulation showed that the GMCs behaved as highly dynamic objects with eventful lives involving collisional build-up, collision-induced star formation, and destruction via stellar feedback. The GMC lifetimes were predicted to be short, only a few tens of millions years. We also found that at least at the resolutions and with the feedback models used in this study, most of the GMCs without H II regions were collapsing, but half of the GMCs with H II regions were expanding owing to the H II-region feedback from stars within them. Our results support the dynamic and feedback-regulated GMC evolution scenario. Although the simulated GMCs were converging rather than virial equilibrium, they followed the observed scaling relationship well. We also analysed the effects of galactic tides and external pressure on GMC evolution and suggested that GMCs cannot be regarded as isolated systems since their evolution in disc galaxies is complicated because of these environmental effects.

  15. Evolution.

    ERIC Educational Resources Information Center

    Mayr, Ernst

    1978-01-01

    Traces the history of evolution theory from Lamarck and Darwin to the present. Discusses natural selection in detail. Suggests that, besides biological evolution, there is also a cultural evolution which is more rapid than the former. (MA)

  16. Teaching Evolution: A Heuristic Study of Personal and Cultural Dissonance

    ERIC Educational Resources Information Center

    Grimes, Larry G.

    2012-01-01

    Darwinian evolution is a robustly supported scientific theory. Yet creationists continue to challenge its teaching in American public schools. Biology teachers in all 50 states are responsible for teaching science content standards that include evolution. As products of their backgrounds and affiliations teachers bring personal attitudes and…

  17. Evolution of a polydnavirus gene in relation to parasitoid-host species immune resistance.

    PubMed

    Dupas, Stéphane; Gitau, Catherine Wanjiru; Branca, Antoine; Le Rü, Bruno Pierre; Silvain, Jean-François

    2008-01-01

    CrV1, a polydisperse DNA virus (polydnavirus or PDV) gene contributes to the suppression of host immunity in Cotesia genus parasitoids. Its molecular evolution was analyzed in relation to levels of resistance in the sympatric host species. Natural selection for nonsynonymous substitutions (positive Darwinian selection) was observed at specific amino acid sites among CrV1 variants; particularly, between parasitoid strains immune suppressive and nonimmune suppressive to the main resistant stem borer host, Busseola fusca. In Cotesia sesamiae, geographic distribution of CrV1 alleles in Kenya was correlated to the relative abundance of B. fusca. These results suggest that PDV genes evolve through natural selection and are genetically linked to factors of suppression of local host resistance. We discuss the forces driving the evolution of CrV1 and its use as a marker to understand parasitoid adaptation to host resistance in biological control.

  18. Historical perspective on the development and evolution of eyes and photoreceptors.

    PubMed

    Gehring, Walter J

    2004-01-01

    The development and evolution of eyes is an "old problem" in biology, which required a special treatment in Charles Darwin's "Origin of the species" (1882) under the heading of "Difficulties of the theory". Darwin postulated a simple and imperfect eye, as a prototype, which can vary and evolve under natural selection into more complex and perfect eyes. Based upon morphological criteria and the different modes of development of the different kinds of eyes, neodarwinists have postulated that the various eye-types are polyphyletic in origin and that the eyes have evolved independently in the various animal phyla. Recent developmental genetic experiments and molecular phylogenetic analyses cast serious doubts on this interpretation and argue strongly for a monophyletic origin of the eyes from a Darwinian prototype and subsequent divergent, parallel and convergent evolution leading to the various eye-types.

  19. On the Evolution of Human Language.

    ERIC Educational Resources Information Center

    Lieberman, Philip

    Human linguistic ability depends, in part, on the gradual evolution of man's supralaryngeal vocal tract. The anatomic basis of human speech production is the result of a long evolutionary process in which the Darwinian process of natural selection acted to retain mutations. For auditory perception, the listener operates in terms of the acoustic…

  20. Nucleotide substitution type dependence of generation time effect of molecular evolution.

    PubMed

    Kisakibaru, Y; Matsuda, H

    1995-06-01

    Using DNA sequence data of 18 genes from 14 mammals, we analyzed how the average molecular evolution rate per year per site (Vy) depends on the generation time (g). (I) Assuming the relation Vy varies; is directly proportional to g(-alpha), the index of generation time effect, (alpha) was estimated to be about 0.14 for amino acid replacement substitutions (A), and about 0.32 for synonymous substitutions (S). (II) Assuming the relation Vy = V(m)g g-1 + V(e)y, where V(m)g and V(e)y are constant independent of g, the fraction, r(e) = V(e)y/Vy, of the mutation rate independent part (V(e)y) in the total evolution rate (Vy) was estimated under the assumptions of the star phylogeny and the constancy of the mutation rate per generation. r(e) was smallest for mouse with the shortest generation time among our analyzed species, and it was estimated to be about 0.57 for A and 0.31 for S. Both results do not support the view that Vy is equal to the neutral mutation rate per site both for A and for S. They are in line with the thesis that, at least for A and probably even for S, the molecular evolution rate is influenced by some causes other than the mutation rate, such as changing environment.

  1. Reptilian heart development and the molecular basis of cardiac chamber evolution.

    PubMed

    Koshiba-Takeuchi, Kazuko; Mori, Alessandro D; Kaynak, Bogac L; Cebra-Thomas, Judith; Sukonnik, Tatyana; Georges, Romain O; Latham, Stephany; Beck, Laurel; Beck, Laural; Henkelman, R Mark; Black, Brian L; Olson, Eric N; Wade, Juli; Takeuchi, Jun K; Nemer, Mona; Gilbert, Scott F; Bruneau, Benoit G

    2009-09-03

    The emergence of terrestrial life witnessed the need for more sophisticated circulatory systems. This has evolved in birds, mammals and crocodilians into complete septation of the heart into left and right sides, allowing separate pulmonary and systemic circulatory systems, a key requirement for the evolution of endothermy. However, the evolution of the amniote heart is poorly understood. Reptilian hearts have been the subject of debate in the context of the evolution of cardiac septation: do they possess a single ventricular chamber or two incompletely septated ventricles? Here we examine heart development in the red-eared slider turtle, Trachemys scripta elegans (a chelonian), and the green anole, Anolis carolinensis (a squamate), focusing on gene expression in the developing ventricles. Both reptiles initially form a ventricular chamber that homogenously expresses the T-box transcription factor gene Tbx5. In contrast, in birds and mammals, Tbx5 is restricted to left ventricle precursors. In later stages, Tbx5 expression in the turtle (but not anole) heart is gradually restricted to a distinct left ventricle, forming a left-right gradient. This suggests that Tbx5 expression was refined during evolution to pattern the ventricles. In support of this hypothesis, we show that loss of Tbx5 in the mouse ventricle results in a single chamber lacking distinct identity, indicating a requirement for Tbx5 in septation. Importantly, misexpression of Tbx5 throughout the developing myocardium to mimic the reptilian expression pattern also results in a single mispatterned ventricular chamber lacking septation. Thus ventricular septation is established by a steep and correctly positioned Tbx5 gradient. Our findings provide a molecular mechanism for the evolution of the amniote ventricle, and support the concept that altered expression of developmental regulators is a key mechanism of vertebrate evolution.

  2. Hepatitis C virus molecular evolution: transmission, disease progression and antiviral therapy.

    PubMed

    Preciado, Maria Victoria; Valva, Pamela; Escobar-Gutierrez, Alejandro; Rahal, Paula; Ruiz-Tovar, Karina; Yamasaki, Lilian; Vazquez-Chacon, Carlos; Martinez-Guarneros, Armando; Carpio-Pedroza, Juan Carlos; Fonseca-Coronado, Salvador; Cruz-Rivera, Mayra

    2014-11-21

    Hepatitis C virus (HCV) infection represents an important public health problem worldwide. Reduction of HCV morbidity and mortality is a current challenge owned to several viral and host factors. Virus molecular evolution plays an important role in HCV transmission, disease progression and therapy outcome. The high degree of genetic heterogeneity characteristic of HCV is a key element for the rapid adaptation of the intrahost viral population to different selection pressures (e.g., host immune responses and antiviral therapy). HCV molecular evolution is shaped by different mechanisms including a high mutation rate, genetic bottlenecks, genetic drift, recombination, temporal variations and compartmentalization. These evolutionary processes constantly rearrange the composition of the HCV intrahost population in a staging manner. Remarkable advances in the understanding of the molecular mechanism controlling HCV replication have facilitated the development of a plethora of direct-acting antiviral agents against HCV. As a result, superior sustained viral responses have been attained. The rapidly evolving field of anti-HCV therapy is expected to broad its landscape even further with newer, more potent antivirals, bringing us one step closer to the interferon-free era.

  3. The molecular biology and evolution of feline immunodeficiency viruses of cougars.

    PubMed

    Poss, Mary; Ross, Howard; Rodrigo, Allen; Terwee, Julie; Vandewoude, Sue; Biek, Roman

    2008-05-15

    Feline immunodeficiency virus (FIV) is a lentivirus that has been identified in many members of the family Felidae but domestic cats are the only FIV host in which infection results in disease. We studied FIVpco infection of cougars (Puma concolor) as a model for asymptomatic lentivirus infections to understand the mechanisms of host-virus coexistence. Several natural cougar populations were evaluated to determine if there are any consequences of FIVpco infection on cougar fecundity, survival, or susceptibility to other infections. We have sequenced full-length viral genomes and conducted a detailed analysis of viral molecular evolution on these sequences and on genome fragments of serially sampled animals to determine the evolutionary forces experienced by this virus in cougars. In addition, we have evaluated the molecular genetics of FIVpco in a new host, domestic cats, to determine the evolutionary consequences to a host-adapted virus associated with cross-species infection. Our results indicate that there are no significant differences in survival, fecundity or susceptibility to other infections between FIVpco-infected and uninfected cougars. The molecular evolution of FIVpco is characterized by a slower evolutionary rate and an absence of positive selection, but also by proviral and plasma viral loads comparable to those of epidemic lentiviruses such as HIV-1 or FIVfca. Evolutionary and recombination rates and selection profiles change significantly when FIVpco replicates in a new host.

  4. Molecular evolution and adaptation of the mitochondrial cytochrome b gene in the subgenus Martes.

    PubMed

    Li, B; Malyarchuk, B; He, X B; Derenko, M

    2013-09-23

    Martes species represent a typical example of rapid evolutionary radiation and a recent speciation event. To identify regions of the genome that experienced adaptive evolution, which might provide clues to their functional importance and may be informative about the features that make each species unique, we sought evidence of molecular adaptation in the mitochondrial DNA (mtDNA) cytochrome b gene in the subgenus Martes. Complete sequences of the cytochrome b gene were obtained from 87 samples, including 49 sables, 28 pine martens, and 10 stone martens, and were combined with mtDNA sequences of other true martens, such as M. melampus and M. americana. Analysis of the cytochrome b gene variation in true martens has shown that the evolution of this gene is under negative selection. In contrast, positive selection on the cytochrome b protein has been detected by means of the software TreeSAAP using a phylogenetic reconstruction of Martes taxa. Signatures of adaptive variation in cytochrome b were restricted to the transmembrane domains, which likely function as proton pumps. We compared results of different methods for testing selection and molecular adaptation, and we supposed that the radical changes of the cytochrome b amino acid residues in the subgenus Martes may be the result of molecular adaptation to specific environmental conditions coupled with species dispersals.

  5. Species-specific size expansion and molecular evolution of the oleosins in angiosperms.

    PubMed

    Liu, Qi; Sun, Yepeng; Su, Wujie; Yang, Jing; Liu, Xiuming; Wang, Yanfang; Wang, Fawei; Li, Haiyan; Li, Xiaokun

    2012-11-10

    Oleosins are hydrophobic plant proteins thought to be important for the formation of oil bodies, which supply energy for seed germination and subsequent seedling growth. To better understand the evolutionary history and diversity of the oleosin gene family in plants, especially angiosperms, we systematically investigated the molecular evolution of this family using eight representative angiosperm species. A total of 73 oleosin members were identified, with six members in each of four monocot species and a greater but variable number in the four eudicots. A phylogenetic analysis revealed that the angiosperm oleosin genes belonged to three monophyletic lineages. Species-specific gene duplications, caused mainly by segmental duplication, led to the great expansion of oleosin genes and occurred frequently in eudicots after the monocot-eudicot divergence. Functional divergence analyses indicate that significant amino acid site-specific selective constraints acted on the different clades of oleosins. Adaptive evolution analyses demonstrate that oleosin genes were subject to strong purifying selection after their species-specific duplications and that rapid evolution occurred with a high degree of evolutionary dynamics in the pollen-specific oleosin genes. In conclusion, this study serves as a foundation for genome-wide analyses of the oleosins. These findings provide insight into the function and evolution of this gene family in angiosperms and pave the way for studies in other plants.

  6. Breeding novel solutions in the brain: a model of Darwinian neurodynamics.

    PubMed

    Szilágyi, András; Zachar, István; Fedor, Anna; de Vladar, Harold P; Szathmáry, Eörs

    2016-01-01

    Background: The fact that surplus connections and neurons are pruned during development is well established. We complement this selectionist picture by a proof-of-principle model of evolutionary search in the brain, that accounts for new variations in theory space. We present a model for Darwinian evolutionary search for candidate solutions in the brain. Methods: We combine known components of the brain - recurrent neural networks (acting as attractors), the action selection loop and implicit working memory - to provide the appropriate Darwinian architecture. We employ a population of attractor networks with palimpsest memory. The action selection loop is employed with winners-share-all dynamics to select for candidate solutions that are transiently stored in implicit working memory. Results: We document two processes: selection of stored solutions and evolutionary search for novel solutions. During the replication of candidate solutions attractor networks occasionally produce recombinant patterns, increasing variation on which selection can act. Combinatorial search acts on multiplying units (activity patterns) with hereditary variation and novel variants appear due to (i) noisy recall of patterns from the attractor networks, (ii) noise during transmission of candidate solutions as messages between networks, and, (iii) spontaneously generated, untrained patterns in spurious attractors. Conclusions: Attractor dynamics of recurrent neural networks can be used to model Darwinian search. The proposed architecture can be used for fast search among stored solutions (by selection) and for evolutionary search when novel candidate solutions are generated in successive iterations. Since all the suggested components are present in advanced nervous systems, we hypothesize that the brain could implement a truly evolutionary combinatorial search system, capable of generating novel variants.

  7. Breeding novel solutions in the brain: a model of Darwinian neurodynamics

    PubMed Central

    Szilágyi, András; Zachar, István; Fedor, Anna; de Vladar, Harold P.; Szathmáry, Eörs

    2016-01-01

    Background: The fact that surplus connections and neurons are pruned during development is well established. We complement this selectionist picture by a proof-of-principle model of evolutionary search in the brain, that accounts for new variations in theory space. We present a model for Darwinian evolutionary search for candidate solutions in the brain. Methods: We combine known components of the brain – recurrent neural networks (acting as attractors), the action selection loop and implicit working memory – to provide the appropriate Darwinian architecture. We employ a population of attractor networks with palimpsest memory. The action selection loop is employed with winners-share-all dynamics to select for candidate solutions that are transiently stored in implicit working memory. Results: We document two processes: selection of stored solutions and evolutionary search for novel solutions. During the replication of candidate solutions attractor networks occasionally produce recombinant patterns, increasing variation on which selection can act. Combinatorial search acts on multiplying units (activity patterns) with hereditary variation and novel variants appear due to (i) noisy recall of patterns from the attractor networks, (ii) noise during transmission of candidate solutions as messages between networks, and, (iii) spontaneously generated, untrained patterns in spurious attractors. Conclusions: Attractor dynamics of recurrent neural networks can be used to model Darwinian search. The proposed architecture can be used for fast search among stored solutions (by selection) and for evolutionary search when novel candidate solutions are generated in successive iterations. Since all the suggested components are present in advanced nervous systems, we hypothesize that the brain could implement a truly evolutionary combinatorial search system, capable of generating novel variants. PMID:27990266

  8. Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia

    PubMed Central

    Janes, Daniel E.; Organ, Christopher L.; Stiglec, Rami; O'Meally, Denis; Sarre, Stephen D.; Georges, Arthur; Graves, Jennifer A. M.; Valenzuela, Nicole; Literman, Robert A.; Rutherford, Kim; Gemmell, Neil; Iverson, John B.; Tamplin, Jeffrey W.; Edwards, Scott V.; Ezaz, Tariq

    2014-01-01

    In reptiles, sex-determining mechanisms have evolved repeatedly and reversibly between genotypic and temperature-dependent sex determination. The gene Dmrt1 directs male determination in chicken (and presumably other birds), and regulates sex differentiation in animals as distantly related as fruit flies, nematodes and humans. Here, we show a consistent molecular difference in Dmrt1 between reptiles with genotypic and temperature-dependent sex determination. Among 34 non-avian reptiles, a convergently evolved pair of amino acids encoded by sequence within exon 2 near the DM-binding domain of Dmrt1 distinguishes species with either type of sex determination. We suggest that this amino acid shift accompanied the evolution of genotypic sex determination from an ancestral condition of temperature-dependent sex determination at least three times among reptiles, as evident in turtles, birds and squamates. This novel hypothesis describes the evolution of sex-determining mechanisms as turnover events accompanied by one or two small mutations. PMID:25540158

  9. Plant hemoglobins: a molecular fossil record for the evolution of oxygen transport.

    PubMed

    Hoy, Julie A; Robinson, Howard; Trent, James T; Kakar, Smita; Smagghe, Benoit J; Hargrove, Mark S

    2007-08-03

    The evolution of oxygen transport hemoglobins occurred on at least two independent occasions. The earliest event led to myoglobin and red blood cell hemoglobin in animals. In plants, oxygen transport "leghemoglobins" evolved much more recently. In both events, pentacoordinate heme sites capable of inert oxygen transfer evolved from hexacoordinate hemoglobins that have unrelated functions. High sequence homology between hexacoordinate and pentacoordinate hemoglobins in plants has poised them for potential structural analysis leading to a molecular understanding of this important evolutionary event. However, the lack of a plant hexacoordinate hemoglobin structure in the exogenously ligand-bound form has prevented such comparison. Here we report the crystal structure of the cyanide-bound hexacoordinate hemoglobin from barley. This presents the first opportunity to examine conformational changes in plant hexacoordinate hemoglobins upon exogenous ligand binding, and reveals structural mechanisms for stabilizing the high-energy pentacoordinate heme conformation critical to the evolution of reversible oxygen binding hemoglobins.

  10. PAL: an object-oriented programming library for molecular evolution and phylogenetics.

    PubMed

    Drummond, A; Strimmer, K

    2001-07-01

    Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers. AVAILIABILTY: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License.

  11. Structural evolution of dilute magnetic (Sn,Mn)Se films grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Kanzyuba, Vasily; Dong, Sining; Liu, Xinyu; Li, Xiang; Rouvimov, Sergei; Okuno, Hanako; Mariette, Henri; Zhang, Xueqiang; Ptasinska, Sylwia; Tracy, Brian D.; Smith, David J.; Dobrowolska, Margaret; Furdyna, Jacek K.

    2017-02-01

    We describe the structural evolution of dilute magnetic (Sn,Mn)Se films grown by molecular beam epitaxy on GaAs (111) substrates, as revealed by transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. When the Mn concentration is increased, the lattice of the ternary (Sn,Mn)Se films evolves quasi-coherently from a SnSe2 two-dimensional (2D) crystal structure into a more complex quasi-2D lattice rearrangement, ultimately transforming into the magnetically concentrated antiferromagnetic MnSe 3D rock-salt structure as Mn approaches 50 at. % of this material. These structural transformations are expected to underlie the evolution of magnetic properties of this ternary system reported earlier in the literature.

  12. Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia.

    PubMed

    Janes, Daniel E; Organ, Christopher L; Stiglec, Rami; O'Meally, Denis; Sarre, Stephen D; Georges, Arthur; Graves, Jennifer A M; Valenzuela, Nicole; Literman, Robert A; Rutherford, Kim; Gemmell, Neil; Iverson, John B; Tamplin, Jeffrey W; Edwards, Scott V; Ezaz, Tariq

    2014-12-01

    In reptiles, sex-determining mechanisms have evolved repeatedly and reversibly between genotypic and temperature-dependent sex determination. The gene Dmrt1 directs male determination in chicken (and presumably other birds), and regulates sex differentiation in animals as distantly related as fruit flies, nematodes and humans. Here, we show a consistent molecular difference in Dmrt1 between reptiles with genotypic and temperature-dependent sex determination. Among 34 non-avian reptiles, a convergently evolved pair of amino acids encoded by sequence within exon 2 near the DM-binding domain of Dmrt1 distinguishes species with either type of sex determination. We suggest that this amino acid shift accompanied the evolution of genotypic sex determination from an ancestral condition of temperature-dependent sex determination at least three times among reptiles, as evident in turtles, birds and squamates. This novel hypothesis describes the evolution of sex-determining mechanisms as turnover events accompanied by one or two small mutations.

  13. Molecular evolution and antigenic variation of European brown hare syndrome virus (EBHSV).

    PubMed

    Lopes, Ana M; Capucci, Lorenzo; Gavier-Widén, Dolores; Le Gall-Reculé, Ghislaine; Brocchi, Emiliana; Barbieri, Ilaria; Quéméner, Agnès; Le Pendu, Jacques; Geoghegan, Jemma L; Holmes, Edward C; Esteves, Pedro J; Abrantes, Joana

    2014-11-01

    European brown hare syndrome virus (EBHSV) is the aetiological agent of European brown hare syndrome (EBHS), a disease affecting Lepus europaeus and Lepus timidus first diagnosed in Sweden in 1980. To characterize EBHSV evolution we studied hare samples collected in Sweden between 1982 and 2008. Our molecular clock dating is compatible with EBHSV emergence in the 1970s. Phylogenetic analysis revealed two lineages: Group A persisted until 1989 when it apparently suffered extinction; Group B emerged in the mid-1980s and contains the most recent strains. Antigenic differences exist between groups, with loss of reactivity of some MAbs over time, which are associated with amino acid substitutions in recognized epitopes. A role for immune selection is also supported by the presence of positively selected codons in exposed regions of the capsid. Hence, EBHSV evolution is characterized by replacement of Group A by Group B viruses, suggesting that the latter possess a selective advantage.

  14. Non-unity molecular heritability demonstrated by continuous evolution in vitro

    NASA Technical Reports Server (NTRS)

    Schmitt, T.; Lehman, N.

    1999-01-01

    INTRODUCTION: When catalytic RNA is evolved in vitro, the molecule's chemical reactivity is usually the desired selection target. Sometimes the phenotype of a particular RNA molecule cannot be unambiguously determined from its genotype, however. This can occur if a nucleotide sequence can adopt multiple folded states, an example of non-unity heritability (i.e. one genotype gives rise to more than one phenotype). In these cases, more rounds of selection are required to achieve a phenotypic shift. We tested the influence of non-unity heritability at the molecular level by selecting for variants of a ligase ribozyme via continuous evolution. RESULTS: During 20 bursts of continuous evolution of a 152-nucleotide ligase ribozyme in which the Mg2+ concentration was periodically lowered, a nine-error variant of the starting 'wild-type' molecule became dominant in the last eight bursts. This variant appears to be more active than the wild type. Kinetic analyses of the mutant suggest that it may not possess a higher first-order catalytic rate constant, however. Examination of the multiple RNA conformations present under the continuous evolution conditions suggests that the mutant is superior to the wild type because it is less likely to misfold into inactive conformers. CONCLUSIONS: The evolution of genotypes that are more likely to exhibit a particular phenotype is an epiphenomenon usually ascribed only to complex living systems. We show that this can occur at the molecular level, demonstrating that in vitro systems may have more life-like characteristics than previously thought, and providing additional support for an RNA world.

  15. Evolution of a single gene highlights the complexity underlying molecular descriptions of fitness

    NASA Astrophysics Data System (ADS)

    Peña, Matthew I.; Van Itallie, Elizabeth; Bennett, Matthew R.; Shamoo, Yousif

    2010-06-01

    Evolution by natural selection is the driving force behind the endless variation we see in nature, yet our understanding of how changes at the molecular level give rise to different phenotypes and altered fitness at the population level remains inadequate. The reproductive fitness of an organism is the most basic metric that describes the chance that an organism will succeed or fail in its environment and it depends upon a complex network of inter- and intramolecular interactions. A deeper understanding of the quantitative relationships relating molecular evolution to adaptation, and consequently fitness, can guide our understanding of important issues in biomedicine such as drug resistance and the engineering of new organisms with applications to biotechnology. We have developed the "weak link" approach to determine how changes in molecular structure and function can relate to fitness and evolutionary outcomes. By replacing adenylate kinase (AK), an essential gene, in a thermophile with a homologous AK from a mesophile we have created a maladapted weak link that produces a temperature-sensitive phenotype. The recombinant strain adapts to nonpermissive temperatures through point mutations to the weak link that increase both stability and activity of the enzyme AK at higher temperatures. Here, we propose a fitness function relating enzyme activity to growth rate and use it to create a dynamic model of a population of bacterial cells. Using metabolic control analysis we show that the growth rate exhibits thresholdlike behavior, saturating at high enzyme activity as other reactions in the energy metabolism pathway become rate limiting. The dynamic model accurately recapitulates observed evolutionary outcomes. These findings suggest that in vitro enzyme kinetic data, in combination with metabolic network analysis, can be used to create fitness functions and dynamic models of evolution within simple metabolic systems.

  16. Molecular dynamics simulations of the structure evolutions of Cu-Zr metallic glasses under irradiation

    NASA Astrophysics Data System (ADS)

    Lang, Lin; Tian, Zean; Xiao, Shifang; Deng, Huiqiu; Ao, Bingyun; Chen, Piheng; Hu, Wangyu

    2017-02-01

    Molecular dynamics simulations have been performed to investigate the structural evolution of Cu64.5Zr35.5 metallic glasses under irradiation. The largest standard cluster analysis (LSCA) method was used to quantify the microstructure within the collision cascade regions. It is found that the majority of clusters within the collision cascade regions are full and defective icosahedrons. Not only the smaller structures (common neighbor subcluster) but also primary clusters greatly changed during the collision cascades; while most of these radiation damages self-recover quickly in the following quench states. These findings indicate the Cu-Zr metallic glasses have excellent irradiation-resistance properties.

  17. Thiol-catalyzed formation of lactate and glycerate from glyceraldehyde. [significance in molecular evolution

    NASA Technical Reports Server (NTRS)

    Weber, A. L.

    1983-01-01

    The rate of lactate formation from glyceraldehyde, catalyzed by N-acetyl-cysteine at ambient temperature in aqueous sodium phosphate (pH 7.0), is more rapid at higher sodium phosphate concentrations and remains essentially the same in the presence and absence of oxygen. The dramatic increase in the rate of glycerate formation that is brought about by this thiol, N-acetylcysteine, is accompanied by commensurate decreases in the rates of glycolate and formate production. It is suggested that the thiol-dependent formation of lactate and glycerate occurs by way of their respective thioesters. Attention is given to the significance of these reactions in the context of molecular evolution.

  18. Evolution and mass extinctions as lognormal stochastic processes

    NASA Astrophysics Data System (ADS)

    Maccone, Claudio

    2014-10-01

    -terrestrial civilizations existing in the Galaxy (as a consequence of the central limit theorem of statistics). (5) But the most striking new result is that the well-known `Molecular Clock of Evolution', namely the `constant rate of Evolution at the molecular level' as shown by Kimura's Neutral Theory of Molecular Evolution, identifies with growth rate of the entropy of our Evo-SETI model, because they both grew linearly in time since the origin of life. (6) Furthermore, we apply our Evo-SETI model to lognormal stochastic processes other than GBMs. For instance, we provide two models for the mass extinctions that occurred in the past: (a) one based on GBMs and (b) the other based on a parabolic mean value capable of covering both the extinction and the subsequent recovery of life forms. (7) Finally, we show that the Markov & Korotayev (2007, 2008) model for Darwinian Evolution identifies with an Evo-SETI model for which the mean value of the underlying lognormal stochastic process is a cubic function of the time. In conclusion: we have provided a new mathematical model capable of embracing molecular evolution, SETI and entropy into a simple set of statistical equations based upon b-lognormals and lognormal stochastic processes with arbitrary mean, of which the GBMs are the particular case of exponential growth.

  19. Evolution of Molecular and Atomic Gas Phases in the Milky Way

    NASA Astrophysics Data System (ADS)

    Koda, Jin; Scoville, Nick; Heyer, Mark

    2016-06-01

    We analyze radial and azimuthal variations of the phase balance between the molecular and atomic interstellar medium (ISM) in the Milky Way (MW) using archival CO(J = 1-0) and HI 21 cm data. In particular, the azimuthal variations—between the spiral arm and interarm regions—are analyzed without any explicit definition of the spiral arm locations. We show that the molecular gas mass fraction, i.e., {f}{{mol}}={{{Σ }}}{{{H}}2}/({{{Σ }}}{HI}+{{{Σ }}}{{{H}}2}), varies predominantly in the radial direction: starting from ˜ 100% at the center, remaining ≳ 50% to R˜ 6 {{kpc}} and decreasing to ˜10%-20% at R=8.5 {{kpc}} when averaged over the whole disk thickness (from ˜100% to ≳60%, then to ˜50% in the midplane). Azimuthal, arm-interarm variations are secondary: only ˜ 20% in the globally molecule-dominated inner MW, but becoming larger, ˜40%-50%, in the atom-dominated outskirts. This suggests that in the inner MW the gas remains highly molecular ({f}{{mol}}\\gt 50%) as it moves from an interarm region into a spiral arm and back into the next interarm region. Stellar feedback does not dissociate molecules much, and the coagulation and fragmentation of molecular clouds dominate the evolution of the ISM at these radii. The trend differs in the outskirts where the gas phase is globally atomic ({f}{{mol}}\\lt 50%). The HI and H2 phases cycle through spiral arm passage there. These different regimes of ISM evolution are also seen in external galaxies (e.g., the LMC, M33, and M51). We explain the radial gradient of {f}{{mol}} using a simple flow continuity model. The effects of spiral arms on this analysis are illustrated in the Appendix.

  20. The genome as a life-history character: why rate of molecular evolution varies between mammal species

    PubMed Central

    Bromham, Lindell

    2011-01-01

    DNA sequences evolve at different rates in different species. This rate variation has been most closely examined in mammals, revealing a large number of characteristics that can shape the rate of molecular evolution. Many of these traits are part of the mammalian life-history continuum: species with small body size, rapid generation turnover, high fecundity and short lifespans tend to have faster rates of molecular evolution. In addition, rate of molecular evolution in mammals might be influenced by behaviour (such as mating system), ecological factors (such as range restriction) and evolutionary history (such as diversification rate). I discuss the evidence for these patterns of rate variation, and the possible explanations of these correlations. I also consider the impact of these systematic patterns of rate variation on the reliability of the molecular date estimates that have been used to suggest a Cretaceous radiation of modern mammals, before the final extinction of the dinosaurs. PMID:21807731

  1. Anticipatory dynamics of biological systems: from molecular quantum states to evolution

    NASA Astrophysics Data System (ADS)

    Igamberdiev, Abir U.

    2015-08-01

    Living systems possess anticipatory behaviour that is based on the flexibility of internal models generated by the system's embedded description. The idea was suggested by Aristotle and is explicitly introduced to theoretical biology by Rosen. The possibility of holding the embedded internal model is grounded in the principle of stable non-equilibrium (Bauer). From the quantum mechanical view, this principle aims to minimize energy dissipation in expense of long relaxation times. The ideas of stable non-equilibrium were developed by Liberman who viewed living systems as subdivided into the quantum regulator and the molecular computer supporting coherence of the regulator's internal quantum state. The computational power of the cell molecular computer is based on the possibility of molecular rearrangements according to molecular addresses. In evolution, the anticipatory strategies are realized both as a precession of phylogenesis by ontogenesis (Berg) and as the anticipatory search of genetic fixation of adaptive changes that incorporates them into the internal model of genetic system. We discuss how the fundamental ideas of anticipation can be introduced into the basic foundations of theoretical biology.

  2. Major Radiations in the Evolution of Caviid Rodents: Reconciling Fossils, Ghost Lineages, and Relaxed Molecular Clocks

    PubMed Central

    Pérez, María Encarnación; Pol, Diego

    2012-01-01

    Background Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America (“eocardiids”). Results A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates. Conclusions The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone. PMID

  3. Molecular evolution of sex-biased genes in the Drosophila ananassae subgroup

    PubMed Central

    2009-01-01

    Background Genes with sex-biased expression often show rapid molecular evolution between species. Previous population genetic and comparative genomic studies of Drosophila melanogaster and D. simulans revealed that male-biased genes have especially high rates of adaptive evolution. To test if this is also the case for other lineages within the melanogaster group, we investigated gene expression in D. ananassae, a species that occurs in structured populations in tropical and subtropical regions. We used custom-made microarrays and published microarray data to characterize the sex-biased expression of 129 D. ananassae genes whose D. melanogaster orthologs had been classified previously as male-biased, female-biased, or unbiased in their expression and had been studied extensively at the population-genetic level. For 43 of these genes we surveyed DNA sequence polymorphism in a natural population of D. ananassae and determined divergence to the sister species D. atripex and D. phaeopleura. Results Sex-biased expression is generally conserved between D. melanogaster and D. ananassae, with the majority of genes exhibiting the same bias in the two species. However, about one-third of the genes have either gained or lost sex-biased expression in one of the species and a small proportion of genes (~4%) have changed bias from one sex to the other. The male-biased genes of D. ananassae show evidence of positive selection acting at the protein level. However, the signal of adaptive protein evolution for male-biased genes is not as strong in D. ananassae as it is in D. melanogaster and is limited to genes with conserved male-biased expression in both species. Within D. ananassae, a significant signal of adaptive evolution is also detected for female-biased and unbiased genes. Conclusions Our findings extend previous observations of widespread adaptive protein evolution to an independent Drosophila lineage, the D. ananassae subgroup. However, the rate of adaptive evolution is

  4. Why mental disorders are just mental dysfunctions (and nothing more): some Darwinian arguments.

    PubMed

    De Block, Andreas

    2008-09-01

    Mental disorders are often thought to be harmful dysfunctions. Jerome Wakefield has argued that such dysfunctions should be understood as failures of naturally selected functions. This suggests, implicitly, that evolutionary biology and other Darwinian disciplines hold important information for anyone working on answering the philosophical question, 'what is a mental disorder?'. In this article, the author argues that Darwinian theory is not only relevant to the understanding of the disrupted functions, but it also sheds light on the disruption itself, as well as on the harm that attends the disruption. The arguments advanced here are partially based on the view that a core feature of Darwinism is that it stresses the environmental relativity of functions and dysfunctions. These arguments show a very close empirical connection between social judgments (values) and dysfunctions (psychopathology), which is of interest for psychiatric theory. Philosophically, they lead to the conclusion that the concept of mental disorder is identical to the concept of mental dysfunction. Consequently, it is both misleading and redundant to conceptualize mental disorders as 'harmful dysfunctions', and not simply as 'mental dysfunctions'.

  5. Molecular Evolution of the Infrared Sensory Gene TRPA1 in Snakes and Implications for Functional Studies

    PubMed Central

    Jiang, Ke; Zhang, Peng

    2011-01-01

    TRPA1 is a calcium ion channel protein recently identified as the infrared receptor in pit organ-containing snakes. Therefore, understanding the molecular evolution of TRPA1 may help to illuminate the origin of “heat vision” in snakes and reveal the molecular mechanism of infrared sensitivity for TRPA1. To this end, we sequenced the infrared sensory gene TRPA1 in 24 snake species, representing nine snake families and multiple non-snake outgroups. We found that TRPA1 is under strong positive selection in the pit-bearing snakes studied, but not in other non-pit snakes and non-snake vertebrates. As a comparison, TRPV1, a gene closely related to TRPA1, was found to be under strong purifying selection in all the species studied, with no difference in the strength of selection between pit-bearing snakes and non-pit snakes. This finding demonstrates that the adaptive evolution of TRPA1 specifically occurred within the pit-bearing snakes and may be related to the functional modification for detecting infrared radiation. In addition, by comparing the TRPA1 protein sequences, we identified 11 amino acid sites that were diverged in pit-bearing snakes but conserved in non-pit snakes and other vertebrates, 21 sites that were diverged only within pit-vipers but conserved in the remaining snakes. These specific amino acid substitutions may be potentially functional important for infrared sensing. PMID:22163322

  6. Molecular timetrees reveal a Cambrian colonization of land and a new scenario for ecdysozoan evolution.

    PubMed

    Rota-Stabelli, Omar; Daley, Allison C; Pisani, Davide

    2013-03-04

    Ecdysozoans have been key components of ecosystems since the early Cambrian, when trilobites and soft-bodied Burgess Shale-type ecdysozoans dominated marine animal communities. Even today, the most abundant animals on Earth are either nematode worms or plankton-forming crustaceans, whereas the most diverse are the insects. Throughout geological time, several ecdysozoan lineages independently colonized land, shaping both marine and terrestrial ecosystems and providing an adequate environment for successive animal terrestrialization. The timing of these events is largely uncertain and has been investigated only partially using molecular data. Here we present a timescale of ecdysozoan evolution based on multiple molecular data sets, the most complete set of fossil calibrations to date, and a thorough series of validation analyses. Results converge on an Ediacaran origin of all major ecdysozoan lineages (∼587-543 million years ago [mya]), followed by a fast Cambrian radiation of the pancrustaceans (∼539-511 mya), a Cambro-Ordovician colonization of land of different arthropod lineages (∼510-471 mya), and a relatively recent radiation of extant nematodes, onychophorans, and tardigrades (∼442 mya). Arthropods colonized land nearly synchronously with land plants. Further diversification within flying insects, nematodes and onychophorans might be related to the evolution of vascular plants and forests.

  7. Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents.

    PubMed

    Huchon, D; Catzeflis, F M; Douzery, E J

    1999-05-01

    Nucleotide sequences of exon 28 of the von Willebrand Factor (vWF) were analyzed for a representative sampling of rodent families and eutherian orders, with one marsupial sequence as outgroup. The aim of this study was to test if inclusion of an increased taxonomic diversity in molecular analyses would shed light on three uncertainties concerning rodent phylogeny: (1) relationships between rodent families, (2) Rodentia monophyly, and (3) the sister group relationship of rodents and lagomorphs. The results did not give evidence of any particular rodent pattern of molecular evolution relative to a general eutherian pattern. Base compositions and rates of evolution of vWF sequences of rodents were in the range of placental variation. The 10 rodent families studied here cluster in five clades: Hystricognathi, Sciuridae and Aplodontidae (Sciuroidea), Muridae, Dipodidae, and Gliridae. Among hystricognaths, the following conclusions are drawn: a single colonization event in South America by Caviomorpha, a paraphyly of Old World and New World porcupines, and an African origin for Old World porcupines. Despite a broader taxonomic sampling diversity, we did not obtain a robust answer to the question of Rodentia monophyly, but in the absence of any other alternative, we cannot reject the hypothesis of a single origin of rodents. Moreover, the phylogenetic position of Lagomorpha remains totally unsettled.

  8. Molecular Evolution of Aralkylamine N-Acetyltransferase in Fish: A Genomic Survey

    PubMed Central

    Li, Jia; You, Xinxin; Bian, Chao; Yu, Hui; Coon, Steven L.; Shi, Qiong

    2015-01-01

    All living organisms synchronize biological functions with environmental changes; melatonin plays a vital role in regulating daily and seasonal variations. Due to rhythmic activity of the timezyme aralkylamine N-acetyltransferase (AANAT), the blood level of melatonin increases at night and decreases during daytime. Whereas other vertebrates have a single form of AANAT, bony fishes possess various isoforms of aanat genes, though the reasons are still unclear. Here, we have taken advantage of multiple unpublished teleost aanat sequences to explore and expand our understanding of the molecular evolution of aanat in fish. Our results confirm that two rounds of whole-genome duplication (WGD) led to the existence of three fish isoforms of aanat, i.e., aanat1a, aanat1b, and aanat2; in addition, gene loss led to the absence of some forms from certain special fish species. Furthermore, we suggest the different roles of two aanat1s in amphibious mudskippers, and speculate that the loss of aanat1a, may be related to terrestrial vision change. Several important sites of AANAT proteins and regulatory elements of aanat genes were analyzed for structural comparison and functional forecasting, respectively, which provides insights into the molecular evolution of the differences between AANAT1 and AANAT2. PMID:26729109

  9. Molecular heterochrony and the evolution of sociality in bumblebees (Bombus terrestris)

    PubMed Central

    Woodard, S. Hollis; Bloch, Guy M.; Band, Mark R.; Robinson, Gene E.

    2014-01-01

    Sibling care is a hallmark of social insects, but its evolution remains challenging to explain at the molecular level. The hypothesis that sibling care evolved from ancestral maternal care in primitively eusocial insects has been elaborated to involve heterochronic changes in gene expression. This elaboration leads to the prediction that workers in these species will show patterns of gene expression more similar to foundress queens, who express maternal care behaviour, than to established queens engaged solely in reproductive behaviour. We tested this idea in bumblebees (Bombus terrestris) using a microarray platform with approximately 4500 genes. Unlike the wasp Polistes metricus, in which support for the above prediction has been obtained, we found that patterns of brain gene expression in foundress and queen bumblebees were more similar to each other than to workers. Comparisons of differentially expressed genes derived from this study and gene lists from microarray studies in Polistes and the honeybee Apis mellifera yielded a shared set of genes involved in the regulation of related social behaviours across independent eusocial lineages. Together, these results suggest that multiple independent evolutions of eusociality in the insects might have involved different evolutionary routes, but nevertheless involved some similarities at the molecular level. PMID:24552837

  10. In vitro molecular evolution yields an NEIBM with a potential novel IgG binding property

    PubMed Central

    Qi, Peipei; Ding, Ying-Ying; He, Ting; Yang, Tong; Chen, Qiuli; Feng, Jiaojiao; Wang, Jinhong; Cao, Mingmei; Li, Xiangyu; Peng, Heng; Zhu, Huaimin; Cao, Jie; Pan, Wei

    2014-01-01

    Staphylococcus aureus protein A (SpA) and protein G of groups C and G streptococci (SpG) are two well-defined bacterial immunoglobulin (Ig)-binding proteins (IBPs) with high affinity for specific sites on IgG from mammalian hosts. Both SpA and SpG contain several highly-homologous IgG-binding domains, each of which possesses similar binding characteristic of the whole corresponding proteins. Whether specific combinations of these domains could generate a molecule with novel IgG-binding properties remained unknown. We constructed a combinatorial phage library displaying randomly-rearranged A, B, C, D and E domains of SpA as well as the B2 (G2) and B3 (G3) domains of SpG. In vitro molecular evolution directed by human, rabbit, bovine, or goat polyclonal IgGs and four subclasses of mouse monoclonal IgGs generated one common combination, D-C-G3. A series of assays demonstrated that D-C-G3 exhibited a potential novel IgG binding property that was obviously different from those of both parent proteins. This study provides an example of successful protein engineering through in vitro molecular evolution and useful approaches for structure and function studies of IBPs. PMID:25366194

  11. Molecular Evolution of Aralkylamine N-Acetyltransferase in Fish: A Genomic Survey.

    PubMed

    Li, Jia; You, Xinxin; Bian, Chao; Yu, Hui; Coon, Steven L; Shi, Qiong

    2015-12-31

    All living organisms synchronize biological functions with environmental changes; melatonin plays a vital role in regulating daily and seasonal variations. Due to rhythmic activity of the timezyme aralkylamine N-acetyltransferase (AANAT), the blood level of melatonin increases at night and decreases during daytime. Whereas other vertebrates have a single form of AANAT, bony fishes possess various isoforms of aanat genes, though the reasons are still unclear. Here, we have taken advantage of multiple unpublished teleost aanat sequences to explore and expand our understanding of the molecular evolution of aanat in fish. Our results confirm that two rounds of whole-genome duplication (WGD) led to the existence of three fish isoforms of aanat, i.e., aanat1a, aanat1b, and aanat2; in addition, gene loss led to the absence of some forms from certain special fish species. Furthermore, we suggest the different roles of two aanat1s in amphibious mudskippers, and speculate that the loss of aanat1a, may be related to terrestrial vision change. Several important sites of AANAT proteins and regulatory elements of aanat genes were analyzed for structural comparison and functional forecasting, respectively, which provides insights into the molecular evolution of the differences between AANAT1 and AANAT2.

  12. In vitro molecular evolution of AL NEIBMs improved immunoglobulin (Ig) binding and antibody detection.

    PubMed

    He, Ting; Ding, Ying-Ying; Feng, Jiao-Jiao; Chen, Qiu-Li; Zhu, Huai-Min; Peng, Heng; Rui, Bing; Li, Xiang-Yu; Cao, Ming-Mei; Pan, Wei

    2014-08-20

    AL (SpA A domain-PpL B3 domain), LD5 (PpL B3 domain-SpA D domain-PpL B3 domain-SpA D domain-PpL B3 domain, L-D-L-D-L) and LD3 (PpL B3 domain-SpA D domain-PpL B3 domain, L-D-L) are novel evolved Ig binding molecules (NEIBMs) derived from the in vitro molecular evolution of combinatorial phage libraries displaying randomly rearranged Ig-binding domains of protein A and protein L. These molecules all showed novel Ig-binding properties of double-site binding to the VH3 and Vκ regions of human Ig Fab and high affinity for human IgM, which enhanced IgM detection in the anti-HCV ELISA assay. In this double-site binding, the A domain binds to the VH3 chain with low affinity. Whether the appropriate mutations in the A domain could improve this binding remains unknown. In this study, four combinatorial phage libraries displaying AL mutants with random mutations at different amino acid positions in the A domain were constructed. Seven AL mutant phages with significantly improved Ig binding activity were obtained from the phage library displaying AL mutants randomly mutated at positions 27 and 34 through human IgM-directed in vitro evolution. Two of the seven prokaryotically expressed AL mutants, AL (VV) and AL (KA), exhibited IgM and IgG binding activities equivalent to those of wild-type AL, whereas other mutants showed attenuated binding. However, after labeling with HRP, AL (VV) and AL (KA) showed improved IgM and IgG binding activity, which significantly improved the detection in the anti-HCV assay. Thus, the present study demonstrates that the binding properties of AL were successfully improved through phage-based molecular evolution, which could substantially contribute to the use of AL in antibody detection, and provides an example of successful protein engineering through in vitro molecular evolution.

  13. Detecting the signatures of adaptive evolution in protein-coding genes.

    PubMed

    Bielawski, Joseph P

    2013-01-01

    The field of molecular evolution, which includes genome evolution, is devoted to finding variation within and between groups of organisms and explaining the processes responsible for generating this variation. Many DNA changes are believed to have little to no functional effect, and a neutral process will best explain their evolution. Thus, a central task is to discover which changes had positive fitness consequences and were subject to Darwinian natural selection during the course of evolution. Due the size and complexity of modern molecular datasets, the field has come to rely extensively on statistical modeling techniques to meet this analytical challenge. For DNA sequences that encode proteins, one of the most powerful approaches is to employ a statistical model of codon evolution. This unit provides a general introduction to the practice of modeling codon evolution using the statistical framework of maximum likelihood. Four real-data analysis activities are used to illustrate the principles of parameter estimation, robustness, hypothesis testing, and site classification. Each activity includes an explicit analytical protocol based on programs provided by the Phylogenetic Analysis by Maximum Likelihood (PAML) package.

  14. Molecular tools and bumble bees: revealing hidden details of ecology and evolution in a model system.

    PubMed

    Woodard, S Hollis; Lozier, Jeffrey D; Goulson, David; Williams, Paul H; Strange, James P; Jha, Shalene

    2015-06-01

    Bumble bees are a longstanding model system for studies on behaviour, ecology and evolution, due to their well-studied social lifestyle, invaluable role as wild and managed pollinators, and ubiquity and diversity across temperate ecosystems. Yet despite their importance, many aspects of bumble bee biology have remained enigmatic until the rise of the genetic and, more recently, genomic eras. Here, we review and synthesize new insights into the ecology, evolution and behaviour of bumble bees that have been gained using modern genetic and genomic techniques. Special emphasis is placed on four areas of bumble bee biology: the evolution of eusociality in this group, population-level processes, large-scale evolutionary relationships and patterns, and immunity and resistance to pesticides. We close with a prospective on the future of bumble bee genomics research, as this rapidly advancing field has the potential to further revolutionize our understanding of bumble bees, particularly in regard to adaptation and resilience. Worldwide, many bumble bee populations are in decline. As such, throughout the review, connections are drawn between new molecular insights into bumble bees and our understanding of the causal factors involved in their decline. Ongoing and potential applications to bumble bee management and conservation are also included to demonstrate how genetics- and genomics-enabled research aids in the preservation of this threatened group.

  15. Molecular Evolution of Drosophila Germline Stem Cell and Neural Stem Cell Regulating Genes.

    PubMed

    Choi, Jae Young; Aquadro, Charles F

    2015-10-27

    Here, we study the molecular evolution of a near complete set of genes that had functional evidence in the regulation of the Drosophila germline and neural stem cell. Some of these genes have previously been shown to be rapidly evolving by positive selection raising the possibility that stem cell genes as a group have elevated signatures of positive selection. Using recent Drosophila comparative genome sequences and population genomic sequences of Drosophila melanogaster, we have investigated both long- and short-term evolution occurring across these two different stem cell systems, and compared them with a carefully chosen random set of genes to represent the background rate of evolution. Our results showed an excess of genes with evidence of a recent selective sweep in both germline and neural stem cells in D. melanogaster. However compared with their control genes, both stem cell systems had no significant excess of genes with long-term recurrent positive selection in D. melanogaster, or across orthologous sequences from the melanogaster group. The evidence of long-term positive selection was limited to a subset of genes with specific functions in both the germline and neural stem cell system.

  16. Adaptive molecular evolution of a defence gene in sexual but not functionally asexual evening primroses.

    PubMed

    Hersch-Green, E I; Myburg, H; Johnson, M T J

    2012-08-01

    Theory predicts that sexual reproduction provides evolutionary advantages over asexual reproduction by reducing mutational load and increasing adaptive potential. Here, we test the latter prediction in the context of plant defences against pathogens because pathogens frequently reduce plant fitness and drive the evolution of plant defences. Specifically, we ask whether sexual evening primrose plant lineages (Onagraceae) have faster rates of adaptive molecular evolution and altered gene expression of a class I chitinase, a gene implicated in defence against pathogens, than functionally asexual evening primrose lineages. We found that the ratio of amino acid to silent substitutions (K(a) /K(s) = 0.19 vs. 0.11 for sexual and asexual lineages, respectively), the number of sites identified to be under positive selection (four vs. zero for sexual and asexual lineages, respectively) and the expression of chitinase were all higher in sexual than in asexual lineages. Our results are congruent with the conclusion that a loss of sexual recombination and segregation in the Onagraceae negatively affects adaptive structural and potentially regulatory evolution of a plant defence protein.

  17. Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life

    PubMed Central

    Pentinsaari, Mikko; Salmela, Heli; Mutanen, Marko; Roslin, Tomas

    2016-01-01

    DNA barcodes are widely used for identification and discovery of species. While such use draws on information at the DNA level, the current amassment of ca. 4.7 million COI barcodes also offers a unique resource for exploring functional constraints on DNA evolution. Here, we explore amino acid variation in a crosscut of the entire animal kingdom. Patterns of DNA variation were linked to functional constraints at the level of the amino acid sequence in functionally important parts of the enzyme. Six amino acid sites show variation with possible effects on enzyme function. Overall, patterns of amino acid variation suggest convergent or parallel evolution at the protein level connected to the transition into a parasitic life style. Denser sampling of two diverse insect taxa revealed that the beetles (Coleoptera) show more amino acid variation than the butterflies and moths (Lepidoptera), indicating fundamental difference in patterns of molecular evolution in COI. Several amino acid sites were found to be under notably strong purifying selection in Lepidoptera as compared to Coleoptera. Overall, these findings demonstrate the utility of the global DNA barcode library to extend far beyond identification and taxonomy, and will hopefully be followed by a multitude of work. PMID:27734964

  18. Evolution of apolar sporocytes in marchantialean liverworts: implications from molecular phylogeny.

    PubMed

    Shimamura, Masaki; Itouga, Misao; Tsubota, Hiromi

    2012-03-01

    In meiosis of basal land plants, meiotic division planes are typically predicted by quadri-lobing of the cytoplasm and/or quadri-partitioning of plastids prior to nuclear divisions. However, sporocytes of several marchantialean liverworts display no indication of premeiotic establishment of quadripolarity, as is observed in flowering plants. In these cases, the shape of sporocytes remains spherical or elliptical and numerous plastids are distributed randomly in the cytoplasm during meiosis. Through a survey of sporocyte morphology in marchantialean liverworts, we newly report the occurrence of apolar sporocytes in Sauteria japonica and Athalamia nana (Cleveaceae; Marchantiales). Molecular phylogenetic analyses revealed that the quadri-lobing of cytoplasm and quadri-partitioning of plastids were lost independently several times during the evolution of marchantialean liverworts. In addition, our phylogenetic analyses indicate that the simplified sporophytes of several marchantialean liverworts are not a primitive condition but rather represent the result of reductive evolution. The loss of the quadripolarity of sporocytes appears to correlate with the evolutionary trend of the sporophyte towards reductions. Through the evolution of the simplified sporophytes, suppression of mitotic divisions of sporogenous cells might had caused not only the modification of sporophyte ontogeny but also the drastic cytological change of sporocyte.

  19. A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution

    PubMed Central

    Danley, Patrick D; Mullen, Sean P; Liu, Fenglong; Nene, Vishvanath; Quackenbush, John; Shaw, Kerry L

    2007-01-01

    Background As the developmental costs of genomic tools decline, genomic approaches to non-model systems are becoming more feasible. Many of these systems may lack advanced genetic tools but are extremely valuable models in other biological fields. Here we report the development of expressed sequence tags (EST's) in an orthopteroid insect, a model for the study of neurobiology, speciation, and evolution. Results We report the sequencing of 14,502 EST's from clones derived from a nerve cord cDNA library, and the subsequent construction of a Gene Index from these sequences, from the Hawaiian trigonidiine cricket Laupala kohalensis. The Gene Index contains 8607 unique sequences comprised of 2575 tentative consensus (TC) sequences and 6032 singletons. For each of the unique sequences, an attempt was made to assign a provisional annotation and to categorize its function using a Gene Ontology-based classification through a sequence-based comparison to known proteins. In addition, a set of unique 70 base pair oligomers that can be used for DNA microarrays was developed. All Gene Index information is posted at the DFCI Gene Indices web page Conclusion Orthopterans are models used to understand the neurophysiological basis of complex motor patterns such as flight and stridulation. The sequences presented in the cricket Gene Index will provide neurophysiologists with many genetic tools that have been largely absent in this field. The cricket Gene Index is one of only two gene indices to be developed in an evolutionary model system. Species within the genus Laupala have speciated recently, rapidly, and extensively. Therefore, the genes identified in the cricket Gene Index can be used to study the genomics of speciation. Furthermore, this gene index represents a significant EST resources for basal insects. As such, this resource is a valuable comparative tool for the understanding of invertebrate molecular evolution. The sequences presented here will provide much needed genomic

  20. Evolution of dark colour in toucans (Ramphastidae): a case of molecular adaptation?

    PubMed

    Corso, J; Mundy, N I; Fagundes, N J R; de Freitas, T R O

    2016-12-01

    In the last decades, researchers have been able to determine the molecular basis of some phenotypes, to test for evidence of natural selection upon them, and to demonstrate that the same genes or genetic pathways can be associated with convergent traits. Colour traits are often subject to natural selection because even small changes in these traits can have a large effect on fitness via camouflage, sexual selection or other mechanisms. The melanocortin-1 receptor locus (MC1R) is frequently associated with intraspecific coat colour variation in vertebrates, but it has been far harder to demonstrate that this locus is involved in adaptive interspecific colour differences. Here, we investigate the contribution of the MC1R gene to the colour diversity found in toucans (Ramphastidae). We found divergent selection on MC1R in the clade represented by the genus Ramphastos and that this coincided with the evolution of darker plumage in members of this genus. Using phylogenetically corrected correlations, we show significant and specific relationships between the rate of nonsynonymous change in MC1R (dN) and plumage darkness across Ramphastidae, and also between the rate of functionally significant amino acid changes in MC1R and plumage darkness. Furthermore, three of the seven amino acid changes in MC1R that occurred in the ancestral Ramphastos branch are associated with melanism in other birds. Taken together, our results suggest that the dark colour of Ramphastos toucans was related to nonsynonymous substitutions in MC1R that may have been subject to positive selection or to a relaxation of selective pressure. These results also demonstrate a quantitative relationship between gene and phenotype evolution, representing an example of how MC1R molecular evolution may affect macroevolution of plumage phenotypes.

  1. Gradual molecular evolution of a sex determination switch through incomplete penetrance of femaleness.

    PubMed

    Beye, Martin; Seelmann, Christine; Gempe, Tanja; Hasselmann, Martin; Vekemans, Xavier; Fondrk, M Kim; Page, Robert E

    2013-12-16

    Some genes regulate phenotypes that are either present or absent. They are often important regulators of developmental switches and are involved in morphological evolution. We have little understanding of the molecular mechanisms by which these absence/presence gene functions have evolved, because the phenotype and fitness of molecular intermediate forms are unknown. Here, we studied the sex-determining switch of 14 natural sequence variants of the csd gene among 76 genotypes of the honeybee (Apis mellifera). Heterozygous genotypes (different specificities) of the csd gene determine femaleness, while hemizygous genotypes (single specificity) determine maleness. Homozygous genotypes of the csd gene (same specificity) are lethal. We found that at least five amino acid differences and length variation between Csd specificities in the specifying domain (PSD) were sufficient to regularly induce femaleness. We estimated that, on average, six pairwise amino acid differences evolved under positive selection. We also identified a natural evolutionary intermediate that showed only three amino acid length differences in the PSD relative to its parental allele. This genotype showed an intermediate fitness because it implemented lethality regularly and induced femaleness infrequently (i.e., incomplete penetrance). We suggest incomplete penetrance as a mechanism through which new molecular switches can gradually and adaptively evolve.

  2. Engineering and Evolution of Molecular Chaperones and Protein Disaggregases with Enhanced Activity

    PubMed Central

    Mack, Korrie L.; Shorter, James

    2016-01-01

    Cells have evolved a sophisticated proteostasis network to ensure that proteins acquire and retain their native structure and function. Critical components of this network include molecular chaperones and protein disaggregases, which function to prevent and reverse deleterious protein misfolding. Nevertheless, proteostasis networks have limits, which when exceeded can have fatal consequences as in various neurodegenerative disorders, including Parkinson's disease and amyotrophic lateral sclerosis. A promising strategy is to engineer proteostasis networks to counter challenges presented by specific diseases or specific proteins. Here, we review efforts to enhance the activity of individual molecular chaperones or protein disaggregases via engineering and directed evolution. Remarkably, enhanced global activity or altered substrate specificity of various molecular chaperones, including GroEL, Hsp70, ClpX, and Spy, can be achieved by minor changes in primary sequence and often a single missense mutation. Likewise, small changes in the primary sequence of Hsp104 yield potentiated protein disaggregases that reverse the aggregation and buffer toxicity of various neurodegenerative disease proteins, including α-synuclein, TDP-43, and FUS. Collectively, these advances have revealed key mechanistic and functional insights into chaperone and disaggregase biology. They also suggest that enhanced chaperones and disaggregases could have important applications in treating human disease as well as in the purification of valuable proteins in the pharmaceutical sector. PMID:27014702

  3. Molecular Corridor Based Approach for Description of Evolution of Secondary Organic Aerosols

    NASA Astrophysics Data System (ADS)

    Li, Y., Sr.; Poeschl, U.; Shiraiwa, M.

    2015-12-01

    Organic aerosol is ubiquitous in the atmosphere and its major component is secondary organic aerosol (SOA). Formation and evolution of SOA is a complex process involving coupled chemical reactions and mass transport in the gas and particle phases (Shiraiwa et al., 2014). Current air quality models do not embody the full spectrum of reaction and transport processes, nor do they identify the dominant rate-limiting steps in SOA formation, resulting in the significant underprediction of observed SOA concentrations, which precludes reliable quantitative predictions of aerosols and their environmental impacts. Recently, it has been suggested that the SOA chemical evolution can be represented well by "molecular corridor" with a tight inverse correlation between molar mass and volatility of SOA oxidation products (Shiraiwa et al., 2014). Here we further analyzed the structure, molar mass and volatility of 31,000 unique organic compounds. These compounds include oxygenated organic compounds as well as nitrogen- and sulfur-containing organics such as amines, organonitrates, and organosulfates. Results show that most of those compounds fall into this two-dimensional (2-D) space, which is constrained by two boundary lines corresponding to the volatility of n -alkanes CnH2n+2 and sugar alcohols CnH2n+2On. A method to predict the volatility of nitrogen- and sulfur- containing compounds is developed based on those 31,000 organic compounds. It is shown that the volatility can be well predicted as a function of chemical composition numbers, providing a way to apply this 2-D space to organic compounds observed in real atmosphere. A comprehensive set of observation data from laboratory experiments, field campaigns and indoor measurements is mapped to the molecular corridor. This 2-D space can successfully grasp the properties of organic compounds formed in different atmospheric conditions. The molecular corridor represents a new framework in which chemical and physical properties as

  4. PyEvolve: a toolkit for statistical modelling of molecular evolution

    PubMed Central

    Butterfield, Andrew; Vedagiri, Vivek; Lang, Edward; Lawrence, Cath; Wakefield, Matthew J; Isaev, Alexander; Huttley, Gavin A

    2004-01-01

    Background Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences – ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. Results Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from ~10 days to ~6 hours. Conclusion PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be

  5. Evolution in an RNA World

    PubMed Central

    Joyce, Gerald F.

    2009-01-01

    A longstanding research goal has been to develop a self-sustained chemical system that is capable of undergoing Darwinian evolution. The notion of primitive RNA-based life suggests this goal might be achieved by constructing an RNA enzyme that catalyzes the replication of RNA molecules, including the RNA enzyme itself. This reaction recently was demonstrated in a cross-catalytic system involving two RNA enzymes that catalyze each other’s synthesis from a total of four component substrates. The cross-replicating RNA enzymes undergo self-sustained exponential amplification at a constant temperature in the absence of proteins or other biological materials. Amplification occurs with a doubling time of 30–60 min, and can be continued indefinitely. Small populations of cross-replicating RNA enzymes can be made to compete for limited resources within a common environment. The molecules reproduce with high fidelity, but occasionally give rise to recombinants that also can replicate. Over the course of many “generations” of selective amplification, novel variants arise and grow to dominate the population based on their relative fitness under the chosen reaction conditions. This is the first example, outside of biology, of evolutionary adaptation in a molecular genetic system. PMID:19667013

  6. How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis

    PubMed Central

    Woese, Carl R.; Goldenfeld, Nigel

    2009-01-01

    Summary: In this commentary, we provide a personal overview of the conceptual history of microbiology and molecular biology over the course of the last hundred years, emphasizing the relationship of these fields to the problem of evolution. We argue that despite their apparent success, all three reached an impasse that arose from the influence of dogmatic or overly narrow perspectives. Finally, we describe how recent developments in microbiology are realizing Beijerinck's vision of a field that is fully integrated with molecular biology, microbial ecology, thereby challenging and extending current thinking in evolution. PMID:19258530

  7. Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms.

    PubMed

    Beaulieu, Jeremy M; O'Meara, Brian C; Crane, Peter; Donoghue, Michael J

    2015-09-01

    Dating analyses based on molecular data imply that crown angiosperms existed in the Triassic, long before their undisputed appearance in the fossil record in the Early Cretaceous. Following a re-analysis of the age of angiosperms using updated sequences and fossil calibrations, we use a series of simulations to explore the possibility that the older age estimates are a consequence of (i) major shifts in the rate of sequence evolution near the base of the angiosperms and/or (ii) the representative taxon sampling strategy employed in such studies. We show that both of these factors do tend to yield substantially older age estimates. These analyses do not prove that younger age estimates based on the fossil record are correct, but they do suggest caution in accepting the older age estimates obtained using current relaxed-clock methods. Although we have focused here on the angiosperms, we suspect that these results will shed light on dating discrepancies in other major clades.

  8. Molecular co-catalyst accelerating hole transfer for enhanced photocatalytic H2 evolution

    PubMed Central

    Bi, Wentuan; Li, Xiaogang; Zhang, Lei; Jin, Tao; Zhang, Lidong; Zhang, Qun; Luo, Yi; Wu, Changzheng; Xie, Yi

    2015-01-01

    In artificial photocatalysis, sluggish kinetics of hole transfer and the resulting high-charge recombination rate have been the Achilles' heel of photocatalytic conversion efficiency. Here we demonstrate water-soluble molecules as co-catalysts to accelerate hole transfer for improved photocatalytic H2 evolution activity. Trifluoroacetic acid (TFA), by virtue of its reversible redox couple TFA·/TFA−, serves as a homogeneous co-catalyst that not only maximizes the contact areas between co-catalysts and reactants but also greatly promotes hole transfer. Thus K4Nb6O17 nanosheet catalysts achieve drastically increased photocatalytic H2 production rate in the presence of TFA, up to 32 times with respect to the blank experiment. The molecular co-catalyst represents a new, simple and highly effective approach to suppress recombination of photogenerated charges, and has provided fertile new ground for creating high-efficiency photosynthesis systems, avoiding use of noble-metal co-catalysts. PMID:26486863

  9. Oxygen evolution on a SrFeO3 anode - Mechanistic considerations from molecular orbital theory

    NASA Technical Reports Server (NTRS)

    Mehandru, S. P.; Anderson, Alfred B.

    1989-01-01

    Various pathways proposed in the literature for the evolution of O2 in electrochemical oxidations are explored using the atom superposition and electron delocalization molecular orbital (ASED-MO) theory and the cluster models of the SrFeO3 surface as a prototype material. Calculations indicate that oxygen atoms can be easily formed on the (100) surface as well as on the edge cation sites of a SrFeO3 anode by the discharge of OH(-), followed by its deprotonation and electron transfer to the electrode. The O atoms can form O2 on the edge and corner sites, where the Fe(4+) is coordinated to four and three bulk oxygen anions, respectively. The calculations strongly disfavor mechanisms involving coupling of oxygen atoms adsorbed on different cations as well as a mechanism featuring an ozone intermediate.

  10. Molecular co-catalyst accelerating hole transfer for enhanced photocatalytic H2 evolution

    NASA Astrophysics Data System (ADS)

    Bi, Wentuan; Li, Xiaogang; Zhang, Lei; Jin, Tao; Zhang, Lidong; Zhang, Qun; Luo, Yi; Wu, Changzheng; Xie, Yi

    2015-10-01

    In artificial photocatalysis, sluggish kinetics of hole transfer and the resulting high-charge recombination rate have been the Achilles' heel of photocatalytic conversion efficiency. Here we demonstrate water-soluble molecules as co-catalysts to accelerate hole transfer for improved photocatalytic H2 evolution activity. Trifluoroacetic acid (TFA), by virtue of its reversible redox couple TFA./TFA-, serves as a homogeneous co-catalyst that not only maximizes the contact areas between co-catalysts and reactants but also greatly promotes hole transfer. Thus K4Nb6O17 nanosheet catalysts achieve drastically increased photocatalytic H2 production rate in the presence of TFA, up to 32 times with respect to the blank experiment. The molecular co-catalyst represents a new, simple and highly effective approach to suppress recombination of photogenerated charges, and has provided fertile new ground for creating high-efficiency photosynthesis systems, avoiding use of noble-metal co-catalysts.

  11. Tethering metal ions to photocatalyst particulate surfaces by bifunctional molecular linkers for efficient hydrogen evolution.

    PubMed

    Yu, Weili; Isimjan, Tayirjan; Del Gobbo, Silvano; Anjum, Dalaver H; Abdel-Azeim, Safwat; Cavallo, Luigi; Garcia-Esparza, Angel T; Domen, Kazunari; Xu, Wei; Takanabe, Kazuhiro

    2014-09-01

    A simple and versatile method for the preparation of photocatalyst particulates modified with effective cocatalysts is presented; the method involves the sequential soaking of photocatalyst particulates in solutions containing bifunctional organic linkers and metal ions. The modification of the particulate surfaces is a universal and reproducible method because the molecular linkers utilize strong covalent bonds, which in turn result in modified monolayer with a small but controlled quantity of metals. The photocatalysis results indicated that the CdS with likely photochemically reduced Pd and Ni, which were initially immobilized via ethanedithiol (EDT) as a linker, were highly efficient for photocatalytic hydrogen evolution from Na2S-Na2SO3-containing aqueous solutions. The method developed in this study opens a new synthesis route for the preparation of effective photocatalysts with various combinations of bifunctional linkers, metals, and photocatalyst particulate materials.

  12. Dynamics of the Eigen and the Crow-Kimura models for molecular evolution

    NASA Astrophysics Data System (ADS)

    Saakian, David B.; Rozanova, Olga; Akmetzhanov, Andrei

    2008-10-01

    We introduce an alternative way to study molecular evolution within well-established Hamilton-Jacobi formalism, showing that for a broad class of fitness landscapes it is possible to derive dynamics analytically within the 1/N accuracy, where N is the genome length. For a smooth and monotonic fitness function this approach gives two dynamical phases: smooth dynamics and discontinuous dynamics. The latter phase arises naturally with no explicite singular fitness function, counterintuitively. The Hamilton-Jacobi method yields straightforward analytical results for the models that utilize fitness as a function of Hamming distance from a reference genome sequence. We also show the way in which this method gives dynamical phase structure for multipeak fitness.

  13. Cosmic Structure and Galaxy Evolution through Intensity Mapping of Molecular Gas

    NASA Astrophysics Data System (ADS)

    Bower, Geoffrey C.; Keating, Garrett K.; Marrone, Daniel P.; YT Lee Array Team, SZA Team

    2016-01-01

    The origin and evolution of structure in the Universe is one of the major challenges of observational astronomy. How does baryonic structure trace the underlying dark matter? How have galaxies evolved to produce the present day Universe? A multi-wavelength, multi-tool approach is necessary to provide the complete story of the evolution of structure in the Universe. Intensity mapping, which relies on the ability to detect many objects at once through their integrated emission rather than direct detection of individual objects, is a critical part of this mosaic. In particular, our understanding of the molecular gas component of massive galaxies is being revolutionized by ALMA and EVLA but the population of smaller, star-forming galaxies, which provide the bulk of star formation cannot be individually probed by these instruments.In this talk, I will summarize two intensity mapping experiments to detect molecular gas through the carbon monoxide (CO) rotational transition. We have completed sensitive observations with the Sunyaev-Zel'dovic Array (SZA) telescope at a wavelength of 1 cm that are sensitive to emission at redshifts 2.3 to 3.3. The SZA experiments sets strong limits on models for the CO emission and demonstrates the ability to reject foregrounds and telescope systematics in very deep integrations. I also describe the development of an intensity mapping capability for the Y.T. Lee Array, a 13-element interferometer located on Mauna Loa. In its first phase, this project focuses on detection of CO at redshifts 2.4 - 3.0 with detection via power spectrum and cross-correlation with other surveys. The project includes a major technical upgrade, a new digital correlator and IF electronics component to be deployed in 2015/2016. The Y.T. Lee Array observations will be more sensitive and extend to larger angular scales than the SZA observations.

  14. Molecular Evolution and Functional Divergence of Trace Amine–Associated Receptors

    PubMed Central

    Eyun, Seong-il; Moriyama, Hideaki; Hoffmann, Federico G.; Moriyama, Etsuko N.

    2016-01-01

    Trace amine-associated receptors (TAARs) are a member of the G-protein-coupled receptor superfamily and are known to be expressed in olfactory sensory neurons. A limited number of molecular evolutionary studies have been done for TAARs so far. To elucidate how lineage-specific evolution contributed to their functional divergence, we examined 30 metazoan genomes. In total, 493 TAAR gene candidates (including 84 pseudogenes) were identified from 26 vertebrate genomes. TAARs were not identified from non-vertebrate genomes. An ancestral-type TAAR-like gene appeared to have emerged in lamprey. We found four therian-specific TAAR subfamilies (one eutherian-specific and three metatherian-specific) in addition to previously known nine subfamilies. Many species-specific TAAR gene duplications and losses contributed to a large variation of TAAR gene numbers among mammals, ranging from 0 in dolphin to 26 in flying fox. TAARs are classified into two groups based on binding preferences for primary or tertiary amines as well as their sequence similarities. Primary amine-detecting TAARs (TAAR1-4) have emerged earlier, generally have single-copy orthologs (very few duplication or loss), and have evolved under strong functional constraints. In contrast, tertiary amine-detecting TAARs (TAAR5-9) have emerged more recently and the majority of them experienced higher rates of gene duplications. Protein members that belong to the tertiary amine-detecting TAAR group also showed the patterns of positive selection especially in the area surrounding the ligand-binding pocket, which could have affected ligand-binding activities and specificities. Expansions of the tertiary amine-detecting TAAR gene family may have played important roles in terrestrial adaptations of therian mammals. Molecular evolution of the TAAR gene family appears to be governed by a complex, species-specific, interplay between environmental and evolutionary factors. PMID:26963722

  15. Molecular Evolution of Slow and Quick Anion Channels (SLACs and QUACs/ALMTs)

    PubMed Central

    Dreyer, Ingo; Gomez-Porras, Judith Lucia; Riaño-Pachón, Diego Mauricio; Hedrich, Rainer; Geiger, Dietmar

    2012-01-01

    Electrophysiological analyses conducted about 25 years ago detected two types of anion channels in the plasma membrane of guard cells. One type of channel responds slowly to changes in membrane voltage while the other responds quickly. Consequently, they were named SLAC, for SLow Anion Channel, and QUAC, for QUick Anion Channel. Recently, genes SLAC1 and QUAC1/ALMT12, underlying the two different anion current components, could be identified in the model plant Arabidopsis thaliana. Expression of the gene products in Xenopus oocytes confirmed the quick and slow current kinetics. In this study we provide an overview on our current knowledge on slow and quick anion channels in plants and analyze the molecular evolution of ALMT/QUAC-like and SLAC-like channels. We discovered fingerprints that allow screening databases for these channel types and were able to identify 192 (177 non-redundant) SLAC-like and 422 (402 non-redundant) ALMT/QUAC-like proteins in the fully sequenced genomes of 32 plant species. Phylogenetic analyses provided new insights into the molecular evolution of these channel types. We also combined sequence alignment and clustering with predictions of protein features, leading to the identification of known conserved phosphorylation sites in SLAC1-like channels along with potential sites that have not been yet experimentally confirmed. Using a similar strategy to analyze the hydropathicity of ALMT/QUAC-like channels, we propose a modified topology with additional transmembrane regions that integrates structure and function of these membrane proteins. Our results suggest that cross-referencing phylogenetic analyses with position-specific protein properties and functional data could be a very powerful tool for genome research approaches in general. PMID:23226151

  16. Molecular evolution of mollusc shell proteins: insights from proteomic analysis of the edible mussel Mytilus.

    PubMed

    Marie, Benjamin; Le Roy, Nathalie; Zanella-Cléon, Isabelle; Becchi, Michel; Marin, Frédéric

    2011-06-01

    Shell matrix proteins (SMPs) that are embedded within calcified layers of mollusc shells are believed to play an essential role in controlling the biomineral synthesis and in increasing its mechanical properties. Among the wide diversity of mollusc shell textures, nacro-prismatic shells represent a tremendous opportunity for the investigation of the SMP evolution. Indeed, nacro-prismatic texture appears early in Cambrian molluscs and is still present in the shell of some bivalves, gastropods, cephalopods and very likely also, of some monoplacophorans. One key question is to know whether these shells are constructed from similar matrix protein assemblages, i.e. whether they share a common origin. Most of the molecular data published so far are restricted to two genera, the bivalve Pinctada and the gastropod Haliotis. The shell protein content of these two genera are clearly different, suggesting independent origins or considerable genetic drift from a common ancestor. In order to describe putatively conserved mollusc shell proteins, here we have investigated the SMP set of a new bivalve model belonging to another genera, the edible mussel Mytilus, using an up-to-date proteomic approach based on the interrogation of more than 70,000 EST sequences, recently available from NCBI public databases. We describe nine novel SMPs, among which three are completely novel, four are homologues of Pinctada SMPs and two are very likely homologues of Haliotis SMPs. This latter result constitutes the first report of conserved SMPs between bivalves and gastropods. More generally, our data suggest that mollusc SMP set may follow a mosaic pattern within the different mollusc models (Mytilus, Pinctada, Haliotis). We discuss the function of such proteins in calcifying matrices, the molecular evolution of SMP genes and the origin of mollusc nacro-prismatic SMPs.

  17. Host shifts and molecular evolution of H7 avian influenza virus hemagglutinin

    PubMed Central

    2011-01-01

    Evolutionary consequences of host shifts represent a challenge to identify the mechanisms involved in the emergence of influenza A (IA) viruses. In this study we focused on the evolutionary history of H7 IA virus in wild and domestic birds, with a particular emphasis on host shifts consequences on the molecular evolution of the hemagglutinin (HA) gene. Based on a dataset of 414 HA nucleotide sequences, we performed an extensive phylogeographic analysis in order to identify the overall genetic structure of H7 IA viruses. We then identified host shift events and investigated viral population dynamics in wild and domestic birds, independently. Finally, we estimated changes in nucleotide substitution rates and tested for positive selection in the HA gene. A strong association between the geographic origin and the genetic structure was observed, with four main clades including viruses isolated in North America, South America, Australia and Eurasia-Africa. We identified ten potential events of virus introduction from wild to domestic birds, but little evidence for spillover of viruses from poultry to wild waterbirds. Several sites involved in host specificity (addition of a glycosylation site in the receptor binding domain) and virulence (insertion of amino acids in the cleavage site) were found to be positively selected in HA nucleotide sequences, in genetically unrelated lineages, suggesting parallel evolution for the HA gene of IA viruses in domestic birds. These results highlight that evolutionary consequences of bird host shifts would need to be further studied to understand the ecological and molecular mechanisms involved in the emergence of domestic bird-adapted viruses. PMID:21711553

  18. Molecular Evolution and Phylodynamics of Acute Hepatitis B Virus in Japan

    PubMed Central

    Lin, Serena Y. C.; Toyoda, Hidenori; Kumada, Takashi; Liu, Hsin-Fu

    2016-01-01

    Hepatitis B virus (HBV) is prevalent worldwide and causes liver diseases, including acute and chronic hepatitis. Ten HBV genotypes (A–J) with distinct geographic distributions have been reported. Cases of acute HBV infection with genotype A have increased in Japan nationwide since the 1990s, mainly through sexual transmission. To investigate the molecular evolution and phylodynamics of HBV genotypes, we collected acute HBV isolates acquired in Japan from 1992–2002. Full genomes were obtained for comprehensive phylogenetic and phylodynamic analysis, with other Japanese HBV sequences from GenBank that were isolated during 1991–2010. HBV genotypes were classified using the maximum-likelihood and Bayesian methods. The GMRF Bayesian Skyride was used to estimate the evolution and population dynamics of HBV. Four HBV genotypes (A, B, C, and H) were identified, of which C was the major genotype. The phylodynamic results indicated an exponential growth between the 1960s and early 1990s; this was followed by a population bottleneck after 1995, possibly linked with successful implementation of a nationwide vaccination program. However, HBV/A increased from 1990 to 2003–2004, and then started to decrease. The prevalence of genotype A has increased over the past 10 years. Phylodynamic inference clearly demonstrates a steady population growth compatible with an ongoing subepidemic; this might be due to the loss of immunity to HBV in adolescents and people being born before the vaccination program. This is the first phylodynamic study of HBV infection in Japan and will facilitate understanding the molecular epidemiology and long-term evolutionary dynamics of this virus in Japan. PMID:27280441

  19. Hypoallergens for allergen-specific immunotherapy by directed molecular evolution of mite group 2 allergens.

    PubMed

    Gafvelin, Guro; Parmley, Stephen; Neimert-Andersson, Theresa; Blank, Ulrich; Eriksson, Tove L J; van Hage, Marianne; Punnonen, Juha

    2007-02-09

    Allergen-specific immunotherapy is the only treatment that provides long lasting relief of allergic symptoms. Currently, it is based on repeated administration of allergen extracts. To improve the safety and efficacy of allergen extract-based immunotherapy, application of hypoallergens, i.e. modified allergens with reduced IgE binding capacity but retained T-cell reactivity, has been proposed. It may, however, be difficult to predict how to modify an allergen to create a hypoallergen. Directed molecular evolution by DNA shuffling and screening provides a means by which to evolve proteins having novel or improved functional properties without knowledge of structure-function relationships of the target molecules. With the aim to generate hypoallergens we applied multigene DNA shuffling on three group 2 dust mite allergen genes, two isoforms of Lep d 2 and Gly d 2. DNA shuffling yielded a library of genes from which encoded shuffled allergens were expressed and screened. A positive selection was made for full-length, high-expressing clones, and screening for low binding to IgE from mite allergic patients was performed using an IgE bead-based binding assay. Nine selected shuffled allergens revealed 80-fold reduced to completely abolished IgE binding compared with the parental allergens in IgE binding competition experiments. Two hypoallergen candidates stimulated allergen-specific T-cell proliferation and cytokine production at comparable levels as the wild-type allergens in patient peripheral blood mononuclear cell cultures. The two candidates also induced blocking Lep d 2-specific IgG antibodies in immunized mice. We conclude that directed molecular evolution is a powerful approach to generate hypoallergens for potential use in allergen-specific immunotherapy.

  20. Molecular metal-Nx centres in porous carbon for electrocatalytic hydrogen evolution

    NASA Astrophysics Data System (ADS)

    Liang, Hai-Wei; Brüller, Sebastian; Dong, Renhao; Zhang, Jian; Feng, Xinliang; Müllen, Klaus

    2015-08-01

    Replacement of precious platinum with efficient and low-cost catalysts for electrocatalytic hydrogen evolution at low overpotentials holds tremendous promise for clean energy devices. Here we report a novel type of robust cobalt-nitrogen/carbon catalyst for the hydrogen evolution reaction (HER) that is prepared by the pyrolysis of cobalt-N4 macrocycles or cobalt/o-phenylenediamine composites and using silica colloids as a hard template. We identify the well-dispersed molecular CoNx sites on the carbon support as the active sites responsible for the HER. The CoNx/C catalyst exhibits extremely high turnover frequencies per cobalt site in acids, for example, 0.39 and 6.5 s-1 at an overpotential of 100 and 200 mV, respectively, which are higher than those reported for other scalable non-precious metal HER catalysts. Our results suggest the great promise of developing new families of non-precious metal HER catalysts based on the controlled conversion of homogeneous metal complexes into solid-state carbon catalysts via economically scalable protocols.

  1. Molecular evolution of colorectal cancer: from multistep carcinogenesis to the big bang.

    PubMed

    Amaro, Adriana; Chiara, Silvana; Pfeffer, Ulrich

    2016-03-01

    Colorectal cancer is characterized by exquisite genomic instability either in the form of microsatellite instability or chromosomal instability. Microsatellite instability is the result of mutation of mismatch repair genes or their silencing through promoter methylation as a consequence of the CpG island methylator phenotype. The molecular causes of chromosomal instability are less well characterized. Genomic instability and field cancerization lead to a high degree of intratumoral heterogeneity and determine the formation of cancer stem cells and epithelial-mesenchymal transition mediated by the TGF-β and APC pathways. Recent analyses using integrated genomics reveal different phases of colorectal cancer evolution. An initial phase of genomic instability that yields many clones with different mutations (big bang) is followed by an important, previously not detected phase of cancer evolution that consists in the stabilization of several clones and a relatively flat outgrowth. The big bang model can best explain the coexistence of several stable clones and is compatible with the fact that the analysis of the bulk of the primary tumor yields prognostic information.

  2. Molecular evolution of plant haemoglobin: two haemoglobin genes in Nymphaeaceae Euryale ferox.

    PubMed

    Guldner, E; Desmarais, E; Galtier, N; Godelle, B

    2004-01-01

    We isolated and sequenced two haemoglobin genes from the early-branching angiosperm Euryale ferox (Nymphaeaceae). The two genes belong to the two known classes of plant haemoglobin. Their existence in Nymphaeaceae supports the theory that class 1 haemoglobin was ancestrally present in all angiosperms, and is evidence for class 2 haemoglobin being widely distributed. These sequences allowed us to unambiguously root the angiosperm haemoglobin phylogeny, and to corroborate the hypothesis that the class 1/class 2 duplication event occurred before the divergence between monocots and eudicots. We addressed the molecular evolution of plant haemoglobin by comparing the synonymous and nonsynonymous substitution rates in various groups of genes. Class 2 haemoglobin genes of legumes (functionally involved in a symbiosis with nitrogen-fixing bacteria) show a higher nonsynonymous substitution rate than class 1 (nonsymbiotic) haemoglobin genes. This suggests that a change in the selective forces applying to plant haemoglobins has occurred during the evolutionary history of this gene family, potentially in relation with the evolution of symbiosis.

  3. Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life.

    PubMed

    Fournier, Gregory P; Andam, Cheryl P; Alm, Eric J; Gogarten, J Peter

    2011-12-01

    Aminoacyl-tRNA synthetases (aaRS) consist of several families of functionally conserved proteins essential for translation and protein synthesis. Like nearly all components of the translation machinery, most aaRS families are universally distributed across cellular life, being inherited from the time of the Last Universal Common Ancestor (LUCA). However, unlike the rest of the translation machinery, aaRS have undergone numerous ancient horizontal gene transfers, with several independent events detected between domains, and some possibly involving lineages diverging before the time of LUCA. These transfers reveal the complexity of molecular evolution at this early time, and the chimeric nature of genomes within cells that gave rise to the major domains. Additionally, given the role of these protein families in defining the amino acids used for protein synthesis, sequence reconstruction of their pre-LUCA ancestors can reveal the evolutionary processes at work in the origin of the genetic code. In particular, sequence reconstructions of the paralog ancestors of isoleucyl- and valyl- RS provide strong empirical evidence that at least for this divergence, the genetic code did not co-evolve with the aaRSs; rather, both amino acids were already part of the genetic code before their cognate aaRSs diverged from their common ancestor. The implications of this observation for the early evolution of RNA-directed protein biosynthesis are discussed.

  4. Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

    NASA Astrophysics Data System (ADS)

    Fournier, Gregory P.; Andam, Cheryl P.; Alm, Eric J.; Gogarten, J. Peter

    2011-12-01

    Aminoacyl-tRNA synthetases (aaRS) consist of several families of functionally conserved proteins essential for translation and protein synthesis. Like nearly all components of the translation machinery, most aaRS families are universally distributed across cellular life, being inherited from the time of the Last Universal Common Ancestor (LUCA). However, unlike the rest of the translation machinery, aaRS have undergone numerous ancient horizontal gene transfers, with several independent events detected between domains, and some possibly involving lineages diverging before the time of LUCA. These transfers reveal the complexity of molecular evolution at this early time, and the chimeric nature of genomes within cells that gave rise to the major domains. Additionally, given the role of these protein families in defining the amino acids used for protein synthesis, sequence reconstruction of their pre-LUCA ancestors can reveal the evolutionary processes at work in the origin of the genetic code. In particular, sequence reconstructions of the paralog ancestors of isoleucyl- and valyl- RS provide strong empirical evidence that at least for this divergence, the genetic code did not co-evolve with the aaRSs; rather, both amino acids were already part of the genetic code before their cognate aaRSs diverged from their common ancestor. The implications of this observation for the early evolution of RNA-directed protein biosynthesis are discussed.

  5. Molecular phylogeny and character evolution in terete-stemmed Andean opuntias (Cactaceae-Opuntioideae).

    PubMed

    Ritz, C M; Reiker, J; Charles, G; Hoxey, P; Hunt, D; Lowry, M; Stuppy, W; Taylor, N

    2012-11-01

    The cacti of tribe Tephrocacteae (Cactaceae-Opuntioideae) are adapted to diverse climatic conditions over a wide area of the southern Andes and adjacent lowlands. They exhibit a range of life forms from geophytes and cushion-plants to dwarf shrubs, shrubs or small trees. To confirm or challenge previous morphology-based classifications and molecular phylogenies, we sampled DNA sequences from the chloroplast trnK/matK region and the nuclear low copy gene phyC and compared the resulting phylogenies with previous data gathered from nuclear ribosomal DNA sequences. The here presented chloroplast and nuclear low copy gene phylogenies were mutually congruent and broadly coincident with the classification based on gross morphology and seed micro-morphology and anatomy. Reconstruction of hypothetical ancestral character states suggested that geophytes and cushion-forming species probably evolved several times from dwarf shrubby precursors. We also traced an increase of embryo size at the expense of the nucellus-derived storage tissue during the evolution of the Tephrocacteae, which is thought to be an evolutionary advantage because nutrients are then more rapidly accessible for the germinating embryo. In contrast to these highly concordant phylogenies, nuclear ribosomal DNA data sampled by a previous study yielded conflicting phylogenetic signals. Secondary structure predictions of ribosomal transcribed spacers suggested that this phylogeny is strongly influenced by the inclusion of paralogous sequence probably arisen by genome duplication during the evolution of this plant group.

  6. Turning points in the evolution of peroxidase-catalase superfamily: molecular phylogeny of hybrid heme peroxidases.

    PubMed

    Zámocký, Marcel; Gasselhuber, Bernhard; Furtmüller, Paul G; Obinger, Christian

    2014-12-01

    Heme peroxidases and catalases are key enzymes of hydrogen peroxide metabolism and signaling. Here, the reconstruction of the molecular evolution of the peroxidase-catalase superfamily (annotated in pfam as PF00141) based on experimentally verified as well as numerous newly available genomic sequences is presented. The robust phylogenetic tree of this large enzyme superfamily was obtained from 490 full-length protein sequences. Besides already well-known families of heme b peroxidases arranged in three main structural classes, completely new (hybrid type) peroxidase families are described being located at the border of these classes as well as forming (so far missing) links between them. Hybrid-type A peroxidases represent a minor eukaryotic subfamily from Excavates, Stramenopiles and Rhizaria sharing enzymatic and structural features of ascorbate and cytochrome c peroxidases. Hybrid-type B peroxidases are shown to be spread exclusively among various fungi and evolved in parallel with peroxidases in land plants. In some ascomycetous hybrid-type B peroxidases, the peroxidase domain is fused to a carbohydrate binding (WSC) domain. Both here described hybrid-type peroxidase families represent important turning points in the complex evolution of the whole peroxidase-catalase superfamily. We present and discuss their phylogeny, sequence signatures and putative biological function.

  7. The molecular origin and evolution of dim-light vision in mammals.

    PubMed

    Bickelmann, Constanze; Morrow, James M; Du, Jing; Schott, Ryan K; van Hazel, Ilke; Lim, Steve; Müller, Johannes; Chang, Belinda S W

    2015-11-01

    The nocturnal origin of mammals is a longstanding hypothesis that is considered instrumental for the evolution of endothermy, a potential key innovation in this successful clade. This hypothesis is primarily based on indirect anatomical inference from fossils. Here, we reconstruct the evolutionary history of rhodopsin--the vertebrate visual pigment mediating the first step in phototransduction at low-light levels--via codon-based model tests for selection, combined with gene resurrection methods that allow for the study of ancient proteins. Rhodopsin coding sequences were reconstructed for three key nodes: Amniota, Mammalia, and Theria. When expressed in vitro, all sequences generated stable visual pigments with λMAX values similar to the well-studied bovine rhodopsin. Retinal release rates of mammalian and therian ancestral rhodopsins, measured via fluorescence spectroscopy, were significantly slower than those of the amniote ancestor, indicating altered molecular function possibly related to nocturnality. Positive selection along the therian branch suggests adaptive evolution in rhodopsin concurrent with therian ecological diversification events during the Mesozoic that allowed for an exploration of the environment at varying light levels.

  8. Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria-plasmid-phage interaction.

    PubMed

    Harrison, Ellie; Hall, James J P; Paterson, Steve; Spiers, Andrew J; Brockhurst, Michael A

    2017-03-01

    Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage SBW25φ2 and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria. We show that, individually, both plasmids and phages impose selection leading to bacterial evolutionary responses that are distinct from bacterial populations evolving without MGEs, but that together, plasmids and phages impose conflicting selection on bacteria, constraining the evolutionary responses observed in pairwise interactions. Our findings highlight the likely difficulties of predicting evolutionary responses to multiple selective pressures from the observed evolutionary responses to each selective pressure alone. Understanding evolution in complex microbial communities comprising many species and MGEs will require that we go beyond studies of pairwise interactions. This article is protected by copyright. All rights reserved.

  9. Bioinspired Molecular Co-Catalysts Bonded to a Silicon Photocathode for Solar Hydrogen Evolution

    SciTech Connect

    Hou, Yidong

    2011-11-08

    The production of fuels from sunlight represents one of the main challenges in the development of a sustainable energy system. Hydrogen is the simplest fuel to produce and although platinum and other noble metals are efficient catalysts for photoelectrochemical hydrogen evolution earth-abundant alternatives are needed for large-scale use. We show that bioinspired molecular clusters based on molybdenum and sulphur evolve hydrogen at rates comparable to that of platinum. The incomplete cubane-like clusters (Mo{sub 3}S{sub 4}) efficiently catalyse the evolution of hydrogen when coupled to a p-type Si semiconductor that harvests red photons in the solar spectrum. The current densities at the reversible potential match the requirement of a photoelectrochemical hydrogen production system with a solar-to-hydrogen efficiency in excess of 10% (ref. 16). The experimental observations are supported by density functional theory calculations of the Mo{sub 3}S{sub 4} clusters adsorbed on the hydrogen-terminated Si(100) surface, providing insights into the nature of the active site.

  10. Molecular metal–Nx centres in porous carbon for electrocatalytic hydrogen evolution

    PubMed Central

    Liang, Hai-Wei; Brüller, Sebastian; Dong, Renhao; Zhang, Jian; Feng, Xinliang; Müllen, Klaus

    2015-01-01

    Replacement of precious platinum with efficient and low-cost catalysts for electrocatalytic hydrogen evolution at low overpotentials holds tremendous promise for clean energy devices. Here we report a novel type of robust cobalt–nitrogen/carbon catalyst for the hydrogen evolution reaction (HER) that is prepared by the pyrolysis of cobalt–N4 macrocycles or cobalt/o-phenylenediamine composites and using silica colloids as a hard template. We identify the well-dispersed molecular CoNx sites on the carbon support as the active sites responsible for the HER. The CoNx/C catalyst exhibits extremely high turnover frequencies per cobalt site in acids, for example, 0.39 and 6.5 s−1 at an overpotential of 100 and 200 mV, respectively, which are higher than those reported for other scalable non-precious metal HER catalysts. Our results suggest the great promise of developing new families of non-precious metal HER catalysts based on the controlled conversion of homogeneous metal complexes into solid-state carbon catalysts via economically scalable protocols. PMID:26250525

  11. Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.

    PubMed

    Kijima, T E; Innan, Hideki

    2013-11-01

    A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

  12. THE GLOBAL EVOLUTION OF GIANT MOLECULAR CLOUDS. II. THE ROLE OF ACCRETION

    SciTech Connect

    Goldbaum, Nathan J.; Krumholz, Mark R.; Matzner, Christopher D.; McKee, Christopher F.

    2011-09-01

    We present virial models for the global evolution of giant molecular clouds (GMCs). Focusing on the presence of an accretion flow and accounting for the amount of mass, momentum, and energy supplied by accretion and star formation feedback, we are able to follow the growth, evolution, and dispersal of individual GMCs. Our model clouds reproduce the scaling relations observed in both galactic and extragalactic clouds. We find that accretion and star formation contribute roughly equal amounts of turbulent kinetic energy over the lifetime of the cloud. Clouds attain virial equilibrium and grow in such a way as to maintain roughly constant surface densities, with typical surface densities of order 50-200 M{sub sun} pc{sup -2}, in good agreement with observations of GMCs in the Milky Way and nearby external galaxies. We find that as clouds grow, their velocity dispersion and radius must also increase, implying that the linewidth-size relation constitutes an age sequence. Lastly, we compare our models to observations of GMCs and associated young star clusters in the Large Magellanic Cloud and find good agreement between our model clouds and the observed relationship between H II regions, young star clusters, and GMCs.

  13. Molecular Evolution and Functional Characterization of a Bifunctional Decarboxylase Involved in Lycopodium Alkaloid Biosynthesis1[OPEN

    PubMed Central

    Bunsupa, Somnuk; Hanada, Kousuke; Maruyama, Akira; Aoyagi, Kaori; Komatsu, Kana; Ueno, Hideki; Yamashita, Madoka; Sasaki, Ryosuke; Oikawa, Akira; Yamazaki, Mami

    2016-01-01

    Lycopodium alkaloids (LAs) are derived from lysine (Lys) and are found mainly in Huperziaceae and Lycopodiaceae. LAs are potentially useful against Alzheimer’s disease, schizophrenia, and myasthenia gravis. Here, we cloned the bifunctional lysine/ornithine decarboxylase (L/ODC), the first gene involved in LA biosynthesis, from the LA-producing plants Lycopodium clavatum and Huperzia serrata. We describe the in vitro and in vivo functional characterization of the L. clavatum L/ODC (LcL/ODC). The recombinant LcL/ODC preferentially catalyzed the decarboxylation of l-Lys over l-ornithine (l-Orn) by about 5 times. Transient expression of LcL/ODC fused with the amino or carboxyl terminus of green fluorescent protein, in onion (Allium cepa) epidermal cells and Nicotiana benthamiana leaves, showed LcL/ODC localization in the cytosol. Transgenic tobacco (Nicotiana tabacum) hairy roots and Arabidopsis (Arabidopsis thaliana) plants expressing LcL/ODC enhanced the production of a Lys-derived alkaloid, anabasine, and cadaverine, respectively, thus, confirming the function of LcL/ODC in plants. In addition, we present an example of the convergent evolution of plant Lys decarboxylase that resulted in the production of Lys-derived alkaloids in Leguminosae (legumes) and Lycopodiaceae (clubmosses). This convergent evolution event probably occurred via the promiscuous functions of the ancestral Orn decarboxylase, which is an enzyme involved in the primary metabolism of polyamine. The positive selection sites were detected by statistical analyses using phylogenetic trees and were confirmed by site-directed mutagenesis, suggesting the importance of those sites in granting the promiscuous function to Lys decarboxylase while retaining the ancestral Orn decarboxylase function. This study contributes to a better understanding of LA biosynthesis and the molecular evolution of plant Lys decarboxylase. PMID:27303024

  14. Molecular evolution and functional divergence of the metallothionein gene family in vertebrates.

    PubMed

    Serén, Nina; Glaberman, Scott; Carretero, Miguel A; Chiari, Ylenia

    2014-04-01

    The metallothionein (MT) gene superfamily consists of metal-binding proteins involved in various metal detoxification and storage mechanisms. The evolution of this gene family in vertebrates has mostly been studied in mammals using sparse taxon or gene sampling. Genomic databases and available data on MT protein function and expression allow a better understanding of the evolution and functional divergence of the different MT types. We recovered 77 MT coding sequences from 20 representative vertebrates with annotated complete genomes. We found multiple MT genes, also in reptiles, which were thought to have only one MT type. Phylogenetic and synteny analyses indicate the existence of a eutherian MT1 and MT2, a tetrapod MT3, an amniote MT4, and fish MT. The optimal gene-tree/species-tree reconciliation analyses identified the best root in the fish clade. Functional analyses reveal variation in hydropathic index among protein domains, likely correlated with their distinct flexibility and metal affinity. Analyses of functional divergence identified amino acid sites correlated with functional divergence among MT types. Uncovering the number of genes and sites possibly correlated with functional divergence will help to design cost-effective MT functional and gene expression studies. This will permit further understanding of the distinct roles and specificity of these proteins and to properly target specific MT for different types of functional studies. Therefore, this work presents a critical background on the molecular evolution and functional divergence of vertebrate MTs to carry out further detailed studies on the relationship between heavy metal metabolism and tolerances among vertebrates.

  15. Evidence for a convergent slowdown in primate molecular rates and its implications for the timing of early primate evolution

    PubMed Central

    Steiper, Michael E.; Seiffert, Erik R.

    2012-01-01

    A long-standing problem in primate evolution is the discord between paleontological and molecular clock estimates for the time of crown primate origins: the earliest crown primate fossils are ∼56 million y (Ma) old, whereas molecular estimates for the haplorhine-strepsirrhine split are often deep in the Late Cretaceous. One explanation for this phenomenon is that crown primates existed in the Cretaceous but that their fossil remains have not yet been found. Here we provide strong evidence that this discordance is better-explained by a convergent molecular rate slowdown in early primate evolution. We show that molecular rates in primates are strongly and inversely related to three life-history correlates: body size (BS), absolute endocranial volume (EV), and relative endocranial volume (REV). Critically, these traits can be reconstructed from fossils, allowing molecular rates to be predicted for extinct primates. To this end, we modeled the evolutionary history of BS, EV, and REV using data from both extinct and extant primates. We show that the primate last common ancestor had a very small BS, EV, and REV. There has been a subsequent convergent increase in BS, EV, and REV, indicating that there has also been a convergent molecular rate slowdown over primate evolution. We generated a unique timescale for primates by predicting molecular rates from the reconstructed phenotypic values for a large phylogeny of living and extinct primates. This analysis suggests that crown primates originated close to the K–Pg boundary and possibly in the Paleocene, largely reconciling the molecular and fossil timescales of primate evolution. PMID:22474376

  16. Evolution of Life and SETI (Evo-SETI)

    NASA Astrophysics Data System (ADS)

    Maccone, Claudio

    forced by us to have their peak value located on the exponential mean-value curve of the GBM (this is the so-called “Peak-Locus Theorem”). In the framework of Darwinian Evolution, the resulting mathematical construction was shown to identify with Cladistics (refs. [2], [3], [4]). 4) The (Shannon) Entropy of such b-lognormals is then seen to represent the “degree of progress” reached by each living organism or by each big set of living organisms, like historic human civilizations. Having understood this fact, Human History may then be cast into the language of b-lognormals that are more and more organized in time (i.e. having smaller and smaller entropy, or smaller and smaller “chaos”), and have their peaks located on the increasing GBM exponential. This exponential is thus the “trend of progress” in Human History. 5) But our most striking new result is about the well-known “Molecular Clock of Evolution”, namely the “constant rate of Evolution at the molecular level” as shown by Kimura’s Neutral Theory of Molecular Evolution. We showed that that the Molecular Clock identifies with Entropy in our Evo-SETI model because they both grew linearly in time since the origin of life. 6) Furthermore, we applid our Evo-SETI model to lognormal stochastic processes other then the GBMs. For instance, we showed that the Markov-Korotayev (2007-2008, refs. [5], [6]) model for Darwinian Evolution identifies with an Evo-SETI model for which the mean value of the lognormal stochastic process is a cubic (third degree polynomial) function of the time. In conclusion: we have provided a vast mathematical model capable of embracing Molecular Evolution, SETI and Entropy into a simple set of statistical equations based upon b-lognormals pdfs and lognormal stochastic processes Keywords: Molecular Clock, Darwinian evolution, statistical Drake equation, lognormal probability densities, geometric Brownian motion, entropy. REFERENCES [1] Maccone, C. (2008), “The Statistical

  17. Evolution of the fruit endocarp: molecular mechanisms underlying adaptations in seed protection and dispersal strategies

    PubMed Central

    Dardick, Chris; Callahan, Ann M.

    2014-01-01

    Plant evolution is largely driven by adaptations in seed protection and dispersal strategies that allow diversification into new niches. This is evident by the tremendous variation in flowering and fruiting structures present both across and within different plant lineages. Within a single plant family a staggering variety of fruit types can be found such as fleshy fruits including berries, pomes, and drupes and dry fruit structures like achenes, capsules, and follicles. What are the evolutionary mechanisms that enable such dramatic shifts to occur in a relatively short period of time? This remains a fundamental question of plant biology today. On the surface it seems that these extreme differences in form and function must be the consequence of very different developmental programs that require unique sets of genes. Yet as we begin to decipher the molecular and genetic basis underlying fruit form it is becoming apparent that simple genetic changes in key developmental regulatory genes can have profound anatomical effects. In this review, we discuss recent advances in understanding the molecular mechanisms of fruit endocarp tissue differentiation that have contributed to species diversification within three plant lineages. PMID:25009543

  18. The Convergent Evolution of Blue Iris Pigmentation in Primates Took Distinct Molecular Paths

    PubMed Central

    Meyer, Wynn K; Zhang, Sidi; Hayakawa, Sachiko; Imai, Hiroo; Przeworski, Molly

    2013-01-01

    How many distinct molecular paths lead to the same phenotype? One approach to this question has been to examine the genetic basis of convergent traits, which likely evolved repeatedly under a shared selective pressure. We investigated the convergent phenotype of blue iris pigmentation, which has arisen independently in four primate lineages: humans, blue-eyed black lemurs, Japanese macaques, and spider monkeys. Characterizing the phenotype across these species, we found that the variation within the blue-eyed subsets of each species occupies strongly overlapping regions of CIE L*a*b* color space. Yet whereas Japanese macaques and humans display continuous variation, the phenotypes of blue-eyed black lemurs and their sister species (whose irises are brown) occupy more clustered subspaces. Variation in an enhancer of OCA2 is primarily responsible for the phenotypic difference between humans with blue and brown irises. In the orthologous region, we found no variant that distinguishes the two lemur species or associates with quantitative phenotypic variation in Japanese macaques. Given the high similarity between the blue iris phenotypes in these species and that in humans, this finding implies that evolution has used different molecular paths to reach the same end. Am J Phys Anthropol 151:398–407, 2013.© 2013 Wiley Periodicals, Inc. PMID:23640739

  19. Rates and patterns of molecular evolution in freshwater versus terrestrial insects.

    PubMed

    Mitterboeck, T Fatima; Fu, Jinzhong; Adamowicz, Sarah J

    2016-11-01

    Insect lineages have crossed between terrestrial and aquatic habitats many times, for both immature and adult life stages. We explore patterns in molecular evolutionary rates between 42 sister pairs of related terrestrial and freshwater insect clades using publicly available protein-coding DNA sequence data from the orders Coleoptera, Diptera, Lepidoptera, Hemiptera, Mecoptera, Trichoptera, and Neuroptera. We furthermore test for habitat-associated convergent molecular evolution in the cytochrome c oxidase subunit I (COI) gene in general and at a particular amino acid site previously reported to exhibit habitat-linked convergence within an aquatic beetle group. While ratios of nonsynonymous-to-synonymous substitutions across available loci were higher in terrestrial than freshwater-associated taxa in 26 of 42 lineage pairs, a stronger trend was observed (20 of 31, pbinomial = 0.15, pWilcoxon = 0.017) when examining only terrestrial-aquatic pairs including fully aquatic taxa. We did not observe any widespread changes at particular amino acid sites in COI associated with habitat shifts, although there may be general differences in selection regime linked to habitat.

  20. Processing of meteoritic organic materials as a possible analog of early molecular evolution in planetary environments

    PubMed Central

    Pizzarello, Sandra; Davidowski, Stephen K.; Holland, Gregory P.; Williams, Lynda B.

    2013-01-01

    The composition of the Sutter’s Mill meteorite insoluble organic material was studied both in toto by solid-state NMR spectroscopy of the powders and by gas chromatography–mass spectrometry analyses of compounds released upon their hydrothermal treatment. Results were compared with those obtained for other meteorites of diverse classifications (Murray, GRA 95229, Murchison, Orgueil, and Tagish Lake) and found to be so far unique in regard to the molecular species released. These include, in addition to O-containing aromatic compounds, complex polyether- and ester-containing alkyl molecules of prebiotic appeal and never detected in meteorites before. The Sutter’s Mill fragments we analyzed had likely been altered by heat, and the hydrothermal conditions of the experiments realistically mimic early Earth settings, such as near volcanic activity or impact craters. On this basis, the data suggest a far larger availability of meteoritic organic materials for planetary environments than previously assumed and that molecular evolution on the early Earth could have benefited from accretion of carbonaceous meteorites both directly with soluble compounds and, for a more protracted time, through alteration, processing, and release from their insoluble organic materials. PMID:24019471

  1. Molecular gas content of H I monsters and implications to cold gas content evolution in galaxies

    NASA Astrophysics Data System (ADS)

    Lee, Cheoljong; Chung, Aeree; Yun, Min S.; Cybulski, Ryan; Narayanan, G.; Erickson, N.

    2014-06-01

    We present 12CO (J = 1 → 0) observations of a sample of local galaxies (0.04 < z < 0.08) with a large neutral hydrogen reservoir, or `H I monsters'. The data were obtained using the redshift search receiver on the five college radio astronomy observatory (FCRAO) 14 m telescope. The sample consists of 20 H I-massive galaxies with MH I > 3 × 1010 M⊙ from the Arecibo Legacy Fast ALFA (ALFALFA) survey and 8 low surface brightness galaxies (LSBs) with a comparable MH I(>1.5 × 1010 M⊙). Our sample selection is purely based on the amount of neutral hydrogen, thereby providing a chance to study how atomic and molecular gas relate to each other in these H I-massive systems. We have detected CO in 15 out of 20 ALFALFA selected galaxies and 4 out of 8 LSBs with molecular gas mass MH2 of (1-11)× 109 M⊙. Their total cold gas masses of (2-7) × 1010 M⊙ make them some of the most gas-massive galaxies identified to date in the Local Universe. Observed trends associated with H I, H2, and stellar properties of the H I massive galaxies and the field comparison sample are analysed in the context of theoretical models of galaxy cold gas content and evolution, and the importance of total gas content and improved recipes for handling spatially differentiated behaviours of disc and halo gas are identified as potential areas of improvement for the modelling.

  2. Molecular evolution and functional divergence of tubulin superfamily in the fungal tree of life

    PubMed Central

    Zhao, Zhongtao; Liu, Huiquan; Luo, Yongping; Zhou, Shanyue; An, Lin; Wang, Chenfang; Jin, Qiaojun; Zhou, Mingguo; Xu, Jin-Rong

    2014-01-01

    Microtubules are essential for various cellular activities and β-tubulins are the target of benzimidazole fungicides. However, the evolution and molecular mechanisms driving functional diversification in fungal tubulins are not clear. In this study, we systematically identified tubulin genes from 59 representative fungi across the fungal kingdom. Phylogenetic analysis showed that α-/β-tubulin genes underwent multiple independent duplications and losses in different fungal lineages and formed distinct paralogous/orthologous clades. The last common ancestor of basidiomycetes and ascomycetes likely possessed two paralogs of α-tubulin (α1/α2) and β-tubulin (β1/β2) genes but α2-tubulin genes were lost in basidiomycetes and β2-tubulin genes were lost in most ascomycetes. Molecular evolutionary analysis indicated that α1, α2, and β2-tubulins have been under strong divergent selection and adaptive positive selection. Many positively selected sites are at or adjacent to important functional sites and likely contribute to functional diversification. We further experimentally confirmed functional divergence of two β-tubulins in Fusarium and identified type II variations in FgTub2 responsible for function shifts. In this study, we also identified δ-/ε-/η-tubulins in Chytridiomycetes. Overall, our results illustrated that different evolutionary mechanisms drive functional diversification of α-/β-tubulin genes in different fungal lineages, and residues under positive selection could provide targets for further experimental study. PMID:25339375

  3. Evolution of the placenta and fetal membranes seen in the light of molecular phylogenetics.

    PubMed

    Carter, A M

    2001-11-01

    Recent analyses of nucleotide sequence data suggest that living placental mammals belong to one of four superorders. The early divergence of these groups was followed by long periods of geographical isolation, due to the break up of continental land masses, allowing for convergent evolution of similar traits in different superorders. As an example, the transition from epitheliochorial to haemochorial placentation occurred independently in bats, rodents, anthropoid primates, armadillos and others. A group of ancient African mammals is suggested by the molecular data, but is not fully supported by morphological evidence. The hypothesis is, however, consistent with some of the data on fetal membranes, suggesting that it would be worthwhile to study the early development of tenrecs, golden moles and elephant shrews. Analyses of fetal membrane traits that group the tarsiers with anthropoid primates, and separate them from the lemurs, are challenged by the molecular data. Other relatives of the primates seem to include tree shrews and flying lemurs, and little is known about the fetal membranes of the latter group. Comparative studies of placental function normally are confined to primates, rodents, lagomorphs and domestic animals: the biological diversity represented by mammals that evolved in ancient Africa and South America is not represented. Therefore, future comparative studies should strive to include species such as the rock hyrax and the armadillo.

  4. Molecular evolution of the metazoan PHD-HIF oxygen-sensing system.

    PubMed

    Rytkönen, Kalle T; Williams, Tom A; Renshaw, Gillian M; Primmer, Craig R; Nikinmaa, Mikko

    2011-06-01

    Metazoans rely on aerobic energy production, which requires an adequate oxygen supply. During reduced oxygen supply (hypoxia), the most profound changes in gene expression are mediated by transcription factors known as hypoxia-inducible factors (HIFs). HIF alpha proteins are commonly posttranslationally regulated by prolyl-4-hydroxylase (PHD) enzymes, which are direct "sensors" of cellular oxygen levels. We examined the molecular evolution of the metazoan PHD-HIF oxygen-sensing system by constructing complete phylogenies for PHD and HIF alpha genes and used computational tools to characterize the molecular changes underlying the functional divergence of PHD and HIF alpha duplicates. The presence of PHDs in metazoan genomes predates the emergence of HIF alphas. Our analysis revealed an unexpected diversity of PHD genes and HIF alpha sequence characteristics in invertebrates, suggesting that the simple oxygen-sensing systems of Caenorhabditis and Drosophila may not be typical of other invertebrate bilaterians. We studied the early vertebrate evolution of the system by sequencing these genes in early-diverging cartilaginous fishes, elasmobranchs. Cartilaginous fishes appear to have three paralogs of both PHD and HIF alpha. The novel sequences were used as outgroups for a detailed molecular analysis of PHD and HIF alpha duplicates in a major air-breathing vertebrate lineage, the mammals, and a major water-breathing vertebrate lineage, the teleosts. In PHDs, functionally divergent amino acid sites were detected near the HIF alpha-binding channel and beta2beta3 loop that defines its substrate specificity. In HIF alphas, more functional divergence was found in teleosts than in mammals, especially in the HIF-1 alpha PAS domain and HIF-2 alpha oxygen-dependent degradation (ODD) domains, which interact with PHDs. Overall, in the vertebrates, elevated substitution rates in the HIF-2 alpha N-terminal ODD domain, together with a functional divergence associated with the known

  5. Molecular epidemiology, phylogeny and evolution of the filarial nematode Wuchereria bancrofti.

    PubMed

    Small, Scott T; Tisch, Daniel J; Zimmerman, Peter A

    2014-12-01

    Wuchereria bancrofti (Wb) is the most widely distributed of the three nematodes known to cause lymphatic filariasis (LF), the other two being Brugia malayi and Brugia timori. Current tools available to monitor LF are limited to diagnostic tests targeting DNA repeats, filarial antigens, and anti-filarial antibodies. While these tools are useful for detection and surveillance, elimination programs have yet to take full advantage of molecular typing for inferring infection history, strain fingerprinting, and evolution. To date, molecular typing approaches have included whole mitochondrial genomes, genotyping, targeted sequencing, and random amplified polymorphic DNA (RAPDs). These studies have revealed much about Wb biology. For example, in one study in Papua New Guinea researchers identified 5 major strains that were widespread and many minor strains some of which exhibit geographic stratification. Genome data, while rare, has been utilized to reconstruct evolutionary relationships among taxa of the Onchocercidae (the clade of filarial nematodes) and identify gene synteny. Their phylogeny reveals that speciation from the common ancestor of both B. malayi and Wb occurred around 5-6 millions years ago with shared ancestry to other filarial nematodes as recent as 15 million years ago. These discoveries hold promise for gene discovery and identifying drug targets in species that are more amenable to in vivo experiments. Continued technological developments in whole genome sequencing and data analysis will likely replace many other forms of molecular typing, multiplying the amount of data available on population structure, genetic diversity, and phylogenetics. Once widely available, the addition of population genetic data from genomic studies should hasten the elimination of LF parasites like Wb. Infectious disease control programs have benefited greatly from population genetics data and recently from population genomics data. However, while there is currently a surplus

  6. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

    PubMed Central

    2011-01-01

    forward the conclusion that this evolutionary scenario has been possible through a complex interplay between adaptive mutations, often structurally destabilizing, and compensatory mutations. Our results unearth patterns of evolution that have likely optimized the Rubisco activity and uncover mutational dynamics useful in the molecular engineering of enzymatic activities. Reviewers This article was reviewed by Prof. Christian Blouin (nominated by Dr W Ford Doolittle), Dr Endre Barta (nominated by Dr Sandor Pongor), and Dr Nicolas Galtier. PMID:21639885

  7. Tracking the Molecular Evolution of Calcium Permeability in a Nicotinic Acetylcholine Receptor

    PubMed Central

    Lipovsek, Marcela; Fierro, Angélica; Pérez, Edwin G.; Boffi, Juan C.; Millar, Neil S.; Fuchs, Paul A.; Katz, Eleonora; Elgoyhen, Ana Belén

    2014-01-01

    Nicotinic acetylcholine receptors are a family of ligand-gated nonselective cationic channels that participate in fundamental physiological processes at both the central and the peripheral nervous system. The extent of calcium entry through ligand-gated ion channels defines their distinct functions. The α9α10 nicotinic cholinergic receptor, expressed in cochlear hair cells, is a peculiar member of the family as it shows differences in the extent of calcium permeability across species. In particular, mammalian α9α10 receptors are among the ligand-gated ion channels which exhibit the highest calcium selectivity. This acquired differential property provides the unique opportunity of studying how protein function was shaped along evolutionary history, by tracking its evolutionary record and experimentally defining the amino acid changes involved. We have applied a molecular evolution approach of ancestral sequence reconstruction, together with molecular dynamics simulations and an evolutionary-based mutagenesis strategy, in order to trace the molecular events that yielded a high calcium permeable nicotinic α9α10 mammalian receptor. Only three specific amino acid substitutions in the α9 subunit were directly involved. These are located at the extracellular vestibule and at the exit of the channel pore and not at the transmembrane region 2 of the protein as previously thought. Moreover, we show that these three critical substitutions only increase calcium permeability in the context of the mammalian but not the avian receptor, stressing the relevance of overall protein structure on defining functional properties. These results highlight the importance of tracking evolutionarily acquired changes in protein sequence underlying fundamental functional properties of ligand-gated ion channels. PMID:25193338

  8. Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges

    PubMed Central

    Schuster, Astrid; Erpenbeck, Dirk; Pisera, Andrzej; Hooper, John; Bryce, Monika; Fromont, Jane; Wörheide, Gert

    2015-01-01

    Reconciling the fossil record with molecular phylogenies to enhance the understanding of animal evolution is a challenging task, especially for taxa with a mostly poor fossil record, such as sponges (Porifera). ‘Lithistida’, a polyphyletic group of recent and fossil sponges, are an exception as they provide the richest fossil record among demosponges. Lithistids, currently encompassing 13 families, 41 genera and >300 recent species, are defined by the common possession of peculiar siliceous spicules (desmas) that characteristically form rigid articulated skeletons. Their phylogenetic relationships are to a large extent unresolved and there has been no (taxonomically) comprehensive analysis to formally reallocate lithistid taxa to their closest relatives. This study, based on the most comprehensive molecular and morphological investigation of ‘lithistid’ demosponges to date, corroborates some previous weakly-supported hypotheses, and provides novel insights into the evolutionary relationships of the previous ‘order Lithistida’. Based on molecular data (partial mtDNA CO1 and 28S rDNA sequences), we show that 8 out of 13 ‘Lithistida’ families belong to the order Astrophorida, whereas Scleritodermidae and Siphonidiidae form a separate monophyletic clade within Tetractinellida. Most lithistid astrophorids are dispersed between different clades of the Astrophorida and we propose to formally reallocate them, respectively. Corallistidae, Theonellidae and Phymatellidae are monophyletic, whereas the families Pleromidae and Scleritodermidae are polyphyletic. Family Desmanthidae is polyphyletic and groups within Halichondriidae – we formally propose a reallocation. The sister group relationship of the family Vetulinidae to Spongillida is confirmed and we propose here for the first time to include Vetulina into a new Order Sphaerocladina. Megascleres and microscleres possibly evolved and/or were lost several times independently in different

  9. Tracking the molecular evolution of calcium permeability in a nicotinic acetylcholine receptor.

    PubMed

    Lipovsek, Marcela; Fierro, Angélica; Pérez, Edwin G; Boffi, Juan C; Millar, Neil S; Fuchs, Paul A; Katz, Eleonora; Elgoyhen, Ana Belén

    2014-12-01

    Nicotinic acetylcholine receptors are a family of ligand-gated nonselective cationic channels that participate in fundamental physiological processes at both the central and the peripheral nervous system. The extent of calcium entry through ligand-gated ion channels defines their distinct functions. The α9α10 nicotinic cholinergic receptor, expressed in cochlear hair cells, is a peculiar member of the family as it shows differences in the extent of calcium permeability across species. In particular, mammalian α9α10 receptors are among the ligand-gated ion channels which exhibit the highest calcium selectivity. This acquired differential property provides the unique opportunity of studying how protein function was shaped along evolutionary history, by tracking its evolutionary record and experimentally defining the amino acid changes involved. We have applied a molecular evolution approach of ancestral sequence reconstruction, together with molecular dynamics simulations and an evolutionary-based mutagenesis strategy, in order to trace the molecular events that yielded a high calcium permeable nicotinic α9α10 mammalian receptor. Only three specific amino acid substitutions in the α9 subunit were directly involved. These are located at the extracellular vestibule and at the exit of the channel pore and not at the transmembrane region 2 of the protein as previously thought. Moreover, we show that these three critical substitutions only increase calcium permeability in the context of the mammalian but not the avian receptor, stressing the relevance of overall protein structure on defining functional properties. These results highlight the importance of tracking evolutionarily acquired changes in protein sequence underlying fundamental functional properties of ligand-gated ion channels.

  10. The role of macromolecular crowding in the evolution of lens crystallins with high molecular refractive index

    NASA Astrophysics Data System (ADS)

    Zhao, Huaying; Magone, M. Teresa; Schuck, Peter

    2011-08-01

    Crystallins are present in the lens at extremely high concentrations in order to provide transparency and generate a high refractive power of the lens. The crystallin families prevalent in the highest density lens tissues are γ-crystallins in vertebrates and S-crystallins in cephalopods. As shown elsewhere, in parallel evolution, both have evolved molecular refractive index increments 5-10% above those of most proteins. Although this is a small increase, it is statistically very significant and can be achieved only by very unusual amino acid compositions. In contrast, such a molecular adaptation to aid in the refractive function of the lens did not occur in crystallins that are preferentially located in lower density lens tissues, such as vertebrate α-crystallin and taxon-specific crystallins. In the current work, we apply a model of non-interacting hard spheres to examine the thermodynamic contributions of volume exclusion at lenticular protein concentrations. We show that the small concentration decrease afforded by the higher molecular refractive index increment of crystallins can amplify nonlinearly to produce order of magnitude differences in chemical activities, and lead to reduced osmotic pressure and the reduced propensity for protein aggregation. Quantitatively, this amplification sets in only at protein concentrations as high as those found in hard lenses or the nucleus of soft lenses, in good correspondence to the observed crystallin properties in different tissues and different species. This suggests that volume exclusion effects provide the evolutionary driving force for the unusual refractive properties and the unusual amino acid compositions of γ-crystallins and S-crystallins.

  11. Molecular Evolution of the Porcine Type I Interferon Family: Subtype-Specific Expression and Antiviral Activity

    PubMed Central

    Sang, Yongming; Bergkamp, Joseph; Blecha, Frank

    2014-01-01

    Type I interferons (IFNs), key antiviral cytokines, evolve to adapt with ever-changing viral threats during vertebrate speciation. Due to novel pathogenic pressure associated with Suidae speciation and domestication, porcine IFNs evolutionarily engender both molecular and functional diversification, which have not been well addressed in pigs, an important livestock species and animal model for biomedical sciences. Annotation of current swine genome assembly Sscrofa10.2 reveals 57 functional genes and 16 pseudogenes of type I IFNs. Subfamilies of multiple IFNA, IFNW and porcine-specific IFND genes are separated into four clusters with ∼60 kb intervals within the IFNB/IFNE bordered region in SSC1, and each cluster contains mingled subtypes of IFNA, IFNW and IFND. Further curation of the 57 functional IFN genes indicates that they include 18 potential artifactual duplicates. We performed phylogenetic construction as well as analyses of gene duplication/conversion and natural selection and showed that porcine type I IFN genes have been undergoing active diversification through both gene duplication and conversion. Extensive analyses of the non-coding sequences proximal to all IFN coding regions identified several genomic repetitive elements significantly associated with different IFN subtypes. Family-wide studies further revealed their molecular diversity with respect to differential expression and restrictive activity on the resurgence of a porcine endogenous retrovirus. Based on predicted 3-D structures of representative animal IFNs and inferred activity, we categorized the general functional propensity underlying the structure-activity relationship. Evidence indicates gene expansion of porcine type I IFNs. Genomic repetitive elements that associated with IFN subtypes may serve as molecular signatures of respective IFN subtypes and genomic mechanisms to mediate IFN gene evolution and expression. In summary, the porcine type I IFN profile has been phylogenetically

  12. Immobilization of a molecular cobalt electrocatalyst by hydrophobic interaction with a hematite photoanode for highly stable oxygen evolution.

    PubMed

    Joya, Khurram S; Morlanés, Natalia; Maloney, Edward; Rodionov, Valentin; Takanabe, Kazuhiro

    2015-09-11

    A unique modification of a hematite photoanode with perfluorinated Co-phthalocyanine (CoFPc) by strong binding associated with hydrophobic interaction is demonstrated. The resultant molecular electrocatalyst - a hematite photoanode hybrid material showed a significant onset shift and high stability for the photoelectrochemical oxidation evolution reaction (OER).

  13. Directed Molecular Evolution Improves the Immunogenicity and Protective Efficacy of a Venezuelan Equine Encephalitis Virus DNA Vaccine

    DTIC Science & Technology

    2009-05-01

    VEEV IA/B challenge. Our results indicate that it is pos- sible to improve the immunogenicity and protective efficacy of alphavirus DNA vaccines using... alphaviruses that ause periodic epizootics in the Americas [1]. These New World lphaviruses cause diseases in humans characterized by fever, eadache...equine encephalitis virus, VEE, alphavirus , DNA vaccine, envelope glycoproteins, directed molecular evolution, efficacy, immunogenicity, laboratory

  14. Science for Survival: The Modern Synthesis of Evolution and the Biological Sciences Curriculum Study

    ERIC Educational Resources Information Center

    Green, Lisa Anne

    2012-01-01

    In this historical dissertation, I examined the process of curriculum development in the Biological Sciences Curriculum Study (BSCS) in the United States during the period 1959-1963. The presentation of evolution in the high school texts was based on a more robust form of Darwinian evolution which developed during the 1930s and 1940s called…

  15. University Student Understanding of Evolutionary Biology's Place in the Creation/Evolution Controversy.

    ERIC Educational Resources Information Center

    Fuerst, Paul A.

    1984-01-01

    A nine-item questionnaire was used to survey 2,387 Ohio State University students in 10 courses about their views on the creation/evolution controversy, especially their acceptance of the concept of Darwinian evolution and on the concept of equal time for "creation science." Results and implications for biology education are presented.…

  16. Reasons Given by UK Churchgoers for Their Stance on Evolution

    ERIC Educational Resources Information Center

    Village, Andrew; Baker, Sylvia

    2013-01-01

    A sample of 661 churchgoers from a range of Christian denominations in the United Kingdom was asked about Darwinian evolution (defined as the common origin of all species, including humans). Respondents were categorised as those who accepted the idea, those who rejected it, and those who were unsure or neutral. People in each category were given a…

  17. Darwinism and the Behavioral Theory of Sociocultural Evolution: An Analysis.

    ERIC Educational Resources Information Center

    Langdon, John

    1979-01-01

    Challenges the view that the social sciences are theoretically impoverished disciplines when compared with the natural sciences. Demonstrates that the synthesis of an abstract Darwinian model of systemic adaptation and the behavioral principles of social learning produces a logical theory of sociocultural evolution. (DB)

  18. Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea).

    PubMed

    Voigt, Oliver; Wülfing, Eilika; Wörheide, Gert

    2012-01-01

    Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a

  19. Direct molecular evolution of detergent-stable G protein-coupled receptors using polymer encapsulated cells.

    PubMed

    Scott, Daniel J; Plückthun, Andreas

    2013-02-08

    G protein-coupled receptors (GPCRs) are the largest class of pharmaceutical protein targets, yet drug development is encumbered by a lack of information about their molecular structure and conformational dynamics. Most mechanistic and structural studies as well as in vitro drug screening with purified receptors require detergent solubilization of the GPCR, but typically, these proteins exhibit only low stability in detergent micelles. We have developed the first directed evolution method that allows the direct selection of GPCRs stable in a chosen detergent from libraries containing over 100 million individual variants. The crucial concept was to encapsulate single Escherichia coli cells of a library, each expressing a different GPCR variant, to form detergent-resistant, semipermeable nano-containers. Unlike naked cells, these containers are not dissolved by detergents, allowing us to solubilize the GPCR proteins in situ while maintaining an association with the protein's genetic information, a prerequisite for directed evolution. The pore size was controlled to permit GPCR ligands to permeate but the solubilized receptor to remain within the nanocapsules. Fluorescently labeled ligands were used to bind to those GPCR variants inside the nano-containers that remained active in the detergent tested. With the use of fluorescence-activated cell sorting, detergent-stable mutants derived from two different family A GPCRs could be identified, some with the highest stability reported in short-chain detergents. In principle, this method (named cellular high-throughput encapsulation, solubilization and screening) is not limited to engineering stabilized GPCRs but could be used to stabilize other proteins for biochemical and structural studies.

  20. Molecular phylogeny of the Tylenchina and evolution of the female gonoduct (Nematoda: Rhabditida).

    PubMed

    Bert, Wim; Leliaert, Frederik; Vierstraete, Andy R; Vanfleteren, Jacques R; Borgonie, Gaetan

    2008-08-01

    Tylenchina are a morphologically and functionally diverse group of nematode species that range from free-living bacteriovores, over transitory grazing root-hair feeders to highly specialized plant-parasites with complex host associations. We performed phylogenetic analyses of small subunit rDNA sequences from 97 species including an analysis that account for the RNA secondary structure in the models of evolution. The present study confirms the sister relationship of the bacteriovore Cephalobidae with the predominantly plant-parasitic Tylenchomorpha. All analyses appoint the fungal-feeding Aphelenchidae and Aphelenchoididae as being polyphyletic but the morphology based hypothesis of their monophyly could not be significantly rejected. Within the Tylenchomorpha, the families that exclusively parasitize higher plants are joined in a single clade. However, only the monophyletic position of the (super)families Hoplolaimidae and Criconematoidea were supported; Anguinidae, Tylenchidae, Belonolaimidae and Pratylenchidae appeared to be paraphyletic or polyphyletic. Parsimony and likelihood ancestral state reconstruction revealed that burrowing endoparasitism and sedentary endoparasitism each evolved, respectively, at least six and at least three times independently, mostly from migratory ectoparasitic ancestors. Only root-knot nematodes have evolved from burrowing endoparasitic nematodes. Traditional classifications are partially misled by this convergent evolution of feeding type and associated morphology. Contrastingly, mapping attributes of the gonoduct cellular architecture, including newly obtained data of 18 species belonging to the Aphelenchoidea, Criconematoidea, Anguinidae and Panagrolaimidae, revealed a broad congruence of the gonoduct characters and the molecular phylogenetic hypothesis. Yet, the presence of an offset spermatheca and proliferation of uterus cells has evolved multiple times, the latter associated with derived endoparasitic feeding specialization

  1. Molecular evolution and functional characterisation of haplotypes of an important rubber biosynthesis gene in Hevea brasiliensis.

    PubMed

    Uthup, T K; Rajamani, A; Ravindran, M; Saha, T

    2016-07-01

    Hydroxy-methylglutaryl coenzyme-A synthase (HMGS) is a rate-limiting enzyme in the cytoplasmic isoprenoid biosynthesis pathway leading to natural rubber production in Hevea brasiliensis (rubber). Analysis of the structural variants of this gene is imperative to understand their functional significance in rubber biosynthesis so that they can be properly utilised for ongoing crop improvement programmes in Hevea. We report here allele richness and diversity of the HMGS gene in selected popular rubber clones. Haplotypes consisting of single nucleotide polymorphisms (SNPs) from the coding and non-coding regions with a high degree of heterozygosity were identified. Segregation and linkage disequilibrium analysis confirmed that recombination is the major contributor to the generation of allelic diversity, rather than point mutations. The evolutionarily conserved nature of some SNPs was identified by comparative DNA sequence analysis of HMGS orthologues from diverse taxa, demonstrating the molecular evolution of rubber biosynthesis genes in general. In silico three-dimensional structural studies highlighting the structural positioning of non-synonymous SNPs from different HMGS haplotypes revealed that the ligand-binding site on the enzyme remains impervious to the reported sequence variations. In contrast, gene expression results indicated the possibility of association between specific haplotypes and HMGS expression in Hevea clones, which may have a downstream impact up to the level of rubber production. Moreover, haplotype diversity of the HMGS gene and its putative association with gene expression can be the basis for further genetic association studies in rubber. Furthermore, the data also show the role of SNPs in the evolution of candidate genes coding for functional traits in plants.

  2. Rates of molecular evolution and diversification in plants: chloroplast substitution rates correlate with species-richness in the Proteaceae

    PubMed Central

    2013-01-01

    Background Many factors have been identified as correlates of the rate of molecular evolution, such as body size and generation length. Analysis of many molecular phylogenies has also revealed correlations between substitution rates and clade size, suggesting a link between rates of molecular evolution and the process of diversification. However, it is not known whether this relationship applies to all lineages and all sequences. Here, in order to investigate how widespread this phenomenon is, we investigate patterns of substitution in chloroplast genomes of the diverse angiosperm family Proteaceae. We used DNA sequences from six chloroplast genes (6278bp alignment with 62 taxa) to test for a correlation between diversification and the rate of substitutions. Results Using phylogenetically-independent sister pairs, we show that species-rich lineages of Proteaceae tend to have significantly higher chloroplast substitution rates, for both synonymous and non-synonymous substitutions. Conclusions We show that the rate of molecular evolution in chloroplast genomes is correlated with net diversification rates in this large plant family. We discuss the possible causes of this relationship, including molecular evolution driving diversification, speciation increasing the rate of substitutions, or a third factor causing an indirect link between molecular and diversification rates. The link between the synonymous substitution rate and clade size is consistent with a role for the mutation rate of chloroplasts driving the speed of reproductive isolation. We find no significant differences in the ratio of non-synonymous to synonymous substitutions between lineages differing in net diversification rate, therefore we detect no signal of population size changes or alteration in selection pressures that might be causing this relationship. PMID:23497266

  3. Structural and Molecular Evidence Suggesting Coronavirus-driven Evolution of Mouse Receptor.

    PubMed

    Peng, Guiqing; Yang, Yang; Pasquarella, Joseph R; Xu, Liqing; Qian, Zhaohui; Holmes, Kathryn V; Li, Fang

    2017-02-10

    Hosts and pathogens are locked in an evolutionary arms race. To infect mice, mouse hepatitis coronavirus (MHV) has evolved to recognize mouse CEACAM1a (mCEACAM1a) as its receptor. To elude MHV infections, mice may have evolved a variant allele from the Ceacam1a gene, called Ceacam1b, producing mCEACAM1b, which is a much poorer MHV receptor than mCEACAM1a. Previous studies showed that sequence differences between mCEACAM1a and mCEACAM1b in a critical MHV-binding CC' loop partially account for the low receptor activity of mCEACAM1b, but detailed structural and molecular mechanisms for the differential MHV receptor activities of mCEACAM1a and mCEACAM1b remained elusive. Here we have determined the crystal structure of mCEACAM1b and identified the structural differences and additional residue differences between mCEACAM1a and mCEACAM1b that affect MHV binding and entry. These differences include conformational alterations of the CC' loop as well as residue variations in other MHV-binding regions, including β-strands C' and C'' and loop C'C''. Using pseudovirus entry and protein-protein binding assays, we show that substituting the structural and residue features from mCEACAM1b into mCEACAM1a reduced the viral receptor activity of mCEACAM1a, whereas substituting the reverse changes from mCEACAM1a into mCEACAM1b increased the viral receptor activity of mCEACAM1b. These results elucidate the detailed molecular mechanism for how mice may have kept pace in the evolutionary arms race with MHV by undergoing structural and residue changes in the MHV receptor, providing insight into this possible example of pathogen-driven evolution of a host receptor protein.

  4. Molecular Evolution and Phylogeography of Co-circulating IHNV and VHSV in Italy.

    PubMed

    Abbadi, Miriam; Fusaro, Alice; Ceolin, Chiara; Casarotto, Claudia; Quartesan, Rosita; Dalla Pozza, Manuela; Cattoli, Giovanni; Toffan, Anna; Holmes, Edward C; Panzarin, Valentina

    2016-01-01

    Infectious haematopoietic necrosis virus (IHNV) and viral haemorrhagic septicaemia virus (VHSV) are the most important viral pathogens impacting rainbow trout farming. These viruses are persistent in Italy, where they are responsible for severe disease outbreaks (epizootics) that affect the profitability of the trout industry. Despite the importance of IHNV and VHSV, little is known about their evolution at a local scale, although this is likely to be important for virus eradication and control. To address this issue we performed a detailed molecular evolutionary and epidemiological analysis of IHNV and VHSV in trout farms from northern Italy. Full-length glycoprotein gene sequences of a selection of VHSV (n = 108) and IHNV (n = 89) strains were obtained. This revealed that Italian VHSV strains belong to sublineages Ia1 and Ia2 of genotype Ia and are distributed into 7 genetic clusters. In contrast, all Italian IHNV isolates fell within genogroup E, for which only a single genetic cluster was identified. More striking was that IHNV has evolved more rapidly than VHSV (mean rates of 11 and 7.3 × 10(-4) nucleotide substitutions per site, per year, respectively), indicating that these viruses exhibit fundamentally different evolutionary dynamics. The time to the most recent common ancestor of both IHNV and VHSV was consistent with the first reports of these pathogens in Italy. By combining sequence data with epidemiological information it was possible to identify different patterns of virus spread among trout farms, in which adjacent facilities can be infected by either genetically similar or different viruses, and farms located in different water catchments can be infected by identical strains. Overall, these findings highlight the importance of combining molecular and epidemiological information to identify the determinants of IHN and VHS spread, and to provide data that is central to future surveillance strategies and possibly control.

  5. Molecular Evolution and Phylogeography of Co-circulating IHNV and VHSV in Italy

    PubMed Central

    Abbadi, Miriam; Fusaro, Alice; Ceolin, Chiara; Casarotto, Claudia; Quartesan, Rosita; Dalla Pozza, Manuela; Cattoli, Giovanni; Toffan, Anna; Holmes, Edward C.; Panzarin, Valentina

    2016-01-01

    Infectious haematopoietic necrosis virus (IHNV) and viral haemorrhagic septicaemia virus (VHSV) are the most important viral pathogens impacting rainbow trout farming. These viruses are persistent in Italy, where they are responsible for severe disease outbreaks (epizootics) that affect the profitability of the trout industry. Despite the importance of IHNV and VHSV, little is known about their evolution at a local scale, although this is likely to be important for virus eradication and control. To address this issue we performed a detailed molecular evolutionary and epidemiological analysis of IHNV and VHSV in trout farms from northern Italy. Full-length glycoprotein gene sequences of a selection of VHSV (n = 108) and IHNV (n = 89) strains were obtained. This revealed that Italian VHSV strains belong to sublineages Ia1 and Ia2 of genotype Ia and are distributed into 7 genetic clusters. In contrast, all Italian IHNV isolates fell within genogroup E, for which only a single genetic cluster was identified. More striking was that IHNV has evolved more rapidly than VHSV (mean rates of 11 and 7.3 × 10−4 nucleotide substitutions per site, per year, respectively), indicating that these viruses exhibit fundamentally different evolutionary dynamics. The time to the most recent common ancestor of both IHNV and VHSV was consistent with the first reports of these pathogens in Italy. By combining sequence data with epidemiological information it was possible to identify different patterns of virus spread among trout farms, in which adjacent facilities can be infected by either genetically similar or different viruses, and farms located in different water catchments can be infected by identical strains. Overall, these findings highlight the importance of combining molecular and epidemiological information to identify the determinants of IHN and VHS spread, and to provide data that is central to future surveillance strategies and possibly control. PMID:27602026

  6. Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba.

    PubMed

    Carretero-Paulet, Lorenzo; Chang, Tien-Hao; Librado, Pablo; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Rozas, Julio; Albert, Victor A

    2015-01-09

    The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compared the U. gibba genome with that of four other eudicot species, defining a total of 17,324 gene families (orthogroups). These families were further classified as either 1) lineage-specific expanded/contracted or 2) stable in size. The U. gibba-expanded families are generically related to three main phenotypic features: 1) trap physiology, 2) key plant morphogenetic/developmental pathways, and 3) response to environmental stimuli, including adaptations to life in aquatic environments. Further scans for signatures of protein functional specialization permitted identification of seven candidate genes with amino acid changes putatively fixed by positive Darwinian selection in the U. gibba lineage. The Arabidopsis orthologs of these genes (AXR, UMAMIT41, IGS, TAR2, SOL1, DEG9, and DEG10) are involved in diverse plant biological functions potentially relevant for U. gibba phenotypic diversification, including 1) auxin metabolism and signal transduction, 2) flowering induction and floral meristem transition, 3) root development, and 4) peptidases. Taken together, our results suggest numerous candidate genes and gene families as interesting targets for further experimental confirmation of their functional and adaptive roles in the U. gibba's unique lifestyle and highly specialized body plan.

  7. Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life

    PubMed Central

    2011-01-01

    Background Seagrasses are a polyphyletic group of monocotyledonous angiosperms that have adapted to a completely submerged lifestyle in marine waters. Here, we exploit two collections of expressed sequence tags (ESTs) of two wide-spread and ecologically important seagrass species, the Mediterranean seagrass Posidonia oceanica (L.) Delile and the eelgrass Zostera marina L., which have independently evolved from aquatic ancestors. This replicated, yet independent evolutionary history facilitates the identification of traits that may have evolved in parallel and are possible instrumental candidates for adaptation to a marine habitat. Results In our study, we provide the first quantitative perspective on molecular adaptations in two seagrass species. By constructing orthologous gene clusters shared between two seagrasses (Z. marina and P. oceanica) and eight distantly related terrestrial angiosperm species, 51 genes could be identified with detection of positive selection along the seagrass branches of the phylogenetic tree. Characterization of these positively selected genes using KEGG pathways and the Gene Ontology uncovered that these genes are mostly involved in translation, metabolism, and photosynthesis. Conclusions These results provide first insights into which seagrass genes have diverged from their terrestrial counterparts via an initial aquatic stage characteristic of the order and to the derived fully-marine stage characteristic of seagrasses. We discuss how adaptive changes in these processes may have contributed to the evolution towards an aquatic and marine existence. PMID:21226908

  8. Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change.

    PubMed

    Morley, Valerie J; Turner, Paul E

    2017-04-01

    Understanding the dynamics of molecular adaptation is a fundamental goal of evolutionary biology. While adaptation to constant environments has been well characterized, the effects of environmental complexity remain seldom studied. One simple but understudied factor is the rate of environmental change. Here we used experimental evolution with RNA viruses to investigate whether evolutionary dynamics varied based on the rate of environmental turnover. We used whole-genome next-generation sequencing to characterize evolutionary dynamics in virus populations adapting to a sudden versus gradual shift onto a novel host cell type. In support of theoretical models, we found that when populations evolved in response to a sudden environmental change, mutations of large beneficial effect tended to fix early, followed by mutations of smaller beneficial effect; as predicted, this pattern broke down in response to a gradual environmental change. Early mutational steps were highly parallel across replicate populations in both treatments. The fixation of single mutations was less common than sweeps of associated "cohorts" of mutations, and this pattern intensified when the environment changed gradually. Additionally, clonal interference appeared stronger in response to a gradual change. Our results suggest that the rate of environmental change is an important determinant of evolutionary dynamics in asexual populations.

  9. Molecular phylogeny, systematics and morphological evolution of the acorn barnacles (Thoracica: Sessilia: Balanomorpha).

    PubMed

    Pérez-Losada, Marcos; Høeg, Jens T; Simon-Blecher, Noa; Achituv, Yair; Jones, Diana; Crandall, Keith A

    2014-12-01

    The Balanomorpha are the largest group of barnacles and rank among the most diverse, commonly encountered and ecologically important marine crustaceans in the world. Paradoxically, despite their relevance and extensive study for over 150years, their evolutionary relationships are still unresolved. Classical morphological systematics was often based on non-cladistic approaches, while modern phylogenetic studies suffer from severe undersampling of taxa and characters (both molecular and morphological). Here we present a phylogenetic analysis of the familial relationships within the Balanomorpha. We estimate divergence times and examine morphological diversity based on five genes, 156 specimens, 10 fossil calibrations, and six key morphological characters. Two balanomorphan superfamilies, eight families and twelve genera were identified as polyphyletic. Chthamaloids, chionelasmatoid and pachylasmatoids split first from the pedunculated ancestors followed by a clade of tetraclitoids and coronuloids, and most of the balanoids. The Balanomorpha split from the Verrucidae (outgroup) in the Lower Cretaceous (139.6 Mya) with all the main lineages, except Pachylasmatoidea, having emerged by the Paleocene (60.9 Mya). Various degrees of convergence were observed in all the assessed morphological characters except the maxillipeds, which suggests that classical interpretations of balanomorphan morphological evolution need to be revised and reinterpreted.

  10. Molecular Evolution of Candidate Genes for Crop-Related Traits in Sunflower (Helianthus annuus L.)

    PubMed Central

    Mandel, Jennifer R.; McAssey, Edward V.; Nambeesan, Savithri; Garcia-Navarro, Elena; Burke, John M.

    2014-01-01

    Evolutionary analyses aimed at detecting the molecular signature of selection during crop domestication and/or improvement can be used to identify genes or genomic regions of likely agronomic importance. Here, we describe the DNA sequence-based characterization of a pool of candidate genes for crop-related traits in sunflower. These genes, which were identified based on homology to genes of known effect in other study systems, were initially sequenced from a panel of improved lines. All genes that exhibited a paucity of sequence diversity, consistent with the possible effects of selection during the evolution of cultivated sunflower, were then sequenced from a panel of wild sunflower accessions an outgroup. These data enabled formal tests for the effects of selection in shaping sequence diversity at these loci. When selection was detected, we further sequenced these genes from a panel of primitive landraces, thereby allowing us to investigate the likely timing of selection (i.e., domestication vs. improvement). We ultimately identified seven genes that exhibited the signature of positive selection during either domestication or improvement. Genetic mapping of a subset of these genes revealed co-localization between candidates for genes involved in the determination of flowering time, seed germination, plant growth/development, and branching and QTL that were previously identified for these traits in cultivated × wild sunflower mapping populations. PMID:24914686

  11. Molecular evolution and functional specialization of chalcone synthase superfamily from Phalaenopsis orchid.

    PubMed

    Han, Ying-Ying; Ming, Feng; Wang, Wei; Wang, Jing-Wen; Ye, Ming-Ming; Shen, Da-Leng

    2006-01-01

    Plant genomes appear to exploit the process of gene duplication as a primary means of acquiring biochemical and developmental flexibility. The best example is the gene encoding chalcone synthase (CHS, EC2.3.1.74), the first committed step in flavonoid biosynthesis. In this study, we examined the molecular evolution of three CHS family members of Phalaenopsis including a novel chs gene (phchs5), which is slowly evolved. The inferred phylogeny of the chs genes of Phalaenopsis with other two orchid plants, Bromoheadia finlaysoniana and Dendrobium hybrid, suggested that gene duplication and divergence have occurred before divergence of these three genera. Relatively quantitative RT-PCR analysis identified expression patterns of these three chs genes in different floral tissues at different developmental stages. Phchs5 was the most abundantly expressed chs gene in floral organs and it was specifically transcribed in petal and lip at the stages when anthocyanin accumulated (stage1-4). Phchs3 and phchs4 were expressed at much lower levels than phchs5. Phchs3 was expressed in pigmented tissue (including lip, petal and sepal) at middle stages (stages 2-4) and in colorless reproductive tissue at late stage (stage 5). Phchs4 was only expressed in petal at earlier stages (stage 1-3) and in lip at middle stage (stage 4). These results present new data on differentiation of gene expression among duplicate copies of chs genes in Phalaenopsis.

  12. Molecular Mixed-Metal Manganese Oxido Cubanes as Precursors to Heterogeneous Oxygen Evolution Catalysts.

    PubMed

    Suseno, Sandy; McCrory, Charles C L; Tran, Rosalie; Gul, Sheraz; Yano, Junko; Agapie, Theodor

    2015-09-14

    Well-defined mixed-metal [CoMn3 O4 ] and [NiMn3 O4 ] cubane complexes were synthesized and used as precursors for heterogeneous oxygen evolution reaction (OER) electrocatalysts. The discrete clusters were dropcasted onto glassy carbon (GC) and indium tin oxide (ITO) electrodes, and the OER activities of the resulting films were evaluated. The catalytic surfaces were analyzed by various techniques to gain insight into the structure-function relationships of the electrocatalysts' heterometallic composition. Depending on preparation conditions, the Co-Mn oxide was found to change metal composition during catalysis, while the Ni-Mn oxides maintained the NiMn3 ratio. XAS studies provided structural insights indicating that the electrocatalysts are different from the molecular precursors, but that the original NiMn3 O4 cubane-like geometry was maintained in the absence of thermal treatment (2-Ni). In contrast, the thermally generated 3-Ni develops an oxide-like extended structure. Both 2-Ni and 3-Ni undergo structural changes upon electrolysis, but they do not convert into the same material. The observed structural motifs in these heterogeneous electrocatalysts are reminiscent of the biological oxygen-evolving complex in Photosystem II, including the MMn3 O4 cubane moiety. The reported studies demonstrate the use of discrete heterometallic oxide clusters as precursors for heterogeneous water oxidation catalysts of novel composition and the distinct behavior of two sets of mixed metal oxides.

  13. Formation and evolution of molecular products in α-pinene secondary organic aerosol.

    PubMed

    Zhang, Xuan; McVay, Renee C; Huang, Dan D; Dalleska, Nathan F; Aumont, Bernard; Flagan, Richard C; Seinfeld, John H

    2015-11-17

    Much of our understanding of atmospheric secondary organic aerosol (SOA) formation from volatile organic compounds derives from laboratory chamber measurements, including mass yield and elemental composition. These measurements alone are insufficient to identify the chemical mechanisms of SOA production. We present here a comprehensive dataset on the molecular identity, abundance, and kinetics of α-pinene SOA, a canonical system that has received much attention owing to its importance as an organic aerosol source in the pristine atmosphere. Identified organic species account for ∼58-72% of the α-pinene SOA mass, and are characterized as semivolatile/low-volatility monomers and extremely low volatility dimers, which exhibit comparable oxidation states yet different functionalities. Features of the α-pinene SOA formation process are revealed for the first time, to our knowledge, from the dynamics of individual particle-phase components. Although monomeric products dominate the overall aerosol mass, rapid production of dimers plays a key role in initiating particle growth. Continuous production of monomers is observed after the parent α-pinene is consumed, which cannot be explained solely by gas-phase photochemical production. Additionally, distinct responses of monomers and dimers to α-pinene oxidation by ozone vs. hydroxyl radicals, temperature, and relative humidity are observed. Gas-phase radical combination reactions together with condensed phase rearrangement of labile molecules potentially explain the newly characterized SOA features, thereby opening up further avenues for understanding formation and evolution mechanisms of α-pinene SOA.

  14. Formation and evolution of molecular products in α-pinene secondary organic aerosol

    PubMed Central

    Zhang, Xuan; McVay, Renee C.; Huang, Dan D.; Dalleska, Nathan F.; Aumont, Bernard; Flagan, Richard C.; Seinfeld, John H.

    2015-01-01

    Much of our understanding of atmospheric secondary organic aerosol (SOA) formation from volatile organic compounds derives from laboratory chamber measurements, including mass yield and elemental composition. These measurements alone are insufficient to identify the chemical mechanisms of SOA production. We present here a comprehensive dataset on the molecular identity, abundance, and kinetics of α-pinene SOA, a canonical system that has received much attention owing to its importance as an organic aerosol source in the pristine atmosphere. Identified organic species account for ∼58–72% of the α-pinene SOA mass, and are characterized as semivolatile/low-volatility monomers and extremely low volatility dimers, which exhibit comparable oxidation states yet different functionalities. Features of the α-pinene SOA formation process are revealed for the first time, to our knowledge, from the dynamics of individual particle-phase components. Although monomeric products dominate the overall aerosol mass, rapid production of dimers plays a key role in initiating particle growth. Continuous production of monomers is observed after the parent α-pinene is consumed, which cannot be explained solely by gas-phase photochemical production. Additionally, distinct responses of monomers and dimers to α-pinene oxidation by ozone vs. hydroxyl radicals, temperature, and relative humidity are observed. Gas-phase radical combination reactions together with condensed phase rearrangement of labile molecules potentially explain the newly characterized SOA features, thereby opening up further avenues for understanding formation and evolution mechanisms of α-pinene SOA. PMID:26578760

  15. The Diversity and Molecular Evolution of B-Cell Receptors during Infection.

    PubMed

    Hoehn, Kenneth B; Fowler, Anna; Lunter, Gerton; Pybus, Oliver G

    2016-05-01

    B-cell receptors (BCRs) are membrane-bound immunoglobulins that recognize and bind foreign proteins (antigens). BCRs are formed through random somatic changes of germline DNA, creating a vast repertoire of unique sequences that enable individuals to recognize a diverse range of antigens. After encountering antigen for the first time, BCRs undergo a process of affinity maturation, whereby cycles of rapid somatic mutation and selection lead to improved antigen binding. This constitutes an accelerated evolutionary process that takes place over days or weeks. Next-generation sequencing of the gene regions that determine BCR binding has begun to reveal the diversity and dynamics of BCR repertoires in unprecedented detail. Although this new type of sequence data has the potential to revolutionize our understanding of infection dynamics, quantitative analysis is complicated by the unique biology and high diversity of BCR sequences. Models and concepts from molecular evolution and phylogenetics that have been applied successfully to rapidly evolving pathogen populations are increasingly being adopted to study BCR diversity and divergence within individuals. However, BCR dynamics may violate key assumptions of many standard evolutionary methods, as they do not descend from a single ancestor, and experience biased mutation. Here, we review the application of evolutionary models to BCR repertoires and discuss the issues we believe need be addressed for this interdisciplinary field to flourish.

  16. Dynamics of Molecular Evolution and Phylogeography of Barley yellow dwarf virus-PAV

    PubMed Central

    Liu, Yan; Zhou, Guanghe; Wang, Xifeng; Elena, Santiago F.

    2011-01-01

    Barley yellow dwarf virus (BYDV) species PAV occurs frequently in irrigated wheat fields worldwide and can be efficiently transmitted by aphids. Isolates of BYDV-PAV from different countries show great divergence both in genomic sequences and pathogenicity. Despite its economical importance, the genetic structure of natural BYDV-PAV populations, as well as of the mechanisms maintaining its high diversity, remain poorly explored. In this study, we investigate the dynamics of BYDV-PAV genome evolution utilizing time-structured data sets of complete genomic sequences from 58 isolates from different hosts obtained worldwide. First, we observed that BYDV-PAV exhibits a high frequency of homologous recombination. Second, our analysis revealed that BYDV-PAV genome evolves under purifying selection and at a substitution rate similar to other RNA viruses (3.158×10−4 nucleotide substitutions/site/year). Phylogeography analyses show that the diversification of BYDV-PAV can be explained by local geographic adaptation as well as by host-driven adaptation. These results increase our understanding of the diversity, molecular evolutionary characteristics and epidemiological properties of an economically important plant RNA virus. PMID:21326861

  17. Structural evolution of nanoscale metallic glasses during high-pressure torsion: A molecular dynamics analysis

    NASA Astrophysics Data System (ADS)

    Feng, S. D.; Jiao, W.; Jing, Q.; Qi, L.; Pan, S. P.; Li, G.; Ma, M. Z.; Wang, W. H.; Liu, R. P.

    2016-11-01

    Structural evolution in nanoscale Cu50Zr50 metallic glasses during high-pressure torsion is investigated using molecular dynamics simulations. Results show that the strong cooperation of shear transformations can be realized by high-pressure torsion in nanoscale Cu50Zr50 metallic glasses at room temperature. It is further shown that high-pressure torsion could prompt atoms to possess lower five-fold symmetries and higher potential energies, making them more likely to participate in shear transformations. Meanwhile, a higher torsion period leads to a greater degree of forced cooperative flow. And the pronounced forced cooperative flow at room temperature under high-pressure torsion permits the study of the shear transformation, its activation and characteristics, and its relationship to the deformations behaviors. This research not only provides an important platform for probing the atomic-level understanding of the fundamental mechanisms of high-pressure torsion in metallic glasses, but also leads to higher stresses and homogeneous flow near lower temperatures which is impossible previously.

  18. Molecular Evolution of a Pervasive Natural Amino-Acid Substitution in Drosophila cryptochrome

    PubMed Central

    Pegoraro, Mirko; Noreen, Shumaila; Bhutani, Supriya; Tsolou, Avgi; Schmid, Ralf; Kyriacou, Charalambos P.; Tauber, Eran

    2014-01-01

    Genetic variations in circadian clock genes may serve as molecular adaptations, allowing populations to adapt to local environments. Here, we carried out a survey of genetic variation in Drosophila cryptochrome (cry), the fly’s dedicated circadian photoreceptor. An initial screen of 10 European cry alleles revealed substantial variation, including seven non-synonymous changes. The SNP frequency spectra and the excessive linkage disequilibrium in this locus suggested that this variation is maintained by natural selection. We focused on a non-conservative SNP involving a leucine - histidine replacement (L232H) and found that this polymorphism is common, with both alleles at intermediate frequencies across 27 populations surveyed in Europe, irrespective of latitude. Remarkably, we were able to reproduce this natural observation in the laboratory using replicate population cages where the minor allele frequency was initially set to 10%. Within 20 generations, the two allelic variants converged to approximately equal frequencies. Further experiments using congenic strains, showed that this SNP has a phenotypic impact, with variants showing significantly different eclosion profiles. At the long term, these phase differences in eclosion may contribute to genetic differentiation among individuals, and shape the evolution of wild populations. PMID:24475129

  19. Molecular evolution and expression of the CRAL_TRIO protein family in insects.

    PubMed

    Smith, Gilbert; Briscoe, Adriana D

    2015-07-01

    CRAL_TRIO domain proteins are known to bind small lipophilic molecules such as retinal, inositol and Vitamin E and include such gene family members as PINTA, α-tocopherol transfer (ATT) proteins, retinoid binding proteins, and clavesins. In insects, very little is known about either the molecular evolution of this family of proteins or their ligand specificity. Here we characterize insect CRAL_TRIO domain proteins and present the first insect CRAL_TRIO protein phylogeny constructed by performing reciprocal BLAST searches of the reference genomes of Drosophila melanogaster, Anopheles gambiae, Apis mellifera, Tribolium castaneum, Bombyx mori, Manduca sexta and Danaus plexippus. We find several highly conserved amino acid residues in the CRAL_TRIO domain-containing genes across insects and a gene expansion resulting in more than twice as many gene family members in lepidopterans than in other surveyed insect species, but no lepidopteran homolog of the PINTA gene in Drosophila. In addition, we examined the expression pattern of CRAL_TRIO domain genes in Manduca sexta heads using RNA-Seq data. Of the 42 gene family members found in the M. sexta reference genome, we found 30 expressed in the head tissue with similar expression profiles between males and females. Our results suggest this gene family underwent a large expansion in lepidopteran, making the lepidopteran CRAL_TRIO domain family distinct from other holometabolous insect lineages.

  20. Molecular phylogenetics and morphological evolution of St. John's wort (Hypericum; Hypericaceae).

    PubMed

    Nürk, Nicolai M; Madriñán, Santiago; Carine, Mark A; Chase, Mark W; Blattner, Frank R

    2013-01-01

    Phylogenetic hypotheses for the large cosmopolitan genus Hypericum (St. John's wort) have previously been based on morphology, and molecular studies have thus far included only a few species. In this study, we used 360 sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) for 206 species representing Hypericum (incl. Triadenum and Thornea) and three other genera of Hypericaceae to generate an explicit phylogenetic hypothesis for the genus using parsimony and model-based methods. The results indicate that the small genus Triadenum is nested in a clade within Hypericum containing most of the New World species. Sister to Hypericum is Thornea from Central America. Within Hypericum, three large clades and two smaller grades were found; these are based on their general morphology, especially characters used previously in taxonomy of the genus. Relative to the most recent classification, around 60% of the sections of Hypericum were monophyletic. We used a Bayesian approach to reconstruct ancestral states of selected morphological characters, which resulted in recognition of characters that support major clades within the genus and a revised interpretation of morphological evolution in Hypericum. The shrubby habit represents the plesiomorphic state from which herbs evolved several times. Arborescent species have radiated convergently in high-elevation habitats in tropical Africa and South America.

  1. Protein sequence conservation and stable molecular evolution reveals influenza virus nucleoprotein as a universal druggable target.

    PubMed

    Babar, Mustafeez Mujtaba; Zaidi, Najam-us-Sahar Sadaf

    2015-08-01

    The high mutation rate in influenza virus genome and appearance of drug resistance calls for a constant effort to identify alternate drug targets and develop new antiviral strategies. The internal proteins of the virus can be exploited as a potential target for therapeutic interventions. Among these, the nucleoprotein (NP) is the most abundant protein that provides structural and functional support to the viral replication machinery. The current study aims at analysis of protein sequence polymorphism patterns, degree of molecular evolution and sequence conservation as a function of potential druggability of nucleoprotein. We analyzed a universal set of amino acid sequences, (n=22,000) and, in order to identify and correlate the functionally conserved, druggable regions across different parameters, classified them on the basis of host organism, strain type and continental region of sample isolation. The results indicated that around 95% of the sequence length was conserved, with at least 7 regions conserved across the protein among various classes. Moreover, the highly variable regions, though very limited in number, were found to be positively selected indicating, thereby, the high degree of protein stability against various hosts and spatio-temporal references. Furthermore, on mapping the conserved regions on the protein, 7 drug binding pockets in the functionally important regions of the protein were revealed. The results, therefore, collectively indicate that nucleoprotein is a highly conserved and stable viral protein that can potentially be exploited for development of broadly effective antiviral strategies.

  2. Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex

    PubMed Central

    2014-01-01

    Background The moss Physcomitrella patens (Hedw.) Bruch & Schimp. is an important experimental model system for evolutionary-developmental studies. In order to shed light on the evolutionary history of Physcomitrella and related species within the Funariaceae, we analyzed the natural genetic diversity of the Physcomitrium-Physcomitrella species complex. Results Molecular analysis of the nuclear single copy gene BRK1 reveals that three Physcomitrium species feature larger genome sizes than Physcomitrella patens and encode two expressed BRK1 homeologs (polyploidization-derived paralogs), indicating that they may be allopolyploid hybrids. Phylogenetic analyses of BRK1 as well as microsatellite simple sequence repeat (SSR) data confirm a polyphyletic origin for three Physcomitrella lineages. Differences in the conservation of mitochondrial editing sites further support hybridization and cryptic speciation within the Physcomitrium-Physcomitrella species complex. Conclusions We propose a revised classification of the previously described four subspecies of Physcomitrella patens into three distinct species, namely Physcomitrella patens, Physcomitrella readeri and Physcomitrella magdalenae. We argue that secondary reduction of sporophyte complexity in these species is due to the establishment of an ecological niche, namely spores resting in mud and possible spore dispersal by migratory birds. Besides the Physcomitrium-Physcomitrella species complex, the Funariaceae are host to their type species, Funaria hygrometrica, featuring a sporophyte morphology which is more complex. Their considerable developmental variation among closely related lineages and remarkable trait evolution render the Funariaceae an interesting group for evolutionary and genetic research. PMID:25015729

  3. A Molecular Approach to the Study of Green Algal Evolution and Early Terrestrial Ecosystems

    NASA Astrophysics Data System (ADS)

    Kodner, R. B.; Summons, R. E.; Knoll, A. H.

    2004-12-01

    The biological nature of pre-land plant terrestrial ecosystems remains an enigmatic chapter of the history of life on earth due to lack of fossil evidence. Molecular phylogenies have shown that Charophycean green algae are the closest relatives of the bryophytes, which have been hypothesized to be the earliest divergent land plants. However, there is no fossil evidence to support this relationship nor is there a reliable fossil record of the earliest land plants. Microfossils representing the earliest land plants appear to have a bryophytes affinity based on limited morphological comparisons but this remains controversial. We are applying a biomolecular approach to study both green algal evolution and its relation to bryophytes using the resistant biopolymer algaenan and phytosterols as biological markers. Algaenan has been shown to have high preservation potential and may be the primary component of enigmatic microfossils assumed to be of algal origin. Algaenan and the green algal sterols, stigmasterol and sitosterol, may also be the precursors of n-alkanes and the hydrocarbon stigmastane that are major components of many Neoproterozoic bitumens. The biological nature and phylogenetic distribution of algaenan is still not well understood. Here we explore the presence and structure of algaenans in terrestrial green algae and bryophytes in relation to their phylogenetic distributions.

  4. Zimmermann's telome theory of megaphyll leaf evolution: a molecular and cellular critique.

    PubMed

    Beerling, David J; Fleming, Andrew J

    2007-02-01

    Megaphyll leaf evolution was a critical event in Earth history that had major consequences for the biotic regulation of the global environment. Zimmermann's telome theory has been widely accepted for over seventy years as the leading explanation for this evolutionary innovation. According to the telome theory, megaphylls evolved from the three-dimensional lateral branches of early vascular land plants in a hypothetical series of three transformations; first, the formation of determinate lateral branches (overtopping); second, the development of 'flattened' branch systems (planation); and third, the fusion of planated branches with lateral outgrowths of photosynthetic mesophyll tissue to form the leaf blade (webbing). A critical review of the molecular and cellular evidence identifies plausible genetic, cellular and physiological mechanisms in extant higher plants for overtopping and planation but more limited evidence for the process of webbing (lateral outgrowth fusion). We highlight key outstanding questions concerning the telome theory that are likely to be resolved when gene identification and functional analysis techniques are applied to photosynthetic organisms that have different evolutionary histories.

  5. Molecular development of fibular reduction in birds and its evolution from dinosaurs.

    PubMed

    Botelho, João Francisco; Smith-Paredes, Daniel; Soto-Acuña, Sergio; O'Connor, Jingmai; Palma, Verónica; Vargas, Alexander O

    2016-03-01

    Birds have a distally reduced, splinter-like fibula that is shorter than the tibia. In embryonic development, both skeletal elements start out with similar lengths. We examined molecular markers of cartilage differentiation in chicken embryos. We found that the distal end of the fibula expresses Indian hedgehog (IHH), undergoing terminal cartilage differentiation, and almost no Parathyroid-related protein (PTHrP), which is required to develop a proliferative growth plate (epiphysis). Reduction of the distal fibula may be influenced earlier by its close contact with the nearby fibulare, which strongly expresses PTHrP. The epiphysis-like fibulare however then separates from the fibula, which fails to maintain a distal growth plate, and fibular reduction ensues. Experimental downregulation of IHH signaling at a postmorphogenetic stage led to a tibia and fibula of equal length: The fibula is longer than in controls and fused to the fibulare, whereas the tibia is shorter and bent. We propose that the presence of a distal fibular epiphysis may constrain greater growth in the tibia. Accordingly, many Mesozoic birds show a fibula that has lost its distal epiphysis, but remains almost as long as the tibia, suggesting that loss of the fibulare preceded and allowed subsequent evolution of great fibulo-tibial disparity.

  6. Molecular Evolution and Expression Divergence of the Aconitase (ACO) Gene Family in Land Plants

    PubMed Central

    Wang, Yi-Ming; Yang, Qi; Liu, Yan-Jing; Yang, Hai-Ling

    2016-01-01

    Aconitase (ACO) is a key enzyme that catalyzes the isomerization of citrate to isocitrate in the tricarboxylic acid (TCA) and glyoxylate cycles. The function of ACOs has been well studied in model plants, such as Arabidopsis. In contrast, the evolutionary patterns of the ACO family in land plants are poorly understood. In this study, we systematically examined the molecular evolution and expression divergence of the ACO gene family in 12 land plant species. Thirty-six ACO genes were identified from the 12 land plant species representing the four major land plant lineages: Bryophytes, lycophytes, gymnosperms, and angiosperms. All of these ACOs belong to the cytosolic isoform. Three gene duplication events contributed to the expansion of the ACO family in angiosperms. The ancestor of angiosperms may have contained only one ACO gene. One gene duplication event split angiosperm ACOs into two distinct clades. Two clades showed a divergence in selective pressure and gene expression patterns. The cis-acting elements that function in light responsiveness were most abundant in the promoter region of the ACO genes, indicating that plant ACO genes might participate in light regulatory pathways. Our findings provide comprehensive insights into the ACO gene family in land plants. PMID:28018410

  7. Molecular evolution and sequence divergence of plant chalcone synthase and chalcone synthase-Like genes.

    PubMed

    Han, Yingying; Zhao, Wenwen; Wang, Zhicui; Zhu, Jingying; Liu, Qisong

    2014-06-01

    Plant chalcone synthase (CHS) and CHS-Like (CHSL) proteins are polyketide synthases. In this study, we evaluated the molecular evolution of this gene family using representative types of CHSL genes, including stilbene synthase (STS), 2-pyrone synthase (2-PS), bibenzyl synthase (BBS), acridone synthase (ACS), biphenyl synthase (BIS), benzalacetone synthase, coumaroyl triacetic acid synthase (CTAS), and benzophenone synthase (BPS), along with their CHS homologs from the same species of both angiosperms and gymnosperms. A cDNA-based phylogeny indicated that CHSLs had diverse evolutionary patterns. STS, ACS, and 2-PS clustered with CHSs from the same species (late diverged pattern), while CTAS, BBS, BPS, and BIS were distant from their CHS homologs (early diverged pattern). The amino-acid phylogeny suggested that CHS and CHSL proteins formed clades according to enzyme function. The CHSs and CHSLs from Polygonaceae and Arachis had unique evolutionary histories. Synonymous mutation rates were lower in late diverged CHSLs than in early diverged ones, indicating that gene duplications occurred more recently in late diverged CHSLs than in early diverged ones. Relative rate tests proved that late diverged CHSLs had unequal rates to CHSs from the same species when using fatty acid synthase, which evolved from the common ancestor with the CHS superfamily, as the outgroup, while the early diverged lineages had equal rates. This indicated that late diverged CHSLs experienced more frequent mutation than early diverged CHSLs after gene duplication, allowing obtaining new functions in relatively short period of time.

  8. Molecular evolution and functional divergence of zebrafish (Danio rerio) cryptochrome genes

    PubMed Central

    Liu, Chao; Hu, Jia; Qu, Chunxiang; Wang, Lin; Huang, Guodong; Niu, Pengfei; Zhong, Zhaomin; Hong, Fashui; Wang, Guanghui; Postlethwait, John H.; Wang, Han

    2015-01-01

    Cryptochromes function in animal circadian regulation. Zebrafish are known to have six cryptochrome (cry) genes but their evolutionary relationships are not yet fully resolved. Here, comparative genomic analyses revealed that a local duplication of ancestral chordate Cry occurred likely before the first round of vertebrate genome duplication (VGD); following two successive rounds of VGD and subsequent gene losses, coelacanths retained cry1a, cry1b, cry2 and cry3; and following the third-round teleost genome duplication (TGD) and subsequent gene losses, zebrafish retained six cry genes, renamed as cry1aa (zcry1a in the old nomenclature), cry1ab (zcry1b), cry1ba (zcry2a), cry1bb (zcry2b), cry2 (zcry3) and cry3 (zcry4). Molecular evolutionary analyses suggested that zebrafish cry genes have evolved divergent functions, which is further supported by their distinct and rhythmic expression patterns as shown by both in situ hybridization and quantitative real-time PCR. Systematic cell transfection assays divided six Cry proteins into repressive Cry1aa, Cry1ab, Cry1ba and Cry1bb, and non-repressive Cry2 and Cry3. Cry2 is non-repressive because it lacks an effective protein-protein interaction domain although it does possess a nuclear localization signal (NLS) motif, whilst Cry3 lacks both an NLS motif and a protein-protein interaction domain. These findings provide a better understanding of evolution of zebrafish cry genes. PMID:25630924

  9. Molecular Evolution and Expansion Analysis of the NAC Transcription Factor in Zea mays

    PubMed Central

    Fan, Kai; Wang, Ming; Miao, Ying; Ni, Mi; Bibi, Noreen; Yuan, Shuna; Li, Feng; Wang, Xuede

    2014-01-01

    NAC (NAM, ATAF1, 2 and CUC2) family is a plant-specific transcription factor and it controls various plant developmental processes. In the current study, 124 NAC members were identified in Zea mays and were phylogenetically clustered into 13 distinct subfamilies. The whole genome duplication (WGD), especially an additional WGD event, may lead to expanding ZmNAC members. Different subfamily has different expansion rate, and NAC subfamily preference was found during the expansion in maize. Moreover, the duplication events might occur after the divergence of the lineages of Z. mays and S. italica, and segmental duplication seemed to be the dominant pattern for the gene duplication in maize. Furthermore, the expansion of ZmNAC members may be also related to gain and loss of introns. Besides, the restriction of functional divergence was discovered after most of the gene duplication events. These results could provide novel insights into molecular evolution and expansion analysis of NAC family in maize, and advance the NAC researches in other plants, especially polyploid plants. PMID:25369196

  10. Heart transplantation in patients with chronic hepatitis B: clinical evolution, molecular analysis, and effect of treatment.

    PubMed

    Zampino, Rosa; Marrone, Aldo; Ragone, Enrico; Costagliola, Loredana; Cirillo, Grazia; Karayiannis, Peter; Ruggiero, Giuseppe; Utili, Riccardo

    2005-11-15

    We evaluated clinical evolution and hepatitis B virus (HBV) molecular changes in heart recipients with chronic HBV infection before transplantation, and studied the effects of lamivudine treatment in patients who experienced HBV reactivation. Nine patients with chronic HBV infection who underwent heart transplantation were investigated. HBV surface/core-promoter/precore/core regions were sequenced. Prior to transplantation, all nine patients had consistently normal ALT and low HBV-DNA levels. Seven experienced HBV reactivation after transplantation (ALT elevated, HBV-DNA>200.000 cps/ml). Lamivudine treatment was initially effective in all patients; three patients during the second year of treatment developed lamivudine resistance-associated mutations (rt-L180M, rt-M204V) with severe disease reactivation, remitted after switch to adefovir treatment. No other significant HBV mutations were identified in the genomic regions studied. Immune suppression is crucial in the reactivation of previous inactive HBV infection and in the liver disease progression in heart recipients. Preemptive lamivudine treatment could be useful in the early management of these patients.

  11. Iron and molecular opacities and the evolution of Population I stars

    NASA Technical Reports Server (NTRS)

    Stothers, Richard B.; Chin, Chao-Wen

    1993-01-01

    Effects of recent opacity revisions on the evolution of Population I stars are explored over the range 1.5-60 solar masses. Opacity parameters considered include the angular momentum coupling scheme for iron, the relative iron abundance, the total metal abundance, and diatomic and triatomic molecular sources. Only the total metal abundance exerts an important control over the evolutionary tracks. Blue loops on the H-R diagram during core helium burning can be very sensitive to opacity, but only insofar as the simple formation or suppression of a blue loop is concerned. The blue loops are most robust for stellar masses around 10 solar masses. We confirm, from a comparison of stellar models with observational data, that the total metal abundance is close to solar and that convective core overshooting is likely to be very slight. The new models predict the existence of an iron convection zone in the envelope and a great widening of the main-sequence band in the H-R diagram at luminosities brighter than 100,000 solar luminosities.

  12. Molecular development of fibular reduction in birds and its evolution from dinosaurs

    PubMed Central

    Botelho, João Francisco; Smith‐Paredes, Daniel; Soto‐Acuña, Sergio; O'Connor, Jingmai; Palma, Verónica; Vargas, Alexander O.

    2016-01-01

    Birds have a distally reduced, splinter‐like fibula that is shorter than the tibia. In embryonic development, both skeletal elements start out with similar lengths. We examined molecular markers of cartilage differentiation in chicken embryos. We found that the distal end of the fibula expresses Indian hedgehog (IHH), undergoing terminal cartilage differentiation, and almost no Parathyroid‐related protein (PTHrP), which is required to develop a proliferative growth plate (epiphysis). Reduction of the distal fibula may be influenced earlier by its close contact with the nearby fibulare, which strongly expresses PTHrP. The epiphysis‐like fibulare however then separates from the fibula, which fails to maintain a distal growth plate, and fibular reduction ensues. Experimental downregulation of IHH signaling at a postmorphogenetic stage led to a tibia and fibula of equal length: The fibula is longer than in controls and fused to the fibulare, whereas the tibia is shorter and bent. We propose that the presence of a distal fibular epiphysis may constrain greater growth in the tibia. Accordingly, many Mesozoic birds show a fibula that has lost its distal epiphysis, but remains almost as long as the tibia, suggesting that loss of the fibulare preceded and allowed subsequent evolution of great fibulo–tibial disparity. PMID:26888088

  13. Structural evolution of nanoscale metallic glasses during high-pressure torsion: A molecular dynamics analysis

    PubMed Central

    Feng, S. D.; Jiao, W.; Jing, Q.; Qi, L.; Pan, S. P.; Li, G.; Ma, M. Z.; Wang, W. H.; Liu, R. P.

    2016-01-01

    Structural evolution in nanoscale Cu50Zr50 metallic glasses during high-pressure torsion is investigated using molecular dynamics simulations. Results show that the strong cooperation of shear transformations can be realized by high-pressure torsion in nanoscale Cu50Zr50 metallic glasses at room temperature. It is further shown that high-pressure torsion could prompt atoms to possess lower five-fold symmetries and higher potential energies, making them more likely to participate in shear transformations. Meanwhile, a higher torsion period leads to a greater degree of forced cooperative flow. And the pronounced forced cooperative flow at room temperature under high-pressure torsion permits the study of the shear transformation, its activation and characteristics, and its relationship to the deformations behaviors. This research not only provides an important platform for probing the atomic-level understanding of the fundamental mechanisms of high-pressure torsion in metallic glasses, but also leads to higher stresses and homogeneous flow near lower temperatures which is impossible previously. PMID:27819352

  14. Periodic Vesicle Formation in Tectonic Fault Zones—an Ideal Scenario for Molecular Evolution

    NASA Astrophysics Data System (ADS)

    Mayer, Christian; Schreiber, Ulrich; Dávila, María J.

    2015-06-01

    Tectonic fault systems in the continental crust offer huge networks of interconnected channels and cavities. Filled mainly with water and carbon dioxide (CO2), containing a wide variety of hydrothermal chemistry and numerous catalytic surfaces, they may offer ideal reaction conditions for prebiotic chemistry. In these systems, an accumulation zone for organic compounds will develop at a depth of approximately 1 km where CO2 turns sub-critical and dissolved components precipitate. At this point, periodic pressure changes caused for example by tidal influences or geyser activity may generate a cyclic process involving repeated phase transitions of carbon dioxide. In the presence of amphiphilic compounds, this will necessarily lead to the transient formation of coated water droplets in the gas phase and corresponding vesicular structures in the aqueous environment. During this process, the concentration of organic components inside the droplets and vesicles would be drastically increased, allowing for favorable reaction conditions and, in case of the vesicles generated, large trans-membrane concentration gradients. Altogether, the process of periodic formation and destruction of vesicles could offer a perfect environment for molecular evolution in small compartments and for the generation of protocells. The basic process of vesicle formation is reproduced experimentally with a lipid in a water/CO2 system.

  15. Periodic Vesicle Formation in Tectonic Fault Zones--an Ideal Scenario for Molecular Evolution.

    PubMed

    Mayer, Christian; Schreiber, Ulrich; Dávila, María J

    2015-06-01

    Tectonic fault systems in the continental crust offer huge networks of interconnected channels and cavities. Filled mainly with water and carbon dioxide (CO2), containing a wide variety of hydrothermal chemistry and numerous catalytic surfaces, they may offer ideal reaction conditions for prebiotic chemistry. In these systems, an accumulation zone for organic compounds will develop at a depth of approximately 1 km where CO2 turns sub-critical and dissolved components precipitate. At this point, periodic pressure changes caused for example by tidal influences or geyser activity may generate a cyclic process involving repeated phase transitions of carbon dioxide. In the presence of amphiphilic compounds, this will necessarily lead to the transient formation of coated water droplets in the gas phase and corresponding vesicular structures in the aqueous environment. During this process, the concentration of organic components inside the droplets and vesicles would be drastically increased, allowing for favorable reaction conditions and, in case of the vesicles generated, large trans-membrane concentration gradients. Altogether, the process of periodic formation and destruction of vesicles could offer a perfect environment for molecular evolution in small compartments and for the generation of protocells. The basic process of vesicle formation is reproduced experimentally with a lipid in a water/CO2 system.

  16. Entropy and charge in molecular evolution--the case of phosphate

    NASA Technical Reports Server (NTRS)

    Arrhenius, G.; Sales, B.; Mojzsis, S.; Lee, T.; Bada, J. L. (Principal Investigator)

    1997-01-01

    Biopoesis, the creation of life, implies molecular evolution from simple components, randomly distributed and in a dilute state, to form highly organized, concentrated systems capable of metabolism, replication and mutation. This chain of events must involve environmental processes that can locally lower entropy in several steps; by specific selection from an indiscriminate mixture, by concentration from dilute solution, and in the case of the mineral-induced processes, by particular effectiveness in ordering and selective reaction, directed toward formation of functional biomolecules. Numerous circumstances provide support for the notion that negatively charged molecules were functionally required and geochemically available for biopoesis. Sulfite ion may have been important in bisulfite complex formation with simple aldehydes, facilitating the initial concentration by sorption of aldehydes in positively charged surface active minerals. Borate ion may have played a similar, albeit less investigated role in forming charged sugar complexes. Among anionic species, oligophosphate ions and charged phosphate esters are likely to have been of even more wide ranging importance, reflected in the continued need for phosphate in a proposed RNA world, and extending its central role to evolved biochemistry. Phosphorylation is shown to result in selective concentration by surface sorption of compounds, otherwise too dilute to support condensation reactions. It provides protection against rapid hydrolysis of sugars and, by selective concentration, induces the oligomerization of aldehydes. As a manifestation of life arisen, phosphate already appears in an organic context in the oldest preserved sedimentary record.

  17. On the evolution and molecular epidemiology of the potyvirus Papaya ringspot virus.

    PubMed

    Bateson, Marion F; Lines, Rosemarie E; Revill, Peter; Chaleeprom, Worawan; Ha, Cuong V; Gibbs, Adrian J; Dale, James L

    2002-10-01

    The potyvirus Papaya ringspot virus (PRSV) is found throughout the tropics and subtropics. Its P biotype is a devastating pathogen of papaya crops and its W biotype of cucurbits. PRSV-P is thought to arise by mutation from PRSV-W. However, the relative impact of mutation and movement on the structure of PRSV populations is not well characterized. To investigate this, we have determined the coat protein sequences of isolates of both biotypes of PRSV from Vietnam (50), Thailand (13), India (1) and the Philippines (1), and analysed them together with 28 PRSV sequences already published, so that we can better understand the molecular epidemiology and evolution of PRSV. In Thailand, variation was greater among PRSV-W isolates (mean nucleotide divergence 7.6%) than PRSV-P isolates (mean 2.6%), but in Vietnamese populations the P and W biotypes were more but similarly diverse. Phylogenetic analyses of PRSV also involving its closest known relative, Moroccan watermelon mosaic virus, indicate that PRSV may have originated in Asia, particularly in the Indian subcontinent, as PRSV populations there are most diverse and hence have probably been present longest. Our analyses show that mutation, together with local and long-distance movement, contributes to population variation, and also confirms an earlier conclusion that populations of the PRSV-P biotype have evolved on several occasions from PRSV-W populations.

  18. Adaptive Molecular Evolution of PHYE in Primulina, a Karst Cave Plant.

    PubMed

    Tao, Junjie; Qi, Qingwen; Kang, Ming; Huang, Hongwen

    2015-01-01

    Limestone Karst areas possess high levels of biodiversity and endemism. Primulina is a typical component of Karst endemic floras. The high species richness and wide distribution in various Karst microenvironments make the genus an idea model for studying speciation and local adaptation. In this study, we obtained 10 full-length sequences of the phytochrome PHYE from available transcriptome resources of Primulina and amplified partial sequences of PHYE from the genomic DNA of 74 Primulina species. Then, we used maximum-likelihood approaches to explore molecular evolution of PHYE in this Karst cave plant. The results showed that PHYE was dominated by purifying selection in both data sets, and two sites were identified as potentially under positive selection. Furthermore, the ω ratio varies greatly among different functional domains of PHYE and among different species lineages. These results suggest that potential positive selection in PHYE might have played an important role in the adaption of Primulina to heterogeneous light environments in Karst regions, and different species lineages might have been subjected to different selective pressures.

  19. Insights into the proline hydroxylase (PHD) family, molecular evolution and its impact on human health.

    PubMed

    Minervini, Giovanni; Quaglia, Federica; Tosatto, Silvio C E

    2015-09-01

    PHDs (proline hydroxylases) are a small protein family found in all organisms, considered the central regulator of the molecular hypoxia response due to PHDs being completely inactivated under low oxygen concentration. At physiological oxygen concentration, PHDs drive the degradation of the HIF-1α (hypoxia-inducible factor 1-α), which is responsible for upregulating the expression of genes involved in the cellular response to hypoxia. Hypoxia is a common feature of most tumors, in particular during metastasis development. Indeed, cancer reacts by activating pathways promoting new blood vessel formation and activating strategies aimed to improve survival. In this scenario, the PHD family regulates the activation of HIF-1α and cell-cycle regulation. Several PHD mutations were found in cancer patients, underlining their importance for human health. Here, we propose a Bayesian model able to predict the pathological effect of human PHD mutations and their correlation with cancer outcome. The model was developed through an integrative in silico approach, where data collected from the literature has been coupled with sequence evolution and structural analysis. The model was used to assess 135 human PHD variants. Finally, bioinformatics characterization was used to demonstrate how few amino acid changes are able to explain the functional specialization of PHD family members and their physiological role in human health.

  20. Molecular evolution of candidate genes for crop-related traits in sunflower (Helianthus annuus L.).

    PubMed

    Mandel, Jennifer R; McAssey, Edward V; Nambeesan, Savithri; Garcia-Navarro, Elena; Burke, John M

    2014-01-01

    Evolutionary analyses aimed at detecting the molecular signature of selection during crop domestication and/or improvement can be used to identify genes or genomic regions of likely agronomic importance. Here, we describe the DNA sequence-based characterization of a pool of candidate genes for crop-related traits in sunflower. These genes, which were identified based on homology to genes of known effect in other study systems, were initially sequenced from a panel of improved lines. All genes that exhibited a paucity of sequence diversity, consistent with the possible effects of selection during the evolution of cultivated sunflower, were then sequenced from a panel of wild sunflower accessions an outgroup. These data enabled formal tests for the effects of selection in shaping sequence diversity at these loci. When selection was detected, we further sequenced these genes from a panel of primitive landraces, thereby allowing us to investigate the likely timing of selection (i.e., domestication vs. improvement). We ultimately identified seven genes that exhibited the signature of positive selection during either domestication or improvement. Genetic mapping of a subset of these genes revealed co-localization between candidates for genes involved in the determination of flowering time, seed germination, plant growth/development, and branching and QTL that were previously identified for these traits in cultivated × wild sunflower mapping populations.

  1. In-situ Mass Spectrometric Determination of Molecular Structural Evolution at the Solid Electrolyte Interphase in Lithium-Ion Batteries

    SciTech Connect

    Zhu, Zihua; Zhou, Yufan; Yan, Pengfei; Vemuri, Venkata Rama Ses; Xu, Wu; Zhao, Rui; Wang, Xuelin; Thevuthasan, Suntharampillai; Baer, Donald R.; Wang, Chong M.

    2015-08-19

    Dynamic molecular evolution at solid/liquid electrolyte interface is always a mystery for a rechargeable battery due to the challenge to directly probe/observe the solid/liquid interface under reaction conditions, which in essence appears to be similarly true for all the fields involving solid/liquid phases, such as electrocatalysis, electrodeposition, biofuel conversion, biofilm, and biomineralization, We use in-situ liquid secondary ion mass spectroscopy (SIMS) for the first time to directly observe the molecular structural evolution at the solid electrode/liquid electrolyte interface for a lithium (Li)-ion battery under dynamic operating conditions. We have discovered that the deposition of Li metal on copper electrode leads to the condensation of solvent molecules around the electrode. Chemically, this layer of solvent condensate tends to deplete the salt anion and with low concentration of Li+ ions, which essentially leads to the formation of a lean electrolyte layer adjacent to the electrode and therefore contributes to the overpotential of the cell. This unprecedented molecular level dynamic observation at the solid electrode/liquid electrolyte interface provides vital chemical information that is needed for designing of better battery chemistry for enhanced performance, and ultimately opens new avenues for using liquid SIMS to probe molecular evolution at solid/liquid interface in general.

  2. Molecular evidence of host influences on the evolution and spread of human tapeworms.

    PubMed

    Michelet, Lorraine; Dauga, Catherine

    2012-08-01

    The taeniasis/cysticercosis complex is included in the list of neglected zoonotic diseases by the World Health Organization due to its significant impact on public health in tropical areas. Cysticercosis is still endemic in many regions of Asia, Africa and Latin America. Long absent in Europe and in other developed countries, cysticercosis has recently re-emerged in the United States and Canada, due to immigration, travel and local transmission. This has encouraged the use of molecular data to understand better the influence of animal and human hosts on the emergence and spread of Taenia species. The increasing number of mitochondrial sequences now available from human tapeworms and recent advances in computational tools has enabled reconstruction of the biogeography and evolutionary history of these organisms. New molecular data have provided insights into the biogeography of T. solium, T. asiatica and T. saginata. A Bayesian statistical framework using variable evolutionary rates from lineage to lineage has allowed an improved timescale analysis of human tapeworms. The dates of divergence obtained were compared to the timing of evolutionary events in the history of their hosts, based on the hypothesis that Taenia spp. and their hosts share a common history. Herein, we review changes in the definitive and secondary hosts and human interactions that underlie the differentiation and evolution of tapeworms. Species diversification of Taenia seems to be closely linked with the evolution of intermediate hosts in response to climatic events during the Pleistocene. Different genotypes of T. solium emerged when European and Asian wild boar Sus spp. populations diverged. Taenia saginata emerged when wild cattle Bos primigenius evolved and when zebu Bos indicus and taurine Bos taurus ancestors separated. Humans through migrations and later with the development of farming and animal husbandry may have had a significant impact on the spread and diversification of tapeworms

  3. The Darwinian muddle on the division of labour: an attempt at clarification.

    PubMed

    D'Hombres, Emmanuel

    2016-04-01

    It is of philosophical and epistemological interest to examine how Darwin conceived the process of division of labour within Natural History. Darwin observed the advantages brought by division of labour to the human economy, and considered that the principle of divergence within nature, which is, according to him, one of the two 'keystones' of his theory, gave comparable advantages. This led him to re-examine Milne-Edwards' view on the notion of division of physiological labour, and to introduce this with modifications into his naturalist writings. After a short review of the Darwinian historiography dealing with this issue, I first show the conceptual confusion into which Darwin plunges, when using a so-called economic argument to defend his thesis of the maximization of beings in a given territory due to division of labour. Following this I propose several hypotheses to explain these shifts, recurring in Darwin's texts, from one conception and from one application to another, of the division of labour.

  4. Adaptive molecular evolution of the Major Histocompatibility Complex genes, DRA and DQA, in the genus Equus

    PubMed Central

    2011-01-01

    Background Major Histocompatibility Complex (MHC) genes are central to vertebrate immune response and are believed to be under balancing selection by pathogens. This hypothesis has been supported by observations of extremely high polymorphism, elevated nonsynonymous to synonymous base pair substitution rates and trans-species polymorphisms at these loci. In equids, the organization and variability of this gene family has been described, however the full extent of diversity and selection is unknown. As selection is not expected to act uniformly on a functional gene, maximum likelihood codon-based models of selection that allow heterogeneity in selection across codon positions can be valuable for examining MHC gene evolution and the molecular basis for species adaptations. Results We investigated the evolution of two class II MHC genes of the Equine Lymphocyte Antigen (ELA), DRA and DQA, in the genus Equus with the addition of novel alleles identified in plains zebra (E. quagga, formerly E. burchelli). We found that both genes exhibited a high degree of polymorphism and inter-specific sharing of allele lineages. To our knowledge, DRA allelic diversity was discovered to be higher than has ever been observed in vertebrates. Evidence was also found to support a duplication of the DQA locus. Selection analyses, evaluated in terms of relative rates of nonsynonymous to synonymous mutations (dN/dS) averaged over the gene region, indicated that the majority of codon sites were conserved and under purifying selection (dN

  5. Molecular phylogeny and genome size evolution of the genus Betula (Betulaceae)

    PubMed Central

    Wang, Nian; McAllister, Hugh A.; Bartlett, Paul R.; Buggs, Richard J. A.

    2016-01-01

    Background and Aims Betula L. (birch) is a genus of approx. 60 species, subspecies or varieties with a wide distribution in the northern hemisphere, of ecological and economic importance. A new classification of Betula has recently been proposed based on morphological characters. This classification differs somewhat from previously published molecular phylogenies, which may be due to factors such as convergent evolution, hybridization, incomplete taxon sampling or misidentification of samples. While chromosome counts have been made for many species, few have had their genome size measured. The aim of this study is to produce a new phylogenetic and genome size analysis of the genus. Methods Internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced for 76 Betula samples verified by taxonomic experts, representing approx. 60 taxa, of which approx. 24 taxa have not been included in previous phylogenetic analyses. A further 49 samples from other collections were also sequenced, and 108 ITS sequences were downloaded from GenBank. Phylogenetic trees were built for these sequences. The genome sizes of 103 accessions representing nearly all described species were estimated using flow cytometry. Key Results As expected for a gene tree of a genus where hybridization and allopolyploidy occur, the ITS tree shows clustering, but not resolved monophyly, for the morphological subgenera recently proposed. Most sections show some clustering, but species of the dwarf section Apterocaryon are unusually scattered. Betula corylifolia (subgenus Nipponobetula) unexpectedly clusters with species of subgenus Aspera. Unexpected placements are also found for B. maximowicziana, B. bomiensis, B. nigra and B. grossa. Biogeographical disjunctions were found within Betula between Europe and North America, and also disjunctions between North-east and South-west Asia. The 2C-values for Betula ranged from 0·88 to 5·33 pg, and polyploids are scattered widely throughout the

  6. Molecular evolution of NASP and conserved histone H3/H4 transport pathway

    PubMed Central

    2014-01-01

    Background NASP is an essential protein in mammals that functions in histone transport pathways and maintenance of a soluble reservoir of histones H3/H4. NASP has been studied exclusively in Opisthokonta lineages where some functional diversity has been reported. In humans, growing evidence implicates NASP miss-regulation in the development of a variety of cancers. Although a comprehensive phylogenetic analysis is lacking, NASP-family proteins that possess four TPR motifs are thought to be widely distributed across eukaryotes. Results We characterize the molecular evolution of NASP by systematically identifying putative NASP orthologs across diverse eukaryotic lineages ranging from excavata to those of the crown group. We detect extensive silent divergence at the nucleotide level suggesting the presence of strong purifying selection acting at the protein level. We also observe a selection bias for high frequencies of acidic residues which we hypothesize is a consequence of their critical function(s), further indicating the role of functional constraints operating on NASP evolution. Our data indicate that TPR1 and TPR4 constitute the most rapidly evolving functional units of NASP and may account for the functional diversity observed among well characterized family members. We also show that NASP paralogs in ray-finned fish have different genomic environments with clear differences in their GC content and have undergone significant changes at the protein level suggesting functional diversification. Conclusion We draw four main conclusions from this study. First, wide distribution of NASP throughout eukaryotes suggests that it was likely present in the last eukaryotic common ancestor (LECA) possibly as an important innovation in the transport of H3/H4. Second, strong purifying selection operating at the protein level has influenced the nucleotide composition of NASP genes. Further, we show that selection has acted to maintain a high frequency of functionally relevant

  7. Molecular phylogenetic approach for studying life-history evolution: the ambiguous example of the genus Medicago L.

    PubMed Central

    Bena, G; Lejeune, B; Prosperi, J M; Olivieri, I

    1998-01-01

    We present a molecular phylogeny including most species of the genus Medicago L. (Fabaceae). Based on the consensus of the 48 most parsimonious trees, life-history and mating-system characters are mapped, and a putative history of the genus is suggested. The most parsimonious reconstruction suggests an ancestral annual and selfing state, and recurrent evolution towards perenniality and outcrossing. Based on theoretical predictions and classical hypotheses of the history of the genus, different assumptions about the ancestral state and different weighting schemes of evolution between the character states are made. Assuming an outcrossing, perennial ancestral state (partly supported by morphological features) does not fundamentally change the reconstruction. To meet theoretical expectations, various weighting schemes favouring evolution towards annuality and selfing are applied. Influence and validity of such weighting schemes are discussed with regard to other studies. PMID:9684377

  8. Evolution of strain and composition of Ge islands on Si (001) grown by molecular beam epitaxy during postgrowth annealing

    SciTech Connect

    Singha, R. K.; Das, S.; Majumdar, S.; Das, K.; Dhar, A.; Ray, S. K.

    2008-06-01

    Self-assembled Ge islands have been grown using a Stranski-Krastanov growth mechanism on Si (001) substrates by solid source molecular beam epitaxy. We performed time varying annealing experiments at a representative temperature of 650 deg. C to study the shape and size evolution of islands for a relatively high Ge coverage. Islands are found to coarsen due to heat treatment via structural and compositional changes through continuous strain relaxation. Different island morphologies, namely, 'pyramids', 'transitional domes', and 'domes' are found during the annealing sequence. The dominant coarsening mechanisms for the temporal evolution of islands of as-grown and annealed samples are explained by the comprehensive analysis of Rutherford back scattering, Raman spectroscopy, high-resolution x-ray diffraction, and atomic force microscopy. A correlation of the morphological evolution with the composition and strain relaxation of grown islands is presented.

  9. Applications of single-strand conformation polymorphism (SSCP) to taxonomy, diagnosis, population genetics and molecular evolution of parasitic nematodes.

    PubMed

    Gasser, R B; Chilton, N B

    2001-11-22

    The analysis of genetic variation in parasitic nematodes has important implications for studying aspects of taxonomy, diagnosis, population genetics, drug resistance and molecular evolution. This article highlights some applications of PCR-based single-strand conformation polymorphism (SSCP) for the analysis of sequence variation in individual parasites (and their populations) to address some of these areas. It also describes the principles and advantages of SSCP, and provides some examples for future applications in parasitology.

  10. The dynamical evolution of molecular clouds near the Galactic Centre - I. Orbital structure and evolutionary timeline

    NASA Astrophysics Data System (ADS)

    Kruijssen, J. M. Diederik; Dale, James E.; Longmore, Steven N.

    2015-02-01

    We recently proposed that the star-forming potential of dense molecular clouds in the Central Molecular Zone (CMZ, i.e. the central few 100 pc) of the Milky Way is intimately linked to their orbital dynamics, potentially giving rise to an absolute-time sequence of star-forming clouds. In this paper, we present an orbital model for the gas stream(s) observed in the CMZ. The model is obtained by integrating orbits in the empirically constrained gravitational potential and represents a good fit (χ _red^2=2.0) to the observed position-velocity distribution of dense (n > several 103 cm-3) gas, reproducing all of its key properties. The orbit is also consistent with observational constraints not included in the fitting process, such as the 3D space velocities of Sgr B2 and the Arches and Quintuplet clusters. It differs from previous, parametric models in several respects: (1) the orbit is open rather than closed due to the extended mass distribution in the CMZ, (2) its orbital velocity (100-200 km s-1) is twice as high as in previous models, and (3) Sgr A* coincides with the focus of the (eccentric) orbit rather than being offset. Our orbital solution supports the recently proposed scenario in which the dust ridge between G0.253+0.016 (`the Brick') and Sgr B2 represents an absolute-time sequence of star-forming clouds, of which the condensation was triggered by the tidal compression during their most recent pericentre passage. We position the clouds on a common timeline and find that their pericentre passages occurred 0.30-0.74 Myr ago. Given their short free-fall times (tff ˜ 0.34 Myr), the quiescent cloud G0.253+0.016 and the vigorously star-forming complex Sgr B2 are separated by a single free-fall time of evolution, implying that star formation proceeds rapidly once collapse has been initiated. We provide the complete orbital solution, as well as several quantitative predictions of our model (e.g. proper motions and the positions of star formation `hotspots'). The

  11. Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles

    PubMed Central

    Fujisawa, Tomochika; Vogler, Alfried P.; Barraclough, Timothy G.

    2015-01-01

    Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution. PMID:25621335

  12. Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles.

    PubMed

    Fujisawa, Tomochika; Vogler, Alfried P; Barraclough, Timothy G

    2015-01-22

    Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.

  13. Molecular evolution of multiple forms of kisspeptins and GPR54 receptors in vertebrates.

    PubMed

    Lee, Yeo Reum; Tsunekawa, Kenta; Moon, Mi Jin; Um, Haet Nim; Hwang, Jong-Ik; Osugi, Tomohiro; Otaki, Naohito; Sunakawa, Yuya; Kim, Kyungjin; Vaudry, Hubert; Kwon, Hyuk Bang; Seong, Jae Young; Tsutsui, Kazuyoshi

    2009-06-01

    Kisspeptin and its receptor GPR54 play important roles in mammalian reproduction and cancer metastasis. Because the KiSS and GPR54 genes have been identified in a limited number of vertebrate species, mainly in mammals, the evolutionary history of these genes is poorly understood. In the present study, we have cloned multiple forms of kisspeptin and GPR54 cDNAs from a variety of vertebrate species. We found that fish have two forms of kisspeptin genes, KiSS-1 and KiSS-2, whereas Xenopus possesses three forms of kisspeptin genes, KiSS-1a, KiSS-1b, and KiSS-2. The nonmammalian KiSS-1 gene was found to be the ortholog of the mammalian KiSS-1 gene, whereas the KiSS-2 gene is a novel form, encoding a C-terminally amidated dodecapeptide in the Xenopus brain. This study is the first to identify a mature form of KiSS-2 product in the brain of any vertebrate. Likewise, fish possess two receptors, GPR54-1 and GPR54-2, whereas Xenopus carry three receptors, GPR54-1a, GPR54-1b, and GPR54-2. Sequence identity and genome synteny analyses indicate that Xenopus GPR54-1a is a human GPR54 ortholog, whereas Xenopus GPR54-1b is a fish GPR54-1 ortholog. Both kisspeptins and GPR54s were abundantly expressed in the Xenopus brain, notably in the hypothalamus, suggesting that these ligand-receptor pairs have neuroendocrine and neuromodulatory roles. Synthetic KiSS-1 and KiSS-2 peptides activated GPR54s expressed in CV-1 cells with different potencies, indicating differential ligand selectivity. These data shed new light on the molecular evolution of the kisspeptin-GPR54 system in vertebrates.

  14. Phylogenetic characterization and molecular evolution of bacterial endosymbionts in psyllids (Hemiptera: Sternorrhyncha).

    PubMed

    Spaulding, A W; von Dohlen, C D

    1998-11-01

    Most sternorrhynchan insects harbor endosymbiotic bacteria in specialized cells (bacteriocytes) near the gut which provide essential nutrients for hosts. In lineages investigated so far with molecular methods (aphids, mealybugs, whiteflies), endosymbionts apparently have arisen from independent infections of common host ancestors and co-speciated with their hosts. Some endosymbionts also exhibit putatively negative genetic effects from their symbiotic association. In this study, the identity of endosymbionts in one major sternorrhynchan lineage, psyllids (Psylloidea), was investigated to determine their position in eubacterial phylogeny and their relationship to other sternorrhynchan endosymbionts. Small-subunit ribosomal RNA genes (16S rDNA) from bacteria in three psyllid species (families Psyllidae and Triozidae) were sequenced and incorporated into an alignment including other insect endosymbionts and free-living bacteria. In phylogenetic analysis, all sequences were placed within the gamma subdivision of the Proteobacteria. Three sequences, one from each psyllid species, formed a highly supported monophyletic group whose branching order matched the host phylogeny, and also exhibited accelerated rates of evolution and mutational bias toward A and T nucleotides. These attributes, characteristic of primary (P) bacteriocyte-dwelling endosymbionts, suggested that these sequences were from the putative psyllid P endosymbiont. Two other sequences were placed within the gamma-3 subgroup of Proteobacteria and were hypothesized to be secondary endosymbionts. The analysis also suggested a sister relationship between P endosymbionts of psyllids and whiteflies. Thus, a continuous mutualistic association between bacteria and insects may have existed since the common ancestor of psyllids and whiteflies. Calculations using a universal substitution rate in bacteria corrected for endosymbiont rate acceleration support the idea that this common ancestor was also the ancestor of

  15. Molecular Evolution and Genetic Variation of G2-Like Transcription Factor Genes in Maize

    PubMed Central

    Han, Guomin; Zhou, Lingyan; Ali, Asif; Zhu, Suwen; Li, Xiaoyu

    2016-01-01

    The productivity of maize (Zea mays L.) depends on the development of chloroplasts, and G2-like transcription factors play a central role in regulating chloroplast development. In this study, we identified 59 G2-like genes in the B73 maize genome and systematically analyzed these genes at the molecular and evolutionary levels. Based on gene structure character, motif compositions and phylogenetic analysis, maize G2-like genes (ZmG1- ZmG59) were divided into seven groups (I-VII). By synteny analysis, 18 collinear gene pairs and strongly conserved microsyntny among regions hosting G2-like genes across maize and sorghum were found. Here, we showed that the vast majority of ZmG gene duplications resulted from whole genome duplication events rather than tandem duplications. After gene duplication events, some ZmG genes were silenced. The functions of G2-like genes were multifarious and most genes that are expressed in green tissues may relate to maize photosynthesis. The qRT-PCR showed that the expression of these genes was sensitive to low temperature and drought. Furthermore, we analyzed differences of ZmGs specific to cultivars in temperate and tropical regions at the population level. Interestingly, the single nucleotide polymorphism (SNP) analysis revealed that nucleotide polymorphism associated with different temperature zones. Above all, G2-like genes were highly conserved during evolution, but polymorphism could be caused due to a different geographical location. Moreover, G2-like genes might be related to cold and drought stresses. PMID:27560803

  16. Rapid molecular evolution across amniotes of the IIS/TOR network.

    PubMed

    McGaugh, Suzanne E; Bronikowski, Anne M; Kuo, Chih-Horng; Reding, Dawn M; Addis, Elizabeth A; Flagel, Lex E; Janzen, Fredric J; Schwartz, Tonia S

    2015-06-02

    The insulin/insulin-like signaling and target of rapamycin (IIS/TOR) network regulates lifespan and reproduction, as well as metabolic diseases, cancer, and aging. Despite its vital role in health, comparative analyses of IIS/TOR have been limited to invertebrates and mammals. We conducted an extensive evolutionary analysis of the IIS/TOR network across 66 amniotes with 18 newly generated transcriptomes from nonavian reptiles and additional available genomes/transcriptomes. We uncovered rapid and extensive molecular evolution between reptiles (including birds) and mammals: (i) the IIS/TOR network, including the critical nodes insulin receptor substrate (IRS) and phosphatidylinositol 3-kinase (PI3K), exhibit divergent evolutionary rates between reptiles and mammals; (ii) compared with a proxy for the rest of the genome, genes of the IIS/TOR extracellular network exhibit exceptionally fast evolutionary rates; and (iii) signatures of positive selection and coevolution of the extracellular network suggest reptile- and mammal-specific interactions between members of the network. In reptiles, positively selected sites cluster on the binding surfaces of insulin-like growth factor 1 (IGF1), IGF1 receptor (IGF1R), and insulin receptor (INSR); whereas in mammals, positively selected sites clustered on the IGF2 binding surface, suggesting that these hormone-receptor binding affinities are targets of positive selection. Further, contrary to reports that IGF2R binds IGF2 only in marsupial and placental mammals, we found positively selected sites clustered on the hormone binding surface of reptile IGF2R that suggest that IGF2R binds to IGF hormones in diverse taxa and may have evolved in reptiles. These data suggest that key IIS/TOR paralogs have sub- or neofunctionalized between mammals and reptiles and that this network may underlie fundamental life history and physiological differences between these amniote sister clades.

  17. Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom.

    PubMed

    Tzou, Wen-Shyong; Chu, Ying; Lin, Tzung-Yi; Hu, Chin-Hwa; Pai, Tun-Wen; Liu, Hsin-Fu; Lin, Han-Jia; Cases, Ildeofonso; Rojas, Ana; Sanchez, Mayka; You, Zong-Ye; Hsu, Ming-Wei

    2014-01-01

    Adaptation of enzymes in a metabolic pathway can occur not only through changes in amino acid sequences but also through variations in transcriptional activation, mRNA splicing and mRNA translation. The heme biosynthesis pathway, a linear pathway comprised of eight consecutive enzymes in animals, provides researchers with ample information for multiple types of evolutionary analyses performed with respect to the position of each enzyme in the pathway. Through bioinformatics analysis, we found that the protein-coding sequences of all enzymes in this pathway are under strong purifying selection, from cnidarians to mammals. However, loose evolutionary constraints are observed for enzymes in which self-catalysis occurs. Through comparative genomics, we found that in animals, the first intron of the enzyme-encoding genes has been co-opted for transcriptional activation of the genes in this pathway. Organisms sense the cellular content of iron, and through iron-responsive elements in the 5' untranslated regions of mRNAs and the intron-exon boundary regions of pathway genes, translational inhibition and exon choice in enzymes may be enabled, respectively. Pathway product (heme)-mediated negative feedback control can affect the transport of pathway enzymes into the mitochondria as well as the ubiquitin-mediated stability of enzymes. Remarkably, the positions of these controls on pathway activity are not ubiquitous but are biased towards the enzymes in the upstream portion of the pathway. We revealed that multiple-level controls on the activity of the heme biosynthesis pathway depend on the linear depth of the enzymes in the pathway, indicating a new strategy for discovering the molecular constraints that shape the evolution of a metabolic pathway.

  18. Is ultra-violet radiation the main force shaping molecular evolution of varicella-zoster virus?

    PubMed Central

    2011-01-01

    Background Varicella (chickenpox) exhibits a characteristic epidemiological pattern which is associated with climate. In general, primary infections in tropical regions are comparatively less frequent among children than in temperate regions. This peculiarity regarding varicella-zoster virus (VZV) infection among certain age groups in tropical regions results in increased susceptibility during adulthood in these regions. Moreover, this disease shows a cyclic behavior in which the number of cases increases significantly during winter and spring. This observation further supports the participation of environmental factors in global epidemiology of chickenpox. However, the underlying mechanisms responsible for this distinctive disease behavior are not understood completely. In a recent publication, Philip S. Rice has put forward an interesting hypothesis suggesting that ultra-violet (UV) radiation is the major environmental factor driving the molecular evolution of VZV. Discussion While we welcomed the attempt to explain the mechanisms controlling VZV transmission and distribution, we argue that Rice's hypothesis takes lightly the circulation of the so called "temperate VZV genotypes" in tropical regions and, to certain degree, overlooks the predominance of such lineages in certain non-temperate areas. Here, we further discuss and present new information about the overwhelming dominance of temperate VZV genotypes in Mexico regardless of geographical location and climate. Summary UV radiation does not satisfactorily explain the distribution of VZV genotypes in different tropical and temperate regions of Mexico. Additionally, the cyclic behavior of varicella does not shown significant differences between regions with different climates in the country. More studies should be conducted to identify the factors directly involved in viral spreading. A better understanding of the modes of transmissions exploited by VZV and their effect on viral fitness is likely to facilitate

  19. Rates of molecular evolution in nuclear genes of east Mediterranean scorpions.

    PubMed

    Gantenbein, Benjamin; Keightley, Peter D

    2004-11-01

    Scorpions of the genus Mesobuthus represent a useful terrestrial model system for studying molecular evolution. They are distributed on several Aegean islands and the adjacent mainland, they are believed to have low rates of dispersal, and evolutionary divergence dates of taxa are available based on biogeographic events that separated islands from each other and the mainland. Here, we present data on polymorphism and synonymous (Ks) and non-synonymous (Ka) substitution rates for nine nuclear protein-coding genes of two east Mediterranean scorpion species, Mesobuthus gibbosus and M. cyprius (Buthidae). Levels of polymorphism tend to be lower in populations from islands (mean nucleotide diversity pi = 0.0071 +/- 0.0028) than in mainland populations (mean pi = 0.0201 +/- 0.0085). By using linear regression of genetic divergence versus isolation time, we estimate Ks to be 3.17 +/- 1.54 per (site x 10(9) years), and Ka to be 0.39 +/- 0.94 per (site x 10(9) years). These estimates for both Ks and Ka are considerably lower than for many other invertebrates, such as Drosophila, and may be attributed to scorpions' mammal-like generation times (approximately 2 years) and low metabolic rates. Phylogenetic analysis using maximum likelihood revealed a phylogeny that is congruent with that expected based on biogeographic events and in which divergences at synonymous sites are proportional to the dates that the taxa are believed to have split. Tests of equality of branch lengths for the Cyprus and Crete lineages revealed that Ks-estimates are about the same in both lineages, as expected from the biogeographic events that separated the islands, but Ka was increased in the Cyprus lineage compared to the Cretan lineage.

  20. Synthetic molecular evolution of pore-forming peptides by iterative combinatorial library screening.

    PubMed

    Krauson, Aram J; He, Jing; Wimley, Andrew W; Hoffmann, Andrew R; Wimley, William C

    2013-04-19

    We previously reported the de novo design of a combinatorial peptide library that was subjected to high-throughput screening to identify membrane-permeabilizing antimicrobial peptides that have β-sheet-like secondary structure. Those peptides do not form discrete pores in membranes but instead partition into membrane interfaces and cause transient permeabilization by membrane disruption, but only when present at high concentration. In this work, we used a consensus sequence from that initial screen as a template to design an iterative, second generation library. In the 24-26-residue, 16,200-member second generation library we varied six residues. Two diad repeat motifs of alternating polar and nonpolar amino acids were preserved to maintain a propensity for non-helical secondary structure. We used a new high-throughput assay to identify members that self-assemble into equilibrium pores in synthetic lipid bilayers. This screen was done at a very stringent peptide to lipid ratio of 1:1000 where most known membrane-permeabilizing peptides, including the template peptide, are not active. In a screen of 10,000 library members we identified 16 (~0.2%) that are equilibrium pore-formers at this high stringency. These rare and highly active peptides, which share a common sequence motif, are as potent as the most active pore-forming peptides known. Furthermore, they are not α-helical, which makes them unusual, as most of the highly potent pore-forming peptides are amphipathic α-helices. Here we demonstrate that this synthetic molecular evolution-based approach, taken together with the new high-throughput tools we have developed, enables the identification, refinement, and optimization of unique membrane active peptides.

  1. A mathematical model for evolution and SETI.

    PubMed

    Maccone, Claudio

    2011-12-01

    Darwinian evolution theory may be regarded as a part of SETI theory in that the factor f(l) in the Drake equation represents the fraction of planets suitable for life on which life actually arose. In this paper we firstly provide a statistical generalization of the Drake equation where the factor f(l) is shown to follow the lognormal probability distribution. This lognormal distribution is a consequence of the Central Limit Theorem (CLT) of Statistics, stating that the product of a number of independent random variables whose probability densities are unknown and independent of each other approached the lognormal distribution when the number of factors increased to infinity. In addition we show that the exponential growth of the number of species typical of Darwinian Evolution may be regarded as the geometric locus of the peaks of a one-parameter family of lognormal distributions (b-lognormals) constrained between the time axis and the exponential growth curve. Finally, since each b-lognormal distribution in the family may in turn be regarded as the product of a large number (actually "an infinity") of independent lognormal probability distributions, the mathematical way is paved to further cast Darwinian Evolution into a mathematical theory in agreement with both its typical exponential growth in the number of living species and the Statistical Drake Equation.

  2. Molecular Evidence for Convergence and Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems.

    PubMed

    Yoshida, M A; Ogura, A; Ikeo, K; Shigeno, S; Moritaki, T; Winters, G C; Kohn, A B; Moroz, L L

    2015-12-01

    Coleoid cephalopods show remarkable evolutionary convergence with vertebrates in their neural organization, including (1) eyes and visual system with optic lobes, (2) specialized parts of the brain controlling learning and memory, such as vertical lobes, and (3) unique vasculature supporting such complexity of the central nervous system. We performed deep sequencing of eye transcriptomes of pygmy squids (Idiosepius paradoxus) and chambered nautiluses (Nautilus pompilius) to decipher the molecular basis of convergent evolution in cephalopods. RNA-seq was complemented by in situ hybridization to localize the expression of selected genes. We found three types of genomic innovations in the evolution of complex brains: (1) recruitment of novel genes into morphogenetic pathways, (2) recombination of various coding and regulatory regions of different genes, often called "evolutionary tinkering" or "co-option", and (3) duplication and divergence of genes. Massive recruitment of novel genes occurred in the evolution of the "camera" eye from nautilus' "pinhole" eye. We also showed that the type-2 co-option of transcription factors played important roles in the evolution of the lens and visual neurons. In summary, the cephalopod convergent morphological evolution of the camera eyes was driven by a mosaic of all types of gene recruitments. In addition, our analysis revealed unexpected variations of squids' opsins, retinochromes, and arrestins, providing more detailed information, valuable for further research on intra-ocular and extra-ocular photoreception of the cephalopods.

  3. Molecular Evidence for Convergence and Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems

    PubMed Central

    Yoshida, M. A.; Ogura, A.; Ikeo, K.; Shigeno, S.; Moritaki, T.; Winters, G. C.; Kohn, A. B.; Moroz, L. L.

    2015-01-01

    Coleoid cephalopods show remarkable evolutionary convergence with vertebrates in their neural organization, including (1) eyes and visual system with optic lobes, (2) specialized parts of the brain controlling learning and memory, such as vertical lobes, and (3) unique vasculature supporting such complexity of the central nervous system. We performed deep sequencing of eye transcriptomes of pygmy squids (Idiosepius paradoxus) and chambered nautiluses (Nautilus pompilius) to decipher the molecular basis of convergent evolution in cephalopods. RNA-seq was complemented by in situ hybridization to localize the expression of selected genes. We found three types of genomic innovations in the evolution of complex brains: (1) recruitment of novel genes into morphogenetic pathways, (2) recombination of various coding and regulatory regions of different genes, often called “evolutionary tinkering” or “co-option”, and (3) duplication and divergence of genes. Massive recruitment of novel genes occurred in the evolution of the “camera” eye from nautilus’ “pinhole” eye. We also showed that the type-2 co-option of transcription factors played important roles in the evolution of the lens and visual neurons. In summary, the cephalopod convergent morphological evolution of the camera eyes was driven by a mosaic of all types of gene recruitments. In addition, our analysis revealed unexpected variations of squids’ opsins, retinochromes, and arrestins, providing more detailed information, valuable for further research on intra-ocular and extra-ocular photoreception of the cephalopods. PMID:26002349

  4. Molecular evolution and expression divergence of the Populus polygalacturonase supergene family shed light on the evolution of increasingly complex organs in plants.

    PubMed

    Yang, Zhi-Ling; Liu, Hai-Jing; Wang, Xiao-Ru; Zeng, Qing-Yin

    2013-03-01

    Plant polygalacturonases (PGs) are involved in cell separation processes during many stages of plant development. Investigation into the diversification of this large gene family in land plants could shed light on the evolution of structural development. We conducted whole-genome annotation, molecular evolution and gene expression analyses of PG genes in five species of land plant: Populus, Arabidopsis, rice, Selaginella and Physcomitrella. We identified 75, 44, 16 and 11 PG genes from Populus, rice, Selaginella and Physcomitrella genomes, respectively, which were divided into three classes. We inferred rapid expansion of class I PG genes in Populus, Arabidopsis and rice, while copy numbers of classes II and III PG genes were relatively conserved in all five species. Populus, Arabidopsis and rice class I PG genes were under more relaxed selection constraints than class II PG genes, while this selective pressure divergence was not observed in Selaginella and Physcomitrella PG families. In addition, class I PG genes underwent marked expression divergence in Populus, rice and Selaginella. Our results suggest that PG gene expansion occurred after the divergence of the lycophytes and euphyllophytes, and this expansion was likely paralleled by the evolution of increasingly complex organs in land plants.

  5. Molecular dynamics simulations of phosphonic acid-aluminum oxide self-organization and their evolution into ordered monolayers.

    PubMed

    Dietrich, H; Schmaltz, T; Halik, M; Zahn, D

    2017-02-15

    We outline an unprejudiced molecular dynamics simulation approach to study the mechanisms of self-organization encompassing the evolution of surfactant-surface interactions to the growth of self-assembled monolayers (SAMs). Therein, the time-length scale problem is tackled by combining an efficient docking-type procedure for implementing surfactant-by-surfactant association with detailed molecular simulations to explore structural relaxation. For this, nanosecond-scale molecular dynamics simulations unravel ordering processes during the gradual assembly of the monolayer. Along this line, different packing motifs of octadecyl phosphonic acid (ODPA) on the (0001) surface of α-alumina and implications for the final density and ordering of the resulting monolayers are elucidated. Moreover, the role of the solvent is discriminated by comparing SAM formation in 2-propanol, hexane and in a vacuum.

  6. The Effects of Molecular Properties on Ready Biodegradation of Aromatic Compounds in the OECD 301B CO2 Evolution Test.

    PubMed

    He, Mei; Mei, Cheng-Fang; Sun, Guo-Ping; Li, Hai-Bei; Liu, Lei; Xu, Mei-Ying

    2016-07-01

    Ready biodegradation is the primary biodegradability of a compound, which is used for discriminating whether a compound could be rapidly and readily biodegraded in the natural ecosystems in a short period and has been applied extensively in the environmental risk assessment of many chemicals. In this study, the effects of 24 molecular properties (including 2 physicochemical parameters, 10 geometrical parameters, 6 topological parameters, and 6 electronic parameters) on the ready biodegradation of 24 kinds of synthetic aromatic compounds were investigated using the OECD 301B CO2 Evolution test. The relationship between molecular properties and ready biodegradation of these aromatic compounds varied with molecular properties. A significant inverse correlation was found for the topological parameter TD, five geometrical parameters (Rad, CAA, CMA, CSEV, and N c), and the physicochemical parameter K ow, and a positive correlation for two topological parameters TC and TVC, whereas no significant correlation was observed for any of the electronic parameters. Based on the correlations between molecular properties and ready biodegradation of these aromatic compounds, the importance of molecular properties was demonstrated as follows: geometrical properties > topological properties > physicochemical properties > electronic properties. Our study first demonstrated the effects of molecular properties on ready biodegradation by a number of experiment data under the same experimental conditions, which should be taken into account to better guide the ready biodegradation tests and understand the mechanisms of the ready biodegradation of aromatic compounds.

  7. Regional differences in rates of plant speciation and molecular evolution: a comparison between eastern Asia and eastern North America.

    PubMed

    Xiang, Qiu-Yun Jenny; Zhang, Wen Heng; Ricklefs, Robert E; Qian, Hong; Chen, Zhi Duan; Wen, Jun; Hua, Jian L

    2004-10-01

    The eastern Asian (EAS)-eastern North American (ENA) floristic disjunction is one of the best-known biogeographic patterns in the Northern Hemisphere. Recent paleontological and molecular analyses have illuminated the origins of the biogeographic pattern, but subsequent diversification and evolution of the disjunct floras in each of the two continents after isolation remains poorly understood. Although similar in climate and floristic composition, EAS has twice as many species as ENA in genera occurring in both regions. Explaining such differences in species diversity between regions with similar environmental conditions (diversity anomalies) is an important goal of the study of the global patterns of biodiversity. We used a phylogenetic approach to compare rates of net speciation and molecular evolution between the two regions. We first identified EAS-ENA disjunct sister clades from ten genera (Asarum, Buckleya, Carpinus, Carya, Cornus, Hamamelis, Illicium, Panax, Stewartia, and Styrax) that represent diverse angiosperm lineages using phylogenetic analyses of ITS (internal transcribed spacer of nuclear ribosomal DNA) sequence data. Species richness and substitution rate of ITS between sister clades were compared. The results revealed a pattern of greater species diversity in the EAS counterparts. A positive relationship between species diversity and ITS substitution rate was also documented. These results suggest greater net speciation and accelerated molecular evolution in EAS. The data support the idea that a regional difference in net speciation rate related to topographic heterogeneity contributes to the diversity anomaly between EAS and ENA. The close relationship between rates of ITS evolution and species richness further suggests that species production may be directly linked to rate of nucleotide substitution.

  8. The roles of atomic and molecular gas on the redshift evolution of star formation and metallicity in galaxy formation models

    NASA Astrophysics Data System (ADS)

    Fu, Jian; Kauffmann, Guinevere

    2013-03-01

    We study the redshift evolution of neutral and molecular gas in the interstellar medium with the results from semi-analytic models of galaxy formation and evolution, which track the cold gas related physical processes in radially resolved galaxy disks. Two kinds of prescriptions are adopted to describe the conversion between molecular and neutral gas in the ISM: one is related to the gas surface density and gas metallicity based on the model results by Krumholz, Mckee & Tumlinson; the other is related the pressure of ISM. We try four types of star formation laws in the models to study the effect of the molecular gas component and the star formation time scale on the model results, and find that the H2 dependent star formation rate with constant star formation efficiency is the preferred star formation law. We run the models based on both Millennium and Millennium II Simulation haloes, and the model parameters are adjusted to fit the observations at z = 0 from THINGS/HERACLES and ALFALFA/COLD GASS. We give predictions for the redshift evolution of cosmic star formation density, H2 to HI cosmic ratios, gas to star mass ratios and gas metallicity vs stellar mass relation. Based on the model results, we find that: (i) the difference in the H2 to HI ratio at z > 3 between the two H2 fraction prescriptions can help future observations to test which prescription is better; (ii) a constant redshift independent star formation time scale will postpone the star formation processes at high redshift and cause obvious redshift evolution for the relation between gas metallicity and stellar mass in galaxies at z < 3.

  9. Outrunning Nature: Directed Evolution of Superior Biocatalysts

    NASA Astrophysics Data System (ADS)

    Woodyer, Ryan; Chen, Wilfred; Zhao, Huimin

    2004-01-01

    Driven by recent technical advances in genetic engineering and new societal needs, the use of enzymes and microorganisms as catalysts to synthesize chemicals and materials is rapidly expanding. One of the key technical drivers is the development of various directed evolution methods for biocatalyst discovery and optimization. Although it essentially replicates the Darwinian evolutionary processes in a test tube, directed evolution can create biocatalysts with better catalytic performance than Nature's own products within weeks or months rather than eons. In this article, both the technologies and applications of directed evolution in biocatalysis are discussed.

  10. The endemic gastropod fauna of Lake Titicaca: correlation between molecular evolution and hydrographic history

    PubMed Central

    Kroll, Oliver; Hershler, Robert; Albrecht, Christian; Terrazas, Edmundo M; Apaza, Roberto; Fuentealba, Carmen; Wolff, Christian; Wilke, Thomas

    2012-01-01

    Lake Titicaca, situated in the Altiplano high plateau, is the only ancient lake in South America. This 2- to 3-My-old (where My is million years) water body has had a complex history that included at least five major hydrological phases during the Pleistocene. It is generally assumed that these physical events helped shape the evolutionary history of the lake's biota. Herein, we study an endemic species assemblage in Lake Titicaca, composed of members of the microgastropod genus Heleobia, to determine whether the lake has functioned as a reservoir of relic species or the site of local diversification, to evaluate congruence of the regional paleohydrology and the evolutionary history of this assemblage, and to assess whether the geographic distributions of endemic lineages are hierarchical. Our phylogenetic analyses indicate that the Titicaca/Altiplano Heleobia fauna (together with few extralimital taxa) forms a species flock. A molecular clock analysis suggests that the most recent common ancestor (MRCAs) of the Altiplano taxa evolved 0.53 (0.28–0.80) My ago and the MRCAs of the Altiplano taxa and their extralimital sister group 0.92 (0.46–1.52) My ago. The endemic species of Lake Titicaca are younger than the lake itself, implying primarily intralacustrine speciation. Moreover, the timing of evolutionary branching events and the ages of two precursors of Lake Titicaca, lakes Cabana and Ballivián, is congruent. Although Lake Titicaca appears to have been the principal site of speciation for the regional Heleobia fauna, the contemporary spatial patterns of endemism have been masked by immigration and/or emigration events of local riverine taxa, which we attribute to the unstable hydrographic history of the Altiplano. Thus, a hierarchical distribution of endemism is not evident, but instead there is a single genetic break between two regional clades. We also discuss our findings in relation to studies of other regional biota and suggest that salinity tolerance

  11. Molecular evolution and the global reemergence of enterovirus D68 by genome-wide analysis

    PubMed Central

    Gong, Yu-Nong; Yang, Shu-Li; Shih, Shin-Ru; Huang, Yhu-Chering; Chang, Pi-Yueh; Huang, Chung-Guei; Kao, Kuo-Chin; Hu, Han-Chung; Liu, Yi-Chun; Tsao, Kuo-Chien

    2016-01-01

    Abstract Human enterovirus D68 (EV-D68) was first reported in the United States in 1962; thereafter, a few cases were reported from 1970 to 2005, but 2 outbreaks occurred in the Philippines (2008) and the United States (2014). However, little is known regarding the molecular evolution of this globally reemerging virus due to a lack of whole-genome sequences and analyses. Here, all publically available sequences including 147 full and 1248 partial genomes from GenBank were collected and compared at the clade and subclade level; 11 whole genomes isolated in Taiwan (TW) in 2014 were also added to the database. Phylogenetic trees were constructed to identify a new subclade, B3, and represent clade circulations among strains. Nucleotide sequence identities of the VP1 gene were 94% to 95% based on a comparison of subclade B3 to B1 and B2 and 87% to 91% when comparing A, C, and D. The patterns of clade circulation need to be clarified to improve global monitoring of EV-D68, even though this virus showed lower diversity among clades compared with the common enterovirus EV-71. Notably, severe cases isolated from Taiwan and China in 2014 were found in subclade B3. One severe case from Taiwan occurred in a female patient with underlying angioimmunoblastic T-cell lymphoma, from whom a bronchoalveolar lavage specimen was obtained. Although host factors play a key role in disease severity, we cannot exclude the possibility that EV-D68 may trigger clinical symptoms or death. To further investigate the genetic diversity of EV-D68, we reported 34 amino acid (aa) polymorphisms identified by comparing subclade B3 to B1 and B2. Clade D strains had a 1-aa deletion and a 2-aa insertion in the VP1 gene, and 1 of our TW/2014 strains had a shorter deletion in the 5′ untranslated region than a previously reported deletion. In summary, a new subclade, genetic indels, and polymorphisms in global strains were discovered elucidating evolutionary and epidemiological trends of EV-D68, and 11

  12. The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla

    PubMed Central

    Fontanillas, Eric; Welch, John J; Thomas, Jessica A; Bromham, Lindell

    2007-01-01

    Background Molecular clock dates, which place the origin of animal phyla deep in the Precambrian, have been used to reject the hypothesis of a rapid evolutionary radiation of animal phyla supported by the fossil record. One possible explanation of the discrepancy is the potential for fast substitution rates early in the metazoan radiation. However, concerted rate variation, occurring simultaneously in multiple lineages, cannot be detected by "clock tests", and so another way to explore such variation is to look for correlated changes between rates and other biological factors. Here we investigate two possible causes of fast early rates: change in average body size or diversification rate of deep metazoan lineages. Results For nine genes for phylogenetically independent comparisons between 50 metazoan phyla, orders, and classes, we find a significant correlation between average body size and rate of molecular evolution of mitochondrial genes. The data also indicate that diversification rate may have a positive effect on rates of mitochondrial molecular evolution. Conclusion If average body sizes were significantly smaller in the early history of the Metazoa, and if rates of diversification were much higher, then it is possible that mitochondrial genes have undergone a slow-down in evolutionary rate, which could affect date estimates made from these genes. PMID:17592650

  13. Structural Evolution of Polylactide Molecular Bottlebrushes: Kinetics Study by Size Exclusion Chromatography, Small Angle Neutron Scattering and Simulations

    SciTech Connect

    Pickel, Deanna L; Kilbey, II, S Michael; Uhrig, David; Hong, Kunlun; Carrillo, Jan-Michael Y; Sumpter, Bobby G; Ahn, Suk-Kyun; Han, Youngkyu; Kim, Dr. Tae-Hwan; Smith, Gregory Scott; Do, Changwoo

    2014-01-01

    Structural evolution from poly(lactide) (PLA) macromonomer to resultant PLA molecular bottlebrush during ring opening metathesis polymerization (ROMP) was investigated for the first time by combining size exclusion chromatography (SEC), small-angle neutron scattering (SANS) and coarse-grained molecular dynamics (CG-MD) simulations. Multiple aliquots were collected at various reaction times during ROMP, and subsequently analyzed by SEC and SANS. The two complementary techniques enable the understanding of systematic changes in conversion, molecular weight and dispersity as well as structural details of PLA molecular bottlebrushes. CG-MD simulation not only predicts the experimental observations, but it also provides further insight into the analysis and interpretation of data obtained in SEC and SANS experiments. We find that PLA molecular bottlebrushes undergo three conformational transitions with increasing conversion (i.e., increasing the backbone length): (1) from an elongated to a globular shape due to longer side chain at lower conversion, (2) from a globular to an elongated shape at intermediate conversion caused by excluded volume of PLA side chain, and (3) the saturation of contour length at higher conversion due to chain transfer reactions.

  14. Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate.

    PubMed

    Villarreal A, Juan Carlos; Crandall-Stotler, Barbara J; Hart, Michelle L; Long, David G; Forrest, Laura L

    2016-03-01

    We present a complete generic-level phylogeny of the complex thalloid liverworts, a lineage that includes the model system Marchantia polymorpha. The complex thalloids are remarkable for their slow rate of molecular evolution and for being the only extant plant lineage to differentiate gas exchange tissues in the gametophyte generation. We estimated the divergence times and analyzed the evolutionary trends of morphological traits, including air chambers, rhizoids and specialized reproductive structures. A multilocus dataset was analyzed using maximum likelihood and Bayesian approaches. Relative rates were estimated using local clocks. Our phylogeny cements the early branching in complex thalloids. Marchantia is supported in one of the earliest divergent lineages. The rate of evolution in organellar loci is slower than for other liverwort lineages, except for two annual lineages. Most genera diverged in the Cretaceous. Marchantia polymorpha diversified in the Late Miocene, giving a minimum age estimate for the evolution of its sex chromosomes. The complex thalloid ancestor, excluding Blasiales, is reconstructed as a plant with a carpocephalum, with filament-less air chambers opening via compound pores, and without pegged rhizoids. Our comprehensive study of the group provides a temporal framework for the analysis of the evolution of critical traits essential for plants during land colonization.

  15. Punctuated equilibrium and shock waves in molecular models of biological evolution

    NASA Astrophysics Data System (ADS)

    Saakian, David B.; Ghazaryan, Makar H.; Hu, Chin-Kun

    2014-08-01

    We consider the dynamics in infinite population evolution models with a general symmetric fitness landscape. We find shock waves, i.e., discontinuous transitions in the mean fitness, in evolution dynamics even with smooth fitness landscapes, which means that the search for the optimal evolution trajectory is more complicated. These shock waves appear in the case of positive epistasis and can be used to represent punctuated equilibria in biological evolution during long geological time scales. We find exact analytical solutions for discontinuous dynamics at the large-genome-length limit and derive optimal mutation rates for a fixed fitness landscape to send the population from the initial configuration to some final configuration in the fastest way.

  16. Punctuated equilibrium and shock waves in molecular models of biological evolution.

    PubMed

    Saakian, David B; Ghazaryan, Makar H; Hu, Chin-Kun

    2014-08-01

    We consider the dynamics in infinite population evolution models with a general symmetric fitness landscape. We find shock waves, i.e., discontinuous transitions in the mean fitness, in evolution dynamics even with smooth fitness landscapes, which means that the search for the optimal evolution trajectory is more complicated. These shock waves appear in the case of positive epistasis and can be used to represent punctuated equilibria in biological evolution during long geological time scales. We find exact analytical solutions for discontinuous dynamics at the large-genome-length limit and derive optimal mutation rates for a fixed fitness landscape to send the population from the initial configuration to some final configuration in the fastest way.

  17. Nothing in the History of Spanish "Anis" Makes Sense, Except in the Light of Evolution

    ERIC Educational Resources Information Center

    Delgado, Juan Antonio; Palma, Ricardo Luis

    2011-01-01

    We describe, discuss and illustrate a metaphoric parallel between the history of the most famous Spanish liqueur, "Anis del Mono" ("Anis" of the Monkey), and the evolution of living organisms in the light of Darwinian theory and other biological hypotheses published subsequent to Charles Darwin's "Origin of Species." Also, we report the use of a…

  18. Iconoclasts of Evolution: Haeckel, Behe, Wells & the Ontogeny of a Fraud

    ERIC Educational Resources Information Center

    Pickett, Kurt M.; Wenzel, John W.; Rissing, Steven W.

    2005-01-01

    Behe (1998) and Wells (1999) claimed that embryological support for Darwinian evolution is based on the drawings of the 19th century embryologist Ernst Haeckel (1834-1919) whose embryological drawings were regarded inaccurate and fraudulent. The history of modern embryology, the roles played by Von Baer and Haeckel in that history and the manner…

  19. Dynamic mixtures and combinatorial libraries: imines as probes for molecular evolution at the interface between chemistry and biology.

    PubMed

    Herrmann, Andreas

    2009-08-21

    In analogy to evolution in biological processes, "molecular evolution", based on the reversible formation of imines, has successfully been explored for drug discovery, receptor design and as a controlled-release vehicle. Multicomponent systems composed of amines and carbonyl compounds generate structural diversity by reversible reaction of the different components to form equilibrated dynamic mixtures or combinatorial libraries (DCLs). Under thermodynamic control and in the presence of an external factor which influences the equilibrium, these systems evolve by selective adaptation to the changing external conditions. This concept allows the casting of biologically or catalytically active substrates and the molding of receptors from DCLs which are composed of smaller non-active amine and carbonyl moieties. Similarly, if the amine or carbonyl compounds are the biologically active compounds of interest, the corresponding dynamic mixtures are found to be efficient delivery systems, allowing their controlled release over time.

  20. PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.

    PubMed

    Lanfear, Robert; Frandsen, Paul B; Wright, April M; Senfeld, Tereza; Calcott, Brett

    2017-03-01

    PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.

  1. Congruence and indifference between two molecular markers for understanding oral evolution in the Marynidae sensu lato (Ciliophora, Colpodea)

    PubMed Central

    Dunthorn, Micah; Katz, Laura A.; Stoeck, Thorsten; Foissner, Wilhelm

    2012-01-01

    Our understanding of the evolution of oral structures within the Colpodida is confounded by the low number of morphological characters that can be used in constructing hypotheses, and by the low taxon and character sampling in molecular phylogenetic analyses designed to assess these hypotheses. Here we increase character sampling by sequencing the mitochondrial SSU-rDNA locus for three isolates of the Marynidae sensu lato. We show that the inferred mitochondrial and nuclear SSU-rDNA trees, as well as concatenated and constrained analyses, are congruent in not recovering a monophyletic Marynidae. However, due to low node support, the trees are indifferent to whether the morphological characters used to unite the Marynidae are the result of retention of ancestral states or convergence. In light of this indifference and an increased amount of nuclear and mitochondrial SSU-rDNA data, alternative hypotheses of oral evolution in the Colpodida are presented. PMID:22356924

  2. Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice.

    PubMed

    Jung, Chang Gyo; Lim, Sung Don; Hwang, Sun-Goo; Jang, Cheol Seong

    2012-08-15

    RING (Really Interesting New Gene) finger proteins are believed to play a critical role in mediating the transfer of ubiquitin to heterogeneous substrate(s). While the two canonical types, RING-H2 and RING-HC, have been well-characterized, the molecular functions of the modified types, particularly the RING-C2 types, remain elusive. We isolated two rice genes harboring the RING-C2 domain on the distal parts of rice chromosomes 11 and 12, termed OsRINGC2-1 and OsRINGC2-2, respectively. A comparison of sequence divergences between 10 duplicate pairs on the distal parts of rice chromosomes 11 and 12 and randomly selected duplicate pairs suggested that OsRINGC2-1 and OsRINGC2-2 have evolved in concert via gene conversion. An in vitro ubiquitination assay revealed that both proteins possess E3 ligase activity, suggesting that the innate functions of these RING domains have not been affected by their modifications during evolution. Subcellular localizations were strikingly different; OsRINGC2-1 was found only in the cytoplasm with many punctate complexes, whereas OsRINGC2-2 was observed in both the nucleus and cytoplasm. The expression patterns of both genes showed striking differences in response to salt stress, whereas plants heterogeneous for both genes mediated salt tolerance in Arabidopsis, supporting the notion of concerted evolution. These results shed light on the molecular functions of OsRINGC2-1 and OsRINGC2-2 and provide insight into their molecular evolution.

  3. Evolution, reproduction and definition of life.

    PubMed

    Chodasewicz, Krzysztof

    2014-03-01

    Synthetic theory of evolution is a superior integrative biological theory. Therefore, there is nothing surprising about the fact that multiple attempts of defining life are based on this theory. One of them even has a status of NASA's working definition. According to this definition, 'life is a self-sustained chemical system capable of undergoing Darwinian evolution' Luisi (Orig Life Evol Bios 28:613-622, 1998); Cleland, Chyba (Orig Life Evol Bios 32:387-393, 2002). This definition is often considered as one of the more theoretically mature definitions of life. This Darwinian definition has nonetheless provoked a lot of criticism. One of the major arguments claims that this definition is wrong due to 'mule's problem'. Mules (and other infertile hybrids), despite being obviously living organisms, in the light of this definition are considered inanimate objects. It is strongly counterintuitive. The aim of this article was to demonstrate that this reasoning is false. In the later part of the text, I also discuss some other arguments against the Darwinian approach to defining life.

  4. Evolution of catalytic function

    NASA Technical Reports Server (NTRS)

    Joyce, G. F.

    1993-01-01

    An RNA-based evolution system was constructed in the laboratory and used to develop RNA enzymes with novel catalytic function. By controlling the nature of the catalytic task that the molecules must perform in order to survive, it is possible to direct the evolving population toward the expression of some desired catalytic behavior. More recently, this system has been coupled to an in vitro translation procedure, raising the possibility of evolving protein enzymes in the laboratory to produce novel proteins with desired catalytic properties. The aim of this line of research is to reduce darwinian evolution, the fundamental process of biology, to a laboratory procedure that can be made to operate in the service of organic synthesis.

  5. Evolution of OH and CO-Dark Molecular Gas Fraction across a Molecular Cloud Boundary in Taurus

    NASA Astrophysics Data System (ADS)

    Xu, Duo; Li, Di; Yue, Nannan; Goldsmith, Paul F.

    2016-03-01

    We present observations of 12CO J = 1-0, 13CO J = 1-0, H i, and all four ground-state transitions of the hydroxyl (OH) radical toward a sharp boundary region of the Taurus molecular cloud. Based on a photodissociation region (PDR) model that reproduces CO and [C i] emission from the same region, we modeled the three OH transitions, 1612, 1665, and 1667 MHz successfully through escape probability non-local thermal equilibrium radiative transfer model calculations. We could not reproduce the 1720 MHz observations, due to unmodeled pumping mechanisms, of which the most likely candidate is a C-shock. The abundance of OH and CO-dark molecular gas is well-constrained. The OH abundance [OH]/[H2] decreases from 8× {10}-7 to 1× {10}-7 as Av increases from 0.4 to 2.7 mag following an empirical law: which is higher than PDR model predictions for low-extinction regions by a factor of 80. The overabundance of OH at extinctions at or below 1 mag is likely the result of a C-shock. The dark gas fraction (DGF, defined as the fraction of molecular gas without detectable CO emission) decreases from 80% to 20% following a Gaussian profile: This trend of the DGF is consistent with our understanding that the DGF drops at low visual extinction due to photodissociation of H2 and drops at high visual extinction due to CO formation. The DGF peaks in the extinction range where H2 has already formed and achieved self-shielding but 12CO has not. Two narrow velocity components with a peak-to-peak spacing of ˜1 km s-1 were clearly identified. Their relative intensity and variation in space and frequency suggest colliding streams or gas flows at the boundary region.

  6. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process.

    PubMed

    Shapiro, James A

    2016-06-08

    The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.

  7. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process

    PubMed Central

    Shapiro, James A.

    2016-01-01

    The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification. PMID:27338490

  8. Molecular evolution of the clustered MMIC-3 multigene family of Gossypium species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Uniqueness, content, localization, and defense-related features of the root-knot nematode resistance-associated MIC-3 supergene cluster in the genus Gossypium are all of interest for molecular evolutionary studies of duplicate supergenes in allopolyploids. Here we report molecular evolutionary rates...

  9. Molecular Evolution of Clustered MIC-3 (Meloidogyne Induced Cotton -3) Multigene Family of Gossypium Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Uniqueness, content, localization, and defense-related features of the root-knot nematode resistance-associated MIC-3 multigene cluster in the genus Gossypium are all of interest for molecular evolutionary studies of duplicate genes in allopolyploids. Here we report molecular evolutionary rates of t...

  10. Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics

    PubMed Central

    Serohijos, Adrian W.R.; Shakhnovich, Eugene I.

    2014-01-01

    The variation among sequences and structures in nature is both determined by physical laws and by evolutionary history. However, these two factors are traditionally investigated by disciplines with different emphasis and philosophy—molecular biophysics on one hand and evolutionary population genetics in another. Here, we review recent theoretical and computational approaches that address the critical need to integrate these two disciplines. We first articulate the elements of these integrated approaches. Then, we survey their contribution to our mechanistic understanding of molecular evolution, the polymorphisms in coding region, the distribution of fitness effects (DFE) of mutations, the observed folding stability of proteins in nature, and the distribution of protein folds in genomes. PMID:24952216

  11. Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.

    PubMed

    Sánchez, Rubén; Serra, François; Tárraga, Joaquín; Medina, Ignacio; Carbonell, José; Pulido, Luis; de María, Alejandro; Capella-Gutíerrez, Salvador; Huerta-Cepas, Jaime; Gabaldón, Toni; Dopazo, Joaquín; Dopazo, Hernán

    2011-07-01

    Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.

  12. Effects of DNA Methylation and Chromatin State on Rates of Molecular Evolution in Insects

    PubMed Central

    Glastad, Karl M.; Goodisman, Michael A. D.; Yi, Soojin V.; Hunt, Brendan G.

    2015-01-01

    Epigenetic information is widely appreciated for its role in gene regulation in eukaryotic organisms. However, epigenetic information can also influence genome evolution. Here, we investigate the effects of epigenetic information on gene sequence evolution in two disparate insects: the fly Drosophila melanogaster, which lacks substantial DNA methylation, and the ant Camponotus floridanus, which possesses a functional DNA methylation system. We found that DNA methylation was positively correlated with the synonymous substitution rate in C. floridanus, suggesting a key effect of DNA methylation on patterns of gene evolution. However, our data suggest the link between DNA methylation and elevated rates of synonymous substitution was explained, in large part, by the targeting of DNA methylation to genes with signatures of transcriptionally active chromatin, rather than the mutational effect of DNA methylation itself. This phenomenon may be explained by an elevated mutation rate for genes residing in transcriptionally active chromatin, or by increased structural constraints on genes in inactive chromatin. This result highlights the importance of chromatin structure as the primary epigenetic driver of genome evolution in insects. Overall, our study demonstrates how different epigenetic systems contribute to variation in the rates of coding sequence evolution. PMID:26637432

  13. Cryptic Species in Tropic Sands - Interactive 3D Anatomy, Molecular Phylogeny and Evolution of Meiofaunal Pseudunelidae (Gastropoda, Acochlidia)

    PubMed Central

    Neusser, Timea P.; Jörger, Katharina M.; Schrödl, Michael

    2011-01-01

    Background Towards realistic estimations of the diversity of marine animals, tiny meiofaunal species usually are underrepresented. Since the biological species concept is hardly applicable on exotic and elusive animals, it is even more important to apply a morphospecies concept on the best level of information possible, using accurate and efficient methodology such as 3D modelling from histological sections. Molecular approaches such as sequence analyses may reveal further, cryptic species. This is the first case study on meiofaunal gastropods to test diversity estimations from traditional taxonomy against results from modern microanatomical methodology and molecular systematics. Results The examined meiofaunal Pseudunela specimens from several Indo-Pacific islands cannot be distinguished by external features. Their 3D microanatomy shows differences in the organ systems and allows for taxonomic separation in some cases. Additional molecular analyses based on partial mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA markers revealed considerable genetic structure that is largely congruent with anatomical or geographical patterns. Two new species (Pseudunela viatoris and P. marteli spp. nov.) are formally described integrating morphological and genetic analyses. Phylogenetic analysis using partial 16S rRNA, COI and the nuclear 18S rRNA markers shows a clade of Pseudunelidae species as the sister group to limnic Acochlidiidae. Within Pseudunela, two subtypes of complex excretory systems occur. A complex kidney already evolved in the ancestor of Hedylopsacea. Several habitat shifts occurred during hedylopsacean evolution. Conclusions Cryptic species occur in tropical meiofaunal Pseudunela gastropods, and likely in other meiofaunal groups with poor dispersal abilities, boosting current diversity estimations. Only a combined 3D microanatomical and molecular approach revealed actual species diversity within Pseudunela reliably. Such integrative methods are

  14. "Plants that Remind Me of Home": Collecting, Plant Geography, and a Forgotten Expedition in the Darwinian Revolution.

    PubMed

    Hung, Kuang-Chi

    2017-02-01

    In 1859, Harvard botanist Asa Gray (1810-1888) published an essay of what he called "the abstract of Japan botany." In it, he applied Charles Darwin's evolutionary theory to explain why strong similarities could be found between the flora of Japan and that of eastern North America, which provoked his famous debate with Louis Agassiz (1807-1873) and initiated Gray's efforts to secure a place for Darwinian biology in the American sciences. Notably, although the Gray-Agassiz debate has become one of the most thoroughly studied scientific debates, historians of science remain unable to answer one critical question: How was Gray able to acquire specimens from Japan? Making use of previously unknown archival materials, this article scrutinizes the institutional, instrumental, financial, and military settings that enabled Gray's collector, Charles Wright (1811-1885), to travel to Japan, as well as examine Wright's collecting practices in Japan. I argue that it is necessary to examine Gray's diagnosis of Japan's flora and the subsequent debate about it from the viewpoint of field sciences. The field-centered approach not only unveils an array of historical significances that have been overshadowed by the analytical framework of the Darwinian revolution and the reception of Darwinism, but also places a seemingly domestic incident in a transnational context.

  15. Molecular Changes During Acute Myeloid Leukemia (AML) Evolution and Identification of Novel Treatment Strategies Through Molecular Stratification.

    PubMed

    Karjalainen, E; Repasky, G A

    2016-01-01

    Acute myeloid leukemia (AML) is a hematopoietic malignancy characterized by impaired differentiation and uncontrollable proliferation of myeloid progenitor cells. Due to high relapse rates, overall survival for this rapidly progressing disease is poor. The significant challenge in AML treatment is disease heterogeneity stemming from variability in maturation state of leukemic cells of origin, genetic aberrations among patients, and existence of multiple disease clones within a single patient. Disease heterogeneity and the lack of biomarkers for drug sensitivity lie at the root of treatment failure as well as selective efficacy of AML chemotherapies and the emergence of drug resistance. Furthermore, standard-of-care treatment is aggressive, presenting significant tolerability concerns to the commonly advanced-age AML patient. In this review, we examine the concept and potential of molecular stratification, particularly with biologically relevant drug responses, in identifying low-toxicity precision therapeutic combinations and clinically relevant biomarkers for AML patient care as a way to overcome these challenges in AML treatment.

  16. Evolution, molecular epidemiology and perspectives on the research of taeniid parasites with special emphasis on Taenia solium.

    PubMed

    Bobes, Raúl J; Fragoso, Gladis; Fleury, Agnès; García-Varela, Martín; Sciutto, Edda; Larralde, Carlos; Laclette, Juan P

    2014-04-01

    Human cysticercosis is known since old historical times in Greece and China; however, human infections by tapeworms have accompanied human beings for more that hundred thousand years. The disease is tightly bound to poverty and lack of hygiene, and has been eradicated in developed countries, but continues being a public health problem in developing countries of Latin-American, Sub-Saharan Africa and Asia, and is also remerging in a number of non endemic countries. It is considered a neglected disease. Here we revise a number of key scientific contributions on taeniid biology that open new avenues for more effective approaches to the control of cysticercosis. The evolution of flatworms and class Cestoda is analyzed, with special emphasis on the emergence of taeniid parasites and the colonization of the human species by tapeworms. The complex molecular host-parasite interplay in this relationship as result of co-evolution between two distantly related organisms. The relevant host and parasite's factors, in the prospect of identifying species-specific molecular markers useful in epidemiological studies carried out in endemic countries. The new possibilities arising with the characterization of the genomes for several species of tapeworms, including a deeper understanding of these organisms, as well as improved tools for diagnosis, vaccination and drug treatment. The need to revise the current control and management strategies for this tropical neglected disease.

  17. Molecular phylogeny and evolution of the proteins encoded by coleoid (cuttlefish, octopus, and squid) posterior venom glands.

    PubMed

    Ruder, Tim; Sunagar, Kartik; Undheim, Eivind A B; Ali, Syed A; Wai, Tak-Cheung; Low, Dolyce H W; Jackson, Timothy N W; King, Glenn F; Antunes, Agostinho; Fry, Bryan G

    2013-04-01

    In this study, we report for the first time a detailed evaluation of the phylogenetic history and molecular evolution of the major coleoid toxins: CAP, carboxypeptidase, chitinase, metalloprotease GON-domain, hyaluronidase, pacifastin, PLA2, SE-cephalotoxin and serine proteases, with the carboxypeptidase and GON-domain documented for the first time in the coleoid venom arsenal. We show that although a majority of sites in these coleoid venom-encoding genes have evolved under the regime of negative selection, a very small proportion of sites are influenced by the transient selection pressures. Moreover, nearly 70 % of these episodically adapted sites are confined to the molecular surface, highlighting the importance of variation of the toxin surface chemistry. Coleoid venoms were revealed to be as complex as other venoms that have traditionally been the recipient of the bulk of research efforts. The presence of multiple peptide/protein types in coleoids similar to those present in other animal venoms identifies a convergent strategy, revealing new information as to what characteristics make a peptide/protein type amenable for recruitment into chemical arsenals. Coleoid venoms have significant potential not only for understanding fundamental aspects of venom evolution but also as an untapped source of novel toxins for use in drug design and discovery.

  18. Molecular evolution of the VP1, VP2, and VP3 genes in human rhinovirus species C.

    PubMed

    Kuroda, Makoto; Niwa, Shoichi; Sekizuka, Tsuyoshi; Tsukagoshi, Hiroyuki; Yokoyama, Masaru; Ryo, Akihide; Sato, Hironori; Kiyota, Naoko; Noda, Masahiro; Kozawa, Kunihisa; Shirabe, Komei; Kusaka, Takashi; Shimojo, Naoki; Hasegawa, Shunji; Sugai, Kazuko; Obuchi, Masatsugu; Tashiro, Masato; Oishi, Kazunori; Ishii, Haruyuki; Kimura, Hirokazu

    2015-02-02

    Human rhinovirus species C (HRV-C) was recently discovered, and this virus has been associated with various acute respiratory illnesses (ARI). However, the molecular evolution of the major antigens of this virus, including VP1, VP2, and VP3, is unknown. Thus, we performed complete VP1, VP2, and VP3 gene analyses of 139 clinical HRV-C strains using RT-PCR with newly designed primer sets and next-generation sequencing. We assessed the time-scale evolution and evolutionary rate of these genes using the Bayesian Markov chain Monte Carlo method. In addition, we calculated the pairwise distance and confirmed the positive/negative selection sites in these genes. The phylogenetic trees showed that the HRV-C strains analyzed using these genes could be dated back approximately 400 to 900 years, and these strains exhibited high evolutionary rates (1.35 to 3.74 × 10(-3) substitutions/site/year). Many genotypes (>40) were confirmed in the phylogenetic trees. Furthermore, no positively selected site was found in the VP1, VP2, and VP3 protein. Molecular modeling analysis combined with variation analysis suggested that the exterior surfaces of the VP1, VP2 and VP3 proteins are rich in loops and are highly variable. These results suggested that HRV-C may have an old history and unique antigenicity as an agent of various ARI.

  19. Molecular variation and evolution of the tyrosine kinase domains of insulin receptor IRa and IRb genes in Cyprinidae.

    PubMed

    Kong, XiangHui; Wang, XuZhen; He, ShunPing

    2011-07-01

    The insulin receptor (IR) gene plays an important role in regulating cell growth, differentiation and development. In the present study, DNA sequences of insulin receptor genes, IRa and IRb, were amplified and sequenced from 37 representative species of the Cyprinidae and from five outgroup species from non-cyprinid Cypriniformes. Based on coding sequences (CDS) of tyrosine kinase regions of IRa and IRb, molecular evolution and phylogenetic relationships were analyzed to better understand the characteristics of IR gene divergence in the family Cyprinidae. IRa and IRb were clustered into one lineage in the gene tree of the IR gene family, reconstructed using the unweighted pair group method with arithmetic mean (UPGMA). IRa and IRb have evolved into distinct genes after IR gene duplication in Cyprinidae. For each gene, molecular evolution analyses showed that there was no significant difference among different groups in the reconstructed maximum parsimony (MP) tree of Cyprinidae; IRa and IRb have been subjected to similar evolutionary pressure among different lineages. Although the amino acid sequences of IRa and IRb tyrosine kinase regions were highly conserved, our analyses showed that there were clear sequence variations between the tyrosine kinase regions of IRa and IRb proteins. This indicates that IRa and IRb proteins might play different roles in the insulin signaling pathway.

  20. Molecular evolution and gene expression differences within the HD-Zip transcription factor family of Zea mays L.

    PubMed

    Mao, Hude; Yu, Lijuan; Li, Zhanjie; Liu, Hui; Han, Ran

    2016-04-01

    Homeodomain-leucine zipper (HD-Zip) transcription factors regulate developmental processes and stress responses in plants, and they vary widely in gene number and family structure. In this study, 55 predicted maize HD-Zip genes were systematically analyzed with respect to their phylogenetic relationships, molecular evolution, and gene expression in order to understand the functional diversification within the family. Phylogenetic analysis of HD-Zip proteins from Zea mays, Oryza sativa, Arabidopsis thaliana, Vitis vinifera, and Physcomitrella patens showed that they group into four classes. We inferred that the copy numbers of classes I and III genes were relatively conserved in all five species. The 55 maize HD-Zip genes are distributed randomly on the ten chromosomes, with 15 segmental duplication and 4 tandem duplication events, suggesting that segmental duplications were the major contributors in the expansion of the maize HD-Zip gene family. Expression analysis of the 55 maize HD-Zip genes in different tissues and drought conditions revealed differences in the expression levels and patterns between the four classes. Promoter analysis revealed that a number of stress response-, hormone response-, light response-, and development-related cis-acting elements were present in their promoters. Our results provide novel insights into the molecular evolution and gene expression within the HD-Zip gene family in maize, and provide a solid foundation for future functional study of the HD-Zip genes in maize.

  1. In Situ Mass Spectrometric Determination of Molecular Structural Evolution at the Solid Electrolyte Interphase in Lithium-Ion Batteries.

    PubMed

    Zhu, Zihua; Zhou, Yufan; Yan, Pengfei; Vemuri, Rama Sesha; Xu, Wu; Zhao, Rui; Wang, Xuelin; Thevuthasan, Suntharampillai; Baer, Donald R; Wang, Chong-Min

    2015-09-09

    Dynamic structural and chemical evolution at solid-liquid electrolyte interface is always a mystery for a rechargeable battery due to the challenge to directly probe a solid-liquid interface under reaction conditions. We describe the creation and usage of in situ liquid secondary ion mass spectroscopy (SIMS) for the first time to directly observe the molecular structural evolution at the solid-liquid electrolyte interface for a lithium (Li)-ion battery under dynamic operating conditions. We have discovered that the deposition of Li metal on copper electrode leads to the condensation of solvent molecules around the electrode. Chemically, this layer of solvent condensate tends to be depleted of the salt anions and with reduced concentration of Li(+) ions, essentially leading to the formation of a lean electrolyte layer adjacent to the electrode and therefore contributing to the overpotential of the cell. This observation provides unprecedented molecular level dynamic information on the initial formation of the solid electrolyte interphase (SEI) layer. The present work also ultimately opens new avenues for implanting the in situ liquid SIMS concept to probe the chemical reaction process that intimately involves solid-liquid interface, such as electrocatalysis, electrodeposition, biofuel conversion, biofilm, and biomineralization.

  2. The geochemical evolution of low-molecular-weight organic acids derived from the degradation of petroleum contaminants in groundwater

    USGS Publications Warehouse

    Cozzarelli, I.M.; Baedecker, M.J.; Eganhouse, R.P.; Goerlitz, D.F.

    1994-01-01

    The geochemical evolution of low-molecular-weight organic acids in groundwater downgradient from a crude-oil spill near Bemidji, Minnesota, was studied over a five year period (1986-1990). The organic acids are metabolic intermediates of the degradation of components of the crude oil and are structurally related to hydrocarbon precursors. The concentrations of organic acids, particularly aliphatic acids, increase as the microbial alteration of hydrocarbons progresses. The organic-acid pool changes in composition and concentration over time and in space as the degradation processes shift from Fe(III) reduction to methanogenesis. Over time, the aquifer system evolves into one in which the groundwater contains more oxidized products of hydrocarbon degradation and the reduced forms of iron, manganese, and nitrogen. Laboratory microcosm experiments with aquifer material support the hypothesis that organic acids observed in the groundwater originate from the microbial degradation of aromatic hydrocarbons under anoxic conditions. The geochemistry of two other shallow aquifers in coastal plain sediments, one contaminated with creosote waste and the other with gasoline, were compared to the Bemidji site. The geochemical evolution of the low-molecular-weight organic acid pool in these systems is controlled, in part, by the presence of electron acceptors available for microbially mediated electron-transfer reactions. The depletion of electron acceptors in aquifers leads to the accumulation of aliphatic organic acids in anoxic groundwater. ?? 1994.

  3. Tracking adaptive evolution in the structure, function and molecular phylogeny of haemoglobin in non-Antarctic notothenioid fish species

    NASA Astrophysics Data System (ADS)

    Verde, Cinzia; Parisi, Elio; di Prisco, Guido

    2006-04-01

    With the notable exception of Antarctic icefishes, haemoglobin (Hb) is present in all vertebrates. In polar fish, Hb evolution has included adaptations with implications at the biochemical, physiological and molecular levels. Cold adaptation has been shown to be also linked to small changes in primary structure and post-translational modifications in proteins, including hydrophobic remodelling and increased flexibility. A wealth of knowledge is available on the oxygen-transport system of fish inhabiting Antarctic waters, but very little is known on the structure and function of Hb of non-Antarctic notothenioid fishes. The comparison of the biochemical and physiological adaptations between cold-adapted and non-cold-adapted species is a powerful tool to understand whether (and to what extent) extreme environments require specific adaptations or simply select for phenotypically different life styles. This study focuses on structure, function and molecular phylogeny of Hb in Antarctic and non-Antarctic notothenioid fishes. The rationale is to use the primary structure of Hb as tool of choice to gain insight into the pathways of the evolution history of α and β globins of notothenioids and also as a basis for reconstructing the phylogenetic relationships among Antarctic and non-Antarctic species.

  4. Molecular phylogeny and character evolution of the chthamaloid barnacles (Cirripedia: Thoracica).

    PubMed

    Pérez-Losada, Marcos; Høeg, Jens T; Crandall, Keith A; Achituv, Yair

    2012-10-01

    The Chthamaloidea (Balanomorpha) present the most plesiomorphic characters in shell plates and cirri, mouthparts, and oral cone within the acorn barnacles (Thoracica: Sessilia). Due to their importance in understanding both the origin and diversification of the Balanomorpha, the evolution of the Chthamaloidea has been debated since Darwin's seminal monographs. Theories of morphological and ontogenetic evolution suggest that the group could have evolved multiple times from pedunculated relatives and that shell plate number diminished gradually (8→6→4) from an ancestral state with eight wall plates surrounded by whorls of small imbricating plates; but this hypothesis has never been subjected to a rigorous phylogenetic test. Here we used multilocus sequence data and extensive taxon sampling to build a comprehensive phylogeny of the Chthamaloidea as a basis for understanding their morphological evolution. Our maximum likelihood and Bayesian analyses separate the Catophragmidae (eight shell plates and imbricating plates) from the Chthamalidae (8-4 shell plates and no imbricating plates), but do no support a gradual reduction in shell plates (8→6→4). This suggests that evolution at the base of the Balanomorpha involved a considerable amount of homoplasy.

  5. Evolution of the fruit endocarp: molecular mechanisms underlying adaptations in seed protection and dispersal strategies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant evolution is largely driven by adaptations in seed protection and dispersal strategies that allow diversification into new niches. This is evident by the tremendous variation in flowering and fruiting structures present both across and within different plant lineages. Within a single plant f...

  6. "DNA Re-EvolutioN": A Game for Learning Molecular Genetics and Evolution

    ERIC Educational Resources Information Center

    Miralles, Laura; Moran, Paloma; Dopico, Eduardo; Garcia-Vazquez, Eva

    2013-01-01

    Evolution is a main concept in biology, but not many students understand how it works. In this article we introduce the game "DNA Re-EvolutioN" as an active learning tool that uses genetic concepts (DNA structure, transcription and translation, mutations, natural selection, etc.) as playing rules. Students will learn about molecular…

  7. Molecular evolution of contracting clouds - Basic methods and initial results. [interstellar processes

    NASA Technical Reports Server (NTRS)

    Gerola, H.; Glassgold, A. E.

    1978-01-01

    The relationship between the dynamics of the interstellar gas and the thermal and chemical effects associated with interstellar molecules and dust is investigated. The evolution of a rather massive isolated initially diffuse cloud under self-gravity is studied, using the equations of hydrodynamics; only radial motions are considered, and the heat, chemical, and radiative-transfer equations are solved simultaneously with the hydrodynamic equations. The relevant chemistry is described along with the thermal model, the radiative-transfer process, and the numerical methods employed. Results for a contracting cloud are discussed in terms of the problem of initial conditions, the dynamical evolution of the cloud, its chemical and thermal evolution, time scales, and column densities. It is shown that the chemical evolution of a massive contracting diffuse cloud is sensitive to such physical properties as temperature and ion abundances, that warm and cool versions of a typical cloud evolve differently, and that the physical origin of this effect is the level of heating due to H2 formation on interstellar dust grains.

  8. Molecular tools and bumble bees: revealing hidden details of ecology and evolution in a model system

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bumble bees are a longstanding model system for studies on behavior, ecology, and evolution, due to their well-studied social lifestyle, invaluable roles as both wild and managed pollinators, and their ubiquity and diversity across temperate ecosystems. Yet despite their importance, many aspects of ...

  9. Scombroid fishes provide novel insights into the trait/rate associations of molecular evolution.

    PubMed

    Qiu, Fan; Kitchen, Andrew; Burleigh, J Gordon; Miyamoto, Michael M

    2014-06-01

    The study of which life history traits primarily affect molecular evolutionary rates is often confounded by the covariance of these traits. Scombroid fishes (billfishes, tunas, barracudas, and their relatives) are unusual in that their mass-specific metabolic rate is positively associated with body size. This study exploits this atypical pattern of trait variation, which allows for direct tests of whether mass-specific metabolic rate or body size is the more important factor of molecular evolutionary rates. We inferred a phylogeny for scombroids from a supermatrix of molecular and morphological characters and used new phylogenetic comparative approaches to assess the associations of body size and mass-specific metabolic rate with substitution rate. As predicted by the body size hypothesis, there is a negative correlation between body size and substitution rate. However, unexpectedly, we also find a negative association between mass-specific metabolic and substitution rates. These relationships are supported by analyses of the total molecular data, separate mitochondrial and nuclear genes, and individual loci, and they are robust to phylogenetic uncertainty. The molecular evolutionary rates of scombroids are primarily tied to body size. This study demonstrates that groups with novel patterns of trait variation can be particularly informative for identifying which life history traits are the primary factors of molecular evolutionary rates.

  10. The evolution of viviparity: molecular and genomic data from squamate reptiles advance understanding of live birth in amniotes.

    PubMed

    Van Dyke, James U; Brandley, Matthew C; Thompson, Michael B

    2014-01-01

    Squamate reptiles (lizards and snakes) are an ideal model system for testing hypotheses regarding the evolution of viviparity (live birth) in amniote vertebrates. Viviparity has evolved over 100 times in squamates, resulting in major changes in reproductive physiology. At a minimum, all viviparous squamates exhibit placentae formed by the appositions of maternal and embryonic tissues, which are homologous in origin with the tissues that form the placenta in therian mammals. These placentae facilitate adhesion of the conceptus to the uterus as well as exchange of oxygen, carbon dioxide, water, sodium, and calcium. However, most viviparous squamates continue to rely on yolk for nearly all of their organic nutrition. In contrast, some species, which rely on the placenta for at least a portion of organic nutrition, exhibit complex placental specializations associated with the transport of amino acids and fatty acids. Some viviparous squamates also exhibit reduced immunocompetence during pregnancy, which could be the result of immunosuppression to protect developing embryos. Recent molecular studies using both candidate-gene and next-generation sequencing approaches have suggested that at least some of the genes and gene families underlying these phenomena play similar roles in the uterus and placenta of viviparous mammals and squamates. Therefore, studies of the evolution of viviparity in squamates should inform hypotheses of the evolution of viviparity in all amniotes, including mammals.

  11. Molecular evolution analysis of WUSCHEL-related homeobox transcription factor family reveals functional divergence among clades in the homeobox region.

    PubMed

    Segatto, Ana Lúcia A; Thompson, Claudia E; Freitas, Loreta B

    2016-07-01

    Gene families have been shown to play important roles in plant evolution and are associated with diversification and speciation. Genes of WUSCHEL-related homeobox family of transcription factors have important functions in plant development and are correlated with the appearance of evolutionary novelties. There are several published studies related to this family, but little is known about the relationships among the main clades in the phylogeny and the molecular evolution of the family. In this study, we obtained a well-resolved Bayesian phylogenetic tree establishing the relationships among the main clades and determining the position of Selaginella moellendorffii WOX genes. Moreover, a correlation was identified between the number of genes in the genomes and the events of whole-genome duplications. The intron-exon structure is more consistent across the modern clade, which appeared more recently in the WOX evolutionary history, and coincides with the development of higher complexity in plant species. No positive selection was detected among sites through the branches in the tree. However, with regard to the main clades, functional divergence among certain amino acids in the homeodomain region was found. Relaxed purifying selection could be the main driving force in the evolution of these genes and in agreement with some genes have been demonstrated to be functionally redundant.

  12. Molecular evolution of a steroid hydroxylating cytochrome P450 using a versatile steroid detection system for screening.

    PubMed

    Virus, Cornelia; Bernhardt, Rita

    2008-12-01

    Molecular evolution is a powerful tool for improving or changing activities of enzymes for their use in biotechnological processes. Cytochromes P450 are highly interesting enzymes for biotechnological purposes because they are able to hydroxylate a broad variety of substrates with high regio- and stereoselectivity. One promising steroid hydroxylating cytochrome P450 for biotechnological applications is CYP106A2 from Bacillus megaterium ATCC 13368. It is one of a few known bacterial cytochromes P450 able to transform steroids such as progesterone and 11-deoxycortisol. CYP106A2 can be easily expressed in Escherichia coli with a high yield and can be reconstituted using the adrenal redox proteins, adrenodoxin and adrenodoxin reductase. We developed a simple screening assay for this system and performed random mutagenesis of CYP106A2, yielding variants with improved 11-deoxycortisol and progesterone hydroxylation activity. After two generations of directed evolution, we were able to improve the k (cat)/K (m) of the 11-deoxycortisol hydroxylation by a factor of more than four. At the same time progesterone conversion was improved about 1.4-fold. Mapping the mutations identified in catalytically improved CYP106A2 variants into the structure of a CYP106A2 model suggests that these mutations influence the mobility of the F/G loop, and the interaction with the redox partner adrenodoxin. The results show the evolution of a soluble steroid hydroxylase as a potential new catalyst for the production of steroidogenic compounds.

  13. Molecular analysis of some camel cytochrome P450 enzymes reveals lower evolution and drug-binding properties.

    PubMed

    Altaher, Yousef; Kandeel, Mahmoud

    2016-01-01

    Camels bear unique genotypes and phenotypes for adaptation of their harsh environment. They have unique visual systems, sniffing, water metabolism, and heat-control mechanisms that are different from other creatures. The recent announcement for the complete sequence of camel genome will allow for the discovery of many secrets of camel life. In this context, the genetic bases of camel drug-metabolizing enzymes are still unknown. Furthermore, the genomic content of camel that rendered it highly susceptible to some drugs (as monensin and salinomycin) and became easily intoxicated needs to be investigated. The objectives of this work are the annotation of camel genome and retrieval of camel for cytochrome P450 (CYP) 1A1, 2C, and 3A enzymes. This is followed by comprehensive phylogenetic, evolution, molecular modeling, and docking studies. In comparison with the human enzymes, camel CYPs showed lower evolution rate, especially CYP1A1. Furthermore, the binding of monensin, salinomycin, alfa-naphthoflavone, felodepine, and ritonavir was weaker in camel enzymes. Interestingly, rerank score indicated instable binding of monensin and salinomycin with camel CYP1A1 as well as salinomycin with camel CYP2C. The results of this work suggest that camels are more susceptible to toxicity with compounds undergoing metabolic oxidation. This conclusion was based on lower evolution rate and lower binding potency of camels compared with the human enzymes.

  14. The evolution of antibiotic resistance: insight into the roles of molecular mechanisms of resistance and treatment context.

    PubMed

    Maclean, R Craig; Hall, Alex R; Perron, Gabriel G; Buckling, Angus

    2010-08-01

    The widespread use of antibiotics has markedly improved public health over the last 60 years. However, the efficacy of antibiotic treatment is rapidly decreasing as a result of the continual spread of antibiotic resistance in pathogen populations. The evolution of antibiotic resistance is an amazingly simple example of adaptation by natural selection, and there is growing interest among evolutionary biologists in using evolutionary principles to help understand and combat the spread of resistance in pathogen populations. In this article, we review recent progress in our understanding of the underlying evolutionary forces that drive antibiotic resistance. Recent work has shown that both the mechanisms of antibiotic action and resistance, as well as the treatment context in which resistance evolves, influence the evolution of resistance in predictable ways. We argue that developing predictive models of resistance evolution that can be used to prevent the spread of resistance in pathogen populations requires integrating the treatment context and the molecular biology of resistance into the same evolutionary framework.

  15. Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular-based research in ecology and evolution

    PubMed Central

    Schlick-Steiner, Birgit C; Arthofer, Wolfgang; Moder, Karl; Steiner, Florian M

    2015-01-01

    Today, the comparative analysis of DNA molecules mainly uses information inferred from nucleotide substitutions. Insertion/deletion (INDEL) mutations, in contrast, are largely considered uninformative and discarded, due to our lacking knowledge on their evolution. However, including rather than discarding INDELs would be relevant to any research area in ecology and evolution that uses molecular data. As a practical approach to better understanding INDEL evolution in general, we propose the study of recent INDEL (reINDEL) mutations – mutations where both ancestral and derived state are seen in the sample. The precondition for reINDEL identification is knowledge about the pedigree of the individuals sampled. Sound reINDEL knowledge will allow the improved modeling needed for including INDELs in the downstream analysis of molecular data. Both microsatellites, currently still the predominant marker system in the analysis of populations, and sequences generated by next-generation sequencing, a promising and rapidly developing range of technologies, offer the opportunity for reINDEL identification. However, a 2013 sample of animal microsatellite studies contained unexpectedly few reINDELs identified. As most likely explanation, we hypothesize that reINDELs are underreported rather than absent and that this underreporting stems from common reINDEL unawareness. If our hypothesis applies, increased reINDEL awareness should allow gathering data rapidly. We recommend the routine reporting of either the absence or presence of reINDELs together with standardized key information on the nature of mutations when they are detected and the use of the keyword “reINDEL” to increase visibility in both instances of successful and unsuccessful search. PMID:25628861

  16. Stress, adaptation, and speciation in the evolution of the blind mole rat, Spalax, in Israel.

    PubMed

    Nevo, Eviatar

    2013-02-01

    Environmental stress played a major role in the evolution of the blind mole rat superspecies Spalax ehrenbergi, affecting its adaptive evolution and ecological speciation underground. Spalax is safeguarded all of its life underground from aboveground climatic fluctuations and predators. However, it encounters multiple stresses in its underground burrows including darkness, energetics, hypoxia, hypercapnia, food scarcity, and pathogenicity. Consequently, it evolved adaptive genomic, proteomic, and phenomic complexes to cope with those stresses. Here I describe some of these adaptive complexes, and their theoretical and applied perspectives. Spalax mosaic molecular and organismal evolution involves reductions or regressions coupled with expansions or progressions caused by evolutionary tinkering and natural genetic engineering. Speciation of Spalax in Israel occurred in the Pleistocene, during the last 2.00-2.35 Mya, generating four species associated intimately with four climatic regimes with increasing aridity stress southwards and eastwards representing an ecological speciational adaptive trend: (Spalax golani, 2n=54→S. galili, 2n=52→S. carmeli, 2n=58→S. judaei, 2n=60). Darwinian ecological speciation occurred gradually with relatively little genetic change by Robertsonian chromosomal and genic mutations. Spalax genome sequencing has just been completed. It involves multiple adaptive complexes to life underground and is an evolutionary model to a few hundred underground mammals. It involves great promise in the future for medicine, space flight, and deep-sea diving.

  17. Corrections to chance fluctuations: quantum mind in biological evolution?

    PubMed

    Damiani, Giuseppe

    2009-01-01

    According to neo-Darwinian theory, biological evolution is produced by natural selection of random hereditary variations. This assumption stems from the idea of a mechanical and deterministic world based on the laws of classic physics. However, the increased knowledge of relationships between metabolism, epigenetic systems, and editing of nucleic acids suggests the existence of self-organized processes of adaptive evolution in response to environmental stresses. Living organisms are open thermodynamic systems which use entropic decay of external source of electromagnetic energy to increase their internal dynamic order and to generate new genetic and epigenetic information with a high degree of coherency and teleonomic creativity. Sensing, information processing, and decision making of biological systems might be mainly quantum phenomena. Amplification of microscopic quantum events using the long-range correlation of fractal structures, at the borderline between deterministic order and unpredictable chaos, may be used to direct a reproducible transition of the biological systems towards a defined macroscopic state. The discoveries of many natural genetic engineering systems, the ability to choose the most effective solutions, and the emergence of complex forms of consciousness at different levels confirm the importance of mind-action directed processes in biological evolution, as suggested by Alfred Russel Wallace. Although the main Darwinian principles will remain a crucial component of our understanding of evolution, a radical rethinking of the conceptual structure of the neo-Darwinian theory is needed.

  18. Molecular and phylogenetic analyses reveal mammalian-like clockwork in the honey bee (Apis mellifera) and shed new light on the molecular evolution of the circadian clock.

    PubMed

    Rubin, Elad B; Shemesh, Yair; Cohen, Mira; Elgavish, Sharona; Robertson, Hugh M; Bloch, Guy

    2006-11-01

    The circadian clock of the honey bee is implicated in ecologically relevant complex behaviors. These include time sensing, time-compensated sun-compass navigation, and social behaviors such as coordination of activity, dance language communication, and division of labor. The molecular underpinnings of the bee circadian clock are largely unknown. We show that clock gene structure and expression pattern in the honey bee are more similar to the mouse than to Drosophila. The honey bee genome does not encode an ortholog of Drosophila Timeless (Tim1), has only the mammalian type Cryptochrome (Cry-m), and has a single ortholog for each of the other canonical "clock genes." In foragers that typically have strong circadian rhythms, brain mRNA levels of amCry, but not amTim as in Drosophila, consistently oscillate with strong amplitude and a phase similar to amPeriod (amPer) under both light-dark and cons