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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. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. Molecular evolution and positive Darwinian selection of the chloroplast maturase matK.

    PubMed

    Hao, Da Cheng; Chen, Shi Lin; Xiao, Pei Gen

    2010-03-01

    It is not clear whether matK evolves under Darwinian selection. In this study, 70 plant groups, representing 2,279 species at various evolutionary levels, were used to illustrate the molecular adaptation and evolutionary dynamics of gene divergence in matKs. Selective influences were investigated using standard dN/dS ratio methods. Analyses revealed the presence of positive selection in matKs of 32 plant groups. More positively selected sites were detected in the N-terminal region than in the RT domain and domain X of matK. Moreover, removing amino acid sites that are under positive selection has a significant effect on the bootstrap values of phylogenetic reconstruction. Our results suggest that the rapidly evolving matK evolves under positive selection in some lineages of land plants. Several regions of matK have experienced molecular adaptation, which fine-tunes maturase performance.

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

    PubMed Central

    Skinner, Michael K.

    2015-01-01

    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. PMID:25917417

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Ago-antagonist theory in Darwinian evolution.

    PubMed

    Bazzani, Armando; Freguglia, Paolo

    2013-01-01

    In this paper we discuss a proposal on the essential structural aspects of Darwinian Evolution Theory. Using this point of view we apply a mathematical ago-antagonist theory inspired by Y. Cherruault's (1998) ideas, which we have extended. In the ago-antagonist model, the phenotype characters measure the individual propensity to perform an innovative x(t) (agonist) or conservative y(t) (antagonist) action with respect to mutation and to speciation process. We have mathematically introduced the conflict concept and we present a model that takes into account the environmental effects by means of a stochastic multiplicative process. We shortly discuss the properties of the related stochastic differential equations.

  13. 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.

  14. 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

  15. 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.

  16. Diversification and enrichment of clinical biomaterials inspired by Darwinian evolution.

    PubMed

    Green, D W; Watson, G S; Watson, J A; Lee, D-J; Lee, J-M; Jung, H-S

    2016-09-15

    Regenerative medicine and biomaterials design are driven by biomimicry. There is the essential requirement to emulate human cell, tissue, organ and physiological complexity to ensure long-lasting clinical success. Biomimicry projects for biomaterials innovation can be re-invigorated with evolutionary insights and perspectives, since Darwinian evolution is the original dynamic process for biological organisation and complexity. Many existing human inspired regenerative biomaterials (defined as a nature generated, nature derived and nature mimicking structure, produced within a biological system, which can deputise for, or replace human tissues for which it closely matches) are without important elements of biological complexity such as, hierarchy and autonomous actions. It is possible to engineer these essential elements into clinical biomaterials via bioinspired implementation of concepts, processes and mechanisms played out during Darwinian evolution; mechanisms such as, directed, computational, accelerated evolutions and artificial selection contrived in the laboratory. These dynamos for innovation can be used during biomaterials fabrication, but also to choose optimal designs in the regeneration process. Further evolutionary information can help at the design stage; gleaned from the historical evolution of material adaptations compared across phylogenies to changes in their environment and habitats. Taken together, harnessing evolutionary mechanisms and evolutionary pathways, leading to ideal adaptations, will eventually provide a new class of Darwinian and evolutionary biomaterials. This will provide bioengineers with a more diversified and more efficient innovation tool for biomaterial design, synthesis and function than currently achieved with synthetic materials chemistry programmes and rational based materials design approach, which require reasoned logic. It will also inject further creativity, diversity and richness into the biomedical technologies that

  17. 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

  18. 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.

  19. 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

  20. "Synergistic selection": a Darwinian frame for the evolution of complexity.

    PubMed

    Corning, Peter A; Szathmáry, Eörs

    2015-04-21

    Non-Darwinian theories about the emergence and evolution of complexity date back at least to Lamarck, and include those of Herbert Spencer and the "emergent evolution" theorists of the later nineteenth and early twentieth centuries. In recent decades, this approach has mostly been espoused by various practitioners in biophysics and complexity theory. However, there is a Darwinian alternative - in essence, an economic theory of complexity - proposing that synergistic effects of various kinds have played an important causal role in the evolution of complexity, especially in the "major transitions". This theory is called the "synergism hypothesis". We posit that otherwise unattainable functional advantages arising from various cooperative phenomena have been favored over time in a dynamic that the late John Maynard Smith characterized and modeled as "synergistic selection". The term highlights the fact that synergistic "wholes" may become interdependent "units" of selection. We provide some historical perspective on this issue, as well as a brief explication of the underlying theory and the concept of synergistic selection, and we describe two relevant models. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Tumor progression: chance and necessity in Darwinian and Lamarckian somatic (mutationless) evolution.

    PubMed

    Huang, Sui

    2012-09-01

    Current investigation of cancer progression towards increasing malignancy focuses on the molecular pathways that produce the various cancerous traits of cells. Their acquisition is explained by the somatic mutation theory: tumor progression is the result of a neo-Darwinian evolution in the tissue. Herein cells are the units of selection. Random genetic mutations permanently affecting these pathways create malignant cell phenotypes that are selected for in the disturbed tissue. However, could it be that the capacity of the genome and its gene regulatory network to generate the vast diversity of cell types during development, i.e., to produce inheritable phenotypic changes without mutations, is harnessed by tumorigenesis to propel a directional change towards malignancy? Here we take an encompassing perspective, transcending the orthodoxy of molecular carcinogenesis and review mechanisms of somatic evolution beyond the Neo-Darwinian scheme. We discuss the central concept of "cancer attractors" - the hidden stable states of gene regulatory networks normally not occupied by cells. Noise-induced transitions into such attractors provide a source for randomness (chance) and regulatory constraints (necessity) in the acquisition of novel expression profiles that can be inherited across cell divisions, and hence, can be selected for. But attractors can also be reached in response to environmental signals - thus offering the possibility for inheriting acquired traits that can also be selected for. Therefore, we face the possibility of non-genetic (mutation-independent) equivalents to both Darwinian and Lamarckian evolution which may jointly explain the arrow of change pointing toward increasing malignancy. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Book review: Darwinian agriculture: How understanding evolution can improve agriculture by R. Ford Dennison

    USDA-ARS?s Scientific Manuscript database

    Agricultural research continually seeks to increase productivity while protecting soil, water and genetic resources. The book Darwinian Agriculture: How Understanding Evolution Can Improve Agriculture, by R. Ford Dennison, delivers a thought-provoking view of how principles of ecology and evolution ...

  3. Understanding protein evolution: from protein physics to Darwinian selection.

    PubMed

    Zeldovich, Konstantin B; Shakhnovich, Eugene I

    2008-01-01

    Efforts in whole-genome sequencing and structural proteomics start to provide a global view of the protein universe, the set of existing protein structures and sequences. However, approaches based on the selection of individual sequences have not been entirely successful at the quantitative description of the distribution of structures and sequences in the protein universe because evolutionary pressure acts on the entire organism, rather than on a particular molecule. In parallel to this line of study, studies in population genetics and phenomenological molecular evolution established a mathematical framework to describe the changes in genome sequences in populations of organisms over time. Here, we review both microscopic (physics-based) and macroscopic (organism-level) models of protein-sequence evolution and demonstrate that bridging the two scales provides the most complete description of the protein universe starting from clearly defined, testable, and physiologically relevant assumptions.

  4. Perspective: is human cultural evolution Darwinian? Evidence reviewed from the perspective of the Origin of Species.

    PubMed

    Mesoudi, Alex; Whiten, Andrew; Laland, Kevin N

    2004-01-01

    The claim that human culture evolves through the differential adoption of cultural variants, in a manner analogous to the evolution of biological species, has been greeted with much resistance and confusion. Here we demonstrate that as compelling a case can now be made that cultural evolution has key Darwinian properties, as Darwin himself presented for biological evolution in The Origin of Species. Culture is shown to exhibit variation, competition, inheritance, and the accumulation of successive cultural modifications over time. Adaptation, convergence, and the loss or change of function can also be identified in culture. Just as Darwin knew nothing of genes or particulate inheritance, a case for Darwinian cultural evolution can be made irrespective of whether unitary cultural replicators exist or whether cultural transmission mechanisms are well understood.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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?

  10. A neo-Darwinian algorithm: asymmetrical mutations due to semiconservative DNA-type replication promote evolution.

    PubMed

    Wada, K N; Doi, H; Tanaka, S; Wada, Y; Furusawa, M

    1993-12-15

    Evolution is, in a sense, to resolve optimization problems. Our neo-Darwinian algorithm based on the mechanics of inheritance and natural selection uses double-stranded DNA-type genetic information to resolve the "knap-sack problem." The algorithm with asymmetrical mutations due to semiconservative DNA-type replication most effectively resolved the problem. Our results strongly suggest that disparity in mutations caused by the asymmetric machinery of DNA replication promotes evolution, in particular of diploid organisms with a high mutation rate, in a small population, and under strong selection pressure.

  11. 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.

  12. 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

  13. 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…

  14. 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…

  15. 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

  16. Non-Darwinian evolution for the source detection of atmospheric releases

    NASA Astrophysics Data System (ADS)

    Cervone, Guido; Franzese, Pasquale

    2011-08-01

    A non-Darwinian evolutionary algorithm is presented as search engine to identify the characteristics of a source of atmospheric pollutants, given a set of concentration measurements. The algorithm drives iteratively a forward dispersion model from tentative sources toward the real source. The solutions of non-Darwinian evolution processes are not generated through pseudo-random operators, unlike traditional evolutionary algorithms, but through a reasoning process based on machine learning rule generation and instantiation. The new algorithm is tested with both a synthetic case and with the Prairie Grass field experiment. To further test the capabilities of the algorithm to work in real-world scenarios, the source identification of all Prairie Grass releases was performed with a decreasing number of sensor measurements, and a relationship is found between the precision of the solution, the number of sensors available, and the levels of concentration measured by the sensors. The proposed methodology can be used for a variety of optimization problems, and is particularly suited for problems where the operations needed for evaluating new candidate solutions are computationally expensive.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. Thermal Solutions for Molecular Evolution

    NASA Astrophysics Data System (ADS)

    Mast, Christof B.; Osterman, Natan; Braun, Dieter

    2012-12-01

    The key requirement to solve the origin of life puzzle are disequilibrium conditions. Early molecular evolution cannot be explained by initial high concentrations of energetic chemicals since they would just react towards their chemical equilibrium allowing no further development. We argue here that persistent disequilibria are needed to increase complexity during molecular evolution. We propose thermal gradients as the disequilibrium setting which drove Darwinian molecular evolution. On the one hand the thermal gradient gives rise to laminar thermal convection flow with highly regular temperature oscillations that allow melting and replication of DNA. On the other hand molecules move along the thermal gradient, a mechanism termed Soret effect or thermophoresis. Inside a long chamber a combination of the convection flow and thermophoresis leads to a very efficient accumulation of molecules. Short DNA is concentrated thousand-fold, whereas longer DNA is exponentially better accumulated. We demonstrated both scenarios in the same micrometer-sized setting. Forthcoming experiments will reveal how replication and accumulation of DNA in a system, driven only by a thermal gradient, could create a Darwinian process of replication and selection.

  2. 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.

  3. 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…

  4. 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…

  5. 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.

  6. 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.

  7. 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.

  8. The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law.

    PubMed

    Denton, Michael J; Marshall, Craig J; Legge, Michael

    2002-12-07

    Before the Darwinian revolution many biologists considered organic forms to be determined by natural law like atoms or crystals and therefore necessary, intrinsic and immutable features of the world order, which will occur throughout the cosmos wherever there is life. The search for the natural determinants of organic form-the celebrated "Laws of Form"-was seen as one of the major tasks of biology. After Darwin, this Platonic conception of form was abandoned and natural selection, not natural law, was increasingly seen to be the main, if not the exclusive, determinant of organic form. However, in the case of one class of very important organic forms-the basic protein folds-advances in protein chemistry since the early 1970s have revealed that they represent a finite set of natural forms, determined by a number of generative constructional rules, like those which govern the formation of atoms or crystals, in which functional adaptations are clearly secondary modifications of primary "givens of physics." The folds are evidently determined by natural law, not natural selection, and are "lawful forms" in the Platonic and pre-Darwinian sense of the word, which are bound to occur everywhere in the universe where the same 20 amino acids are used for their construction. We argue that this is a major discovery which has many important implications regarding the origin of proteins, the origin of life and the fundamental nature of organic form. We speculate that it is unlikely that the folds will prove to be the only case in nature where a set of complex organic forms is determined by natural law, and suggest that natural law may have played a far greater role in the origin and evolution of life than is currently assumed.

  9. 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.

  10. 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.

  11. A Scoring Rubric for Students' Responses to Simple Evolution Questions: Darwinian Components

    ERIC Educational Resources Information Center

    Jensen, Murray; Moore, Randy; Hatch, Jay; Hsu, Leon

    2007-01-01

    The call to teach students Darwin's theory of evolution by natural selection has been made by a variety of professional organizations. In addition to these national organizations, almost every state has science education guidelines calling for the teaching of evolution. Many administrators and policymakers believe that evolution is being taught,…

  12. The "sensational" power of movement in plants: A Darwinian system for studying the evolution of behavior.

    PubMed

    Whippo, Craig W; Hangarter, Roger P

    2009-12-01

    Darwin's research on botany and plant physiology was a landmark attempt to integrate plant movements into a biological perspective of behavior. Since antiquity, people have sought to explain plant movements via mechanical or physiological forces, and yet they also constructed analogies between plant and animal behavior. During the Renaissance and Enlightenment, thinkers began to see that physiochemical explanations of plant movements could equally apply to animal behavior and even human thought. Darwin saw his research on plant movements as a strategic front against those who argued that his theory of evolution could not account for the acquisition of new behavioral traits. He believed that his research explained how the different forms of plant movement evolved as modified habits of circumnutation, and he presented evidence that plants might have a brain-like organ, which could have acquired various types of plant sensitivity during evolution. Upon publication of The Power of Movement in Plants, his ideas were overwhelmingly rejected by plant physiologists. Subsequently, plant biologists came to view the work as an important contribution to plant physiology and biology, but its intended contribution to the field of evolution and behavior has been largely overlooked.

  13. 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,…

  14. 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,…

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. [Haeckel: a German Darwinian?].

    PubMed

    Schmitt, Stéphane

    2009-01-01

    German biologist Ernst Haeckel (1834-1919) is often considered the most renowned Darwinian in his country since, as early as 1862, he declared that he accepted the conclusions Darwin had reached three years before in On the Origin of Species, and afterwards, he continuously proclaimed himself a supporter of the English naturalist and championed the evolutionary theory. Nevertheless, if we examine carefully his books, in particular his General Morphology (1866), we can see that he carries on a tradition very far from Darwin's thoughts. In spite of his acceptance of the idea of natural selection, that he establishes as an argument for materialism, he adopts, indeed, a conception of evolution that is, in some respects, rather close to Lamarck's views. He is, thus, a good example of the ambiguities of the reception of Darwinism in Germany in the second part of the 19th century.

  20. 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)

  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. The neutral theory of molecular evolution in the genomic era.

    PubMed

    Nei, Masatoshi; Suzuki, Yoshiyuki; Nozawa, Masafumi

    2010-01-01

    The neutral theory of molecular evolution has been widely accepted and is the guiding principle for studying evolutionary genomics and the molecular basis of phenotypic evolution. Recent data on genomic evolution are generally consistent with the neutral theory. However, many recently published papers claim the detection of positive Darwinian selection via the use of new statistical methods. Examination of these methods has shown that their theoretical bases are not well established and often result in high rates of false-positive and false-negative results. When the deficiencies of these statistical methods are rectified, the results become largely consistent with the neutral theory. At present, genome-wide analyses of natural selection consist of collections of single-locus analyses. However, because phenotypic evolution is controlled by the interaction of many genes, the study of natural selection ought to take such interactions into account. Experimental studies of evolution will also be crucial.

  3. 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.

  4. 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.

  5. 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.

  6. The statesman and the ophthalmologist: Gladstone and Magnus on the evolution of human colour vision, one small episode of the nineteenth-century Darwinian debate.

    PubMed

    Bellmer, E H

    1999-01-01

    Among the numerous nineteenth-century sorties into particular aspects of the Darwinian debate are two 1877 publications. The first, Die Geschichtliche Entwickelung des Farbensinnes, was a treatise on the evolutionary development of human colour vision by Hugo Magnus, an obscure German ophthalmologist. The other, The Colour-Sense, was an article by William Ewart Gladstone, the great British statesman. Magnus, working from linguistic science and optical physiology, developed the theory that humankind had passed through successive stages of colour recognition, from none to full perception, brightest colours first. Gladstone supported the theory with data from his studies of Homeric colour words, placing Homer at a very early stage. Their theory was not accepted. It assumed colour vocabulary to be an index of colour recognition, and too little was known about the nature or age of early man. The present study intends to follow this particular episode as an excellent example of the scholarship, argumentation, and limited scientific knowledge of the time, as applied to human evolution.

  7. 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

  8. Usefulness of a Darwinian system in a biotechnological application: evolution of optical window fluorescent protein variants under selective pressure.

    PubMed

    Schoetz, Ulrike; Deliolanis, Nikolaos C; 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.

  9. 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

  10. 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.

  11. 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)

  12. 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)

  13. Molecular Evolution in Historical Perspective.

    PubMed

    Suárez-Díaz, Edna

    2016-12-01

    In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms. These developments sparked important debates between defendants of the molecular and organismic approaches. The most vocal confrontations focused on the relation between primates and humans, and the neutral theory of molecular evolution. By the 1980s and 1990s, the construction of large protein and DNA sequences databases, and the development of computer-based statistical tools, facilitated the coming together of molecular and evolutionary biology. Although in its contemporary form the field of molecular evolution can be traced back to the last five decades, the field has deep roots in twentieth century experimental life sciences. For historians of science, the origins and consolidation of molecular evolution provide a privileged field for the study of scientific debates, the relation between technological advances and scientific knowledge, and the connection between science and broader social concerns.

  14. Chemistry and the missing era of evolution.

    PubMed

    Cairns-Smith, A Graham

    2008-01-01

    The Darwinian evolution of life on earth depends utterly on complex molecular machinery, which, it seems, could only have arisen through a Darwinian evolution. The "RNA world" idea reduces this paradox, but requires a geochemically implausible supply of RNA monomers. A pre-RNA era of natural selection is implied. I suggest that originally this was based on inorganic materials that came to replicate permutations with specific (e.g. catalytic) effects.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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…

  3. 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…

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. The Evolution of Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Wannier, Peter

    2002-07-01

    How is the evolution of dense clouds affected by their surrounding, more diffuse gas? Without an answer, it is not possible to understand the evolution of the ISM. Dense clouds can end their lives through the combined actions of star formation, violent disruption, and ablation. If ablation is an important process, then it is not a foregone conclusion that the dense clouds we see today will ever form stars. We will learn about the ablation process using STIS observations toward 18 stars for which we have existing FUSE observations, sightlines selected to lie behind the extended halos of four widely separated, molecular clouds. Our primary goal is to measure the gas pressure, the key to driving gas flows; secondary goals are to estimate the prevailing radiation and the CO column density. We have completed a pilot study of three stars in B5/Perseus, which enabled us to infer the presence near that cloud, of an isobaric, evaporative outflow, probably driven by UV irradiation. The 18 proposed sightlines lie near four dense clouds which have been well studied at radio, mm and far-IR wavelengths, providing needed auxiliary information about morphology and kinematics. The clouds {1} are nearby, {2} are unperturbed by massive star formation, and {3} sample a range of external environments. The combined STIS, FUSE and ground-based results will yield information needed to understand the role of ablation in the evolution of the central clouds.

  13. 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.

  14. 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

  15. 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

  16. Dracula's children: molecular evolution of vampire bat venom.

    PubMed

    Low, Dolyce H W; Sunagar, Kartik; Undheim, Eivind A B; Ali, Syed A; Alagon, Alejandro C; Ruder, Tim; Jackson, Timothy N W; Pineda Gonzalez, Sandy; King, Glenn F; Jones, Alun; Antunes, Agostinho; Fry, Bryan G

    2013-08-26

    While vampire bat oral secretions have been the subject of intense research, efforts have concentrated only on two components: DSPA (Desmodus rotundus salivary plasminogen activator) and Draculin. The molecular evolutionary history of DSPA has been elucidated, while conversely draculin has long been known from only a very small fragment and thus even the basic protein class was not even established. Despite the fact that vampire bat venom has a multitude of effects unaccounted by the documented bioactivities of DSPA and draculin, efforts have not been made to establish what other bioactive proteins are secreted by their submaxillary gland. In addition, it has remained unclear whether the anatomically distinct anterior and posterior lobes of the submaxillary gland are evolving on separate gene expression trajectories or if they remain under the shared genetic control. Using a combined proteomic and transcriptomic approach, we show that identical proteins are simultaneously expressed in both lobes. In addition to recovering the known structural classes of DSPA, we recovered a novel DSPA isoform as well as obtained a very large sequence stretch of draculin and thus established that it is a mutated version of the lactotransferrin scaffold. This study reveals a much more complex secretion profile than previously recognised. In addition to obtaining novel versions of scaffolds convergently recruited into other venoms (allergen-like, CRiSP, kallikrein, Kunitz, lysozyme), we also documented novel expression of small peptides related to calcitonin, PACAP, and statherin. Other overexpressed protein types included BPI-fold, lacritin, and secretoglobin. Further, we investigate the molecular evolution of various vampire bat venom-components and highlight the dominant role of positive selection in the evolution of these proteins. Conspicuously many of the proteins identified in the proteome were found to be homologous to proteins with known activities affecting vasodilation and

  17. 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.

  18. 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

  19. 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

  20. 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…

  1. 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…

  2. 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…

  3. Elements for a theory of molecular evolution.

    PubMed

    Arber, Werner

    2003-10-23

    Biological evolution is known to be driven by the availability of genetic variants. Spontaneous genetic variation can be the result of a number of specific molecular mechanisms. These can be grouped into three qualitatively different natural strategies of generating genetic variations, namely local sequence changes, DNA rearrangement within the genome and horizontal gene transfer, which is referred to here as DNA acquisition. All of these strategies bring about alterations in the DNA sequences of the genome, thus corresponding to the molecular genetic definition of the term mutation. A detailed inspection of specific mechanisms of mutagenesis reveals on the one hand the impact of non-genetic internal and environmental factors, and on the other hand the specific involvement of gene products. The underlying so-called evolution genes can be classified into generators of genetic variations and into modulators of the frequency of genetic variation. These evolution genes are postulated to have themselves undergone biological evolution under the pressure of second-order selection. On the basis of a few selected examples of mutagenesis, elements for a theory of molecular evolution are collected without a claim for completeness. Philosophical dimensions as well as practical aspects of the advanced knowledge on specific molecular mechanisms involved in molecular evolution are also briefly discussed.

  4. 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.

  5. [Debating Darwin in Spain: anti-Darwinian evolutionary theories and modern synthesis].

    PubMed

    Pelayo, Francisco

    2009-01-01

    Centenary celebrations of Darwin's birth were held in Valencia and Lorca in 1909. Fifty years later, the meetings and the publications of the Spanish scientific community on the occasion of the centenary of the publication of "On the Origin of Species" showed a proximity and an acceptance towards the theses of the evolutionary modern synthesis. During the first half of the 20th century, there were controversies in Spain between the Darwinian and anti-Darwinian positions. In addition, non-Darwinian evolutionary theories were spread and supported. Though the assumptions of the synthetic theory of evolution were soon known, commented and discussed, the majority trend in the 40s and 50s was to incline towards finalist and vitalist interpretations of evolution.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. Molecular signatures of ribosomal evolution.

    PubMed

    Roberts, Elijah; Sethi, Anurag; Montoya, Jonathan; Woese, Carl R; Luthey-Schulten, Zaida

    2008-09-16

    Ribosomal signatures, idiosyncrasies in the ribosomal RNA (rRNA) and/or proteins, are characteristic of the individual domains of life. As such, insight into the early evolution of the domains can be gained from a comparative analysis of their respective signatures in the translational apparatus. In this work, we identify signatures in both the sequence and structure of the rRNA and analyze their contributions to the universal phylogenetic tree using both sequence- and structure-based methods. Domain-specific ribosomal proteins can be considered signatures in their own right. Although it is commonly assumed that they developed after the universal ribosomal proteins, we present evidence that at least one may have been present before the divergence of the organismal lineages. We find correlations between the rRNA signatures and signatures in the ribosomal proteins showing that the rRNA signatures coevolved with both domain-specific and universal ribosomal proteins. Finally, we show that the genomic organization of the universal ribosomal components contains these signatures as well. From these studies, we propose the ribosomal signatures are remnants of an evolutionary-phase transition that occurred as the cell lineages began to coalesce and so should be reflected in corresponding signatures throughout the fabric of the cell and its genome.

  18. Molecular signatures of ribosomal evolution

    PubMed Central

    Roberts, Elijah; Sethi, Anurag; Montoya, Jonathan; Woese, Carl R.; Luthey-Schulten, Zaida

    2008-01-01

    Ribosomal signatures, idiosyncrasies in the ribosomal RNA (rRNA) and/or proteins, are characteristic of the individual domains of life. As such, insight into the early evolution of the domains can be gained from a comparative analysis of their respective signatures in the translational apparatus. In this work, we identify signatures in both the sequence and structure of the rRNA and analyze their contributions to the universal phylogenetic tree using both sequence- and structure-based methods. Domain-specific ribosomal proteins can be considered signatures in their own right. Although it is commonly assumed that they developed after the universal ribosomal proteins, we present evidence that at least one may have been present before the divergence of the organismal lineages. We find correlations between the rRNA signatures and signatures in the ribosomal proteins showing that the rRNA signatures coevolved with both domain-specific and universal ribosomal proteins. Finally, we show that the genomic organization of the universal ribosomal components contains these signatures as well. From these studies, we propose the ribosomal signatures are remnants of an evolutionary-phase transition that occurred as the cell lineages began to coalesce and so should be reflected in corresponding signatures throughout the fabric of the cell and its genome. PMID:18768810

  19. 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…

  20. 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…

  1. 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)

  2. 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)

  3. The First Darwinian Phylogenetic Tree of Plants.

    PubMed

    Hoßfeld, Uwe; Watts, Elizabeth; Levit, Georgy S

    2017-02-01

    In 1866, the German zoologist Ernst Haeckel (1834-1919) published the first Darwinian trees of life in the history of biology in his book General Morphology of Organisms. We take a specific look at the first phylogenetic trees for the plant kingdom that Haeckel created as part of this two-volume work. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. 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.

  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. The Molecular Basis of Human Brain Evolution.

    PubMed

    Enard, Wolfgang

    2016-10-24

    Humans are a remarkable species, especially because of the remarkable properties of their brain. Since the split from the chimpanzee lineage, the human brain has increased three-fold in size and has acquired abilities for vocal learning, language and intense cooperation. To better understand the molecular basis of these changes is of great biological and biomedical interest. However, all the about 16 million fixed genetic changes that occurred during human evolution are fully correlated with all molecular, cellular, anatomical and behavioral changes that occurred during this time. Hence, as humans and chimpanzees cannot be crossed or genetically manipulated, no direct evidence for linking particular genetic and molecular changes to human brain evolution can be obtained. Here, I sketch a framework how indirect evidence can be obtained and review findings related to the molecular basis of human cognition, vocal learning and brain size. In particular, I discuss how a comprehensive comparative approach, leveraging cellular systems and genomic technologies, could inform the evolution of our brain in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  9. Molecular evolution of color vision in vertebrates.

    PubMed

    Yokoyama, Shozo

    2002-10-30

    Visual systems of vertebrates exhibit a striking level of diversity, reflecting their adaptive responses to various color environments. The photosensitive molecules, visual pigments, can be synthesized in vitro and their absorption spectra can be determined. Comparing the amino acid sequences and absorption spectra of various visual pigments, we can identify amino acid changes that have modified the absorption spectra of visual pigments. These hypotheses can then be tested using the in vitro assay. This approach has been a powerful tool in elucidating not only the molecular bases of color vision, but the processes of adaptive evolution at the molecular level.

  10. 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.

  11. 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.

  12. 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.

  13. Time-dependent rates of molecular evolution.

    PubMed

    Ho, Simon Y W; Lanfear, Robert; Bromham, Lindell; Phillips, Matthew J; Soubrier, Julien; Rodrigo, Allen G; Cooper, Alan

    2011-08-01

    For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events. © 2011 Blackwell Publishing Ltd.

  14. Molecular evolution of prolactin in primates.

    PubMed

    Wallis, O Caryl; Mac-Kwashie, Akofa O; Makri, Georgia; Wallis, Michael

    2005-05-01

    Pituitary prolactin, like growth hormone (GH) and several other protein hormones, shows an episodic pattern of molecular evolution in which sustained bursts of rapid change contrast with long periods of slow evolution. A period of rapid change occurred in the evolution of prolactin in primates, leading to marked sequence differences between human prolactin and that of nonprimate mammals. We have defined this burst more precisely by sequencing the coding regions of prolactin genes for a prosimian, the slow loris (Nycticebus pygmaeus), and a New World monkey, the marmoset (Callithrix jacchus). Slow loris prolactin is very similar in sequence to pig prolactin, so the episode of rapid change occurred during primate evolution, after the separation of lines leading to prosimians and higher primates. Marmoset prolactin is similar in sequence to human prolactin, so the accelerated evolution occurred before divergence of New World monkeys and Old World monkeys/apes. The burst of change was confined largely to coding sequence (nonsynonymous sites) for mature prolactin and is not marked in other components of the gene sequence. This and the observations that (1) there was no apparent loss of function during the episode of rapid evolution, (2) the rate of evolution slowed toward the basal rate after this burst, and (3) the distribution of substitutions in the prolactin molecule is very uneven support the idea that this episode of rapid change was due to positive adaptive selection. In the slow loris and marmoset there is no evidence for duplication of the prolactin gene, and evidence from another New World monkey (Cebus albifrons) and from the chimpanzee and human genome sequences, suggests that this is the general position in primates, contrasting with the situation for GH genes. The chimpanzee prolactin sequence differs from that of human at two residues and comparison of human and chimpanzee prolactin gene sequences suggests that noncoding regions associated with regulating

  15. 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.

  16. Molecular evolution of human species D adenoviruses

    PubMed Central

    Robinson, Christopher M.; Seto, Donald; Jones, Morris S.; Dyer, David W.; Chodosh, James

    2011-01-01

    Adenoviruses are medium-sized double stranded DNA viruses that infect vertebrates. Human adenoviruses cause an array of diseases. Currently there are 56 human adenovirus types recognized and characterized within seven species (A-G). Of those types, a majority belongs to species D. In this review, the genomic conservation and diversity are examined amongst human adenoviruses within species D, particularly in contrast to other human adenovirus species. Specifically, homologous recombination is presented as a driving force for the molecular evolution of human adenoviruses and the emergence of new adenovirus pathogens. PMID:21570490

  17. Evolution - A Theory Evolving

    ERIC Educational Resources Information Center

    Weinberg, Janet H.

    1975-01-01

    Presented is an explanation of a non-Darwinian theory of evolution based on the premise that functional differences are the result of many small mutations such as the substitution of one amino acid for another in a large protein molecule. A brief overview of Darwinian evolution and other theories are presented. (EB)

  18. Chemical Evolution and the Evolutionary Definition of Life.

    PubMed

    Higgs, Paul G

    2017-06-01

    Darwinian evolution requires a mechanism for generation of diversity in a population, and selective differences between individuals that influence reproduction. In biology, diversity is generated by mutations and selective differences arise because of the encoded functions of the sequences (e.g., ribozymes or proteins). Here, I draw attention to a process that I will call chemical evolution, in which the diversity is generated by random chemical synthesis instead of (or in addition to) mutation, and selection acts on physicochemical properties, such as hydrolysis, photolysis, solubility, or surface binding. Chemical evolution applies to short oligonucleotides that can be generated by random polymerization, as well as by template-directed replication, and which may be too short to encode a specific function. Chemical evolution is an important stage on the pathway to life, between the stage of "just chemistry" and the stage of full biological evolution. A mathematical model is presented here that illustrates the differences between these three stages. Chemical evolution leads to much larger differences in molecular concentrations than can be achieved by selection without replication. However, chemical evolution is not open-ended, unlike biological evolution. The ability to undergo Darwinian evolution is often considered to be a defining feature of life. Here, I argue that chemical evolution, although Darwinian, does not quite constitute life, and that a good place to put the conceptual boundary between non-life and life is between chemical and biological evolution.

  19. Amino Acid Properties Conserved in Molecular Evolution

    PubMed Central

    Rudnicki, Witold R.; Mroczek, Teresa; Cudek, Paweł

    2014-01-01

    That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts – one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications. PMID:24967708

  20. 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

  1. 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

  2. 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

  3. Becoming a Darwinian: the micro-politics of Sir Francis Galton's scientific career 1859-65.

    PubMed

    Waller, John C

    2004-04-01

    In 1865 Francis Galton (1822-1911) published 'Hereditary Talent and Character', an elaborate attempt to prove the heritability of intelligence on the basis of pedigree data. It was the start of Galton's lifelong commitment to investigating the statistical patterns and physiological mechanisms of hereditary transmission. Most existing attempts to explain Galton's fascination for heredity have argued that he was driven by a commitment to conservative political ideologies to seek means of naturalizing human inequality. However, this paper shows that another factor of at least equal importance has been overlooked by Galton scholars: his determination during the 1860s to be accepted among the ranks of the Darwinian inner circle. By hitching his career to the fortunes of what looked likely to emerge as a new scientific elite, Galton felt that he could bypass the typically slow and uncertain route to achieving scientific distinction. For this essentially strategic reason, between 1860 and 1865 he drifted away from a set of existing scientific concerns that were failing to deliver the approbation that he desired. Earnestly seeking to ingratiate himself with the Darwinian lobby, he then toyed with a variety of potential research projects relevant to Darwinian evolution. Yet Galton consistently failed to stimulate the enthusiasm of the Darwinians. Finally, however, after several months of ruminating, in 1864 he settled on a study of eminent pedigrees as a subject that was both germane and highly useful to the Darwinian enterprise. Galton's willingness to shift the direction of his scientific career during the 1860s underscores the importance of examining the micro-politics of scientific careers in addition to their broader social and political context. This account also emphasizes the limitations of class-based explanations even when considering scientists whose work seems so manifestly indicative of ideological motivation.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. The evolution of giant molecular filaments

    NASA Astrophysics Data System (ADS)

    Duarte-Cabral, Ana; Dobbs, C. L.

    2017-10-01

    In recent years, there has been a growing interest in studying giant molecular filaments (GMFs), which are extremely elongated (>100 pc in length) giant molecular clouds (GMCs). They are often seen as inter-arm features in external spiral galaxies, but have been tentatively associated with spiral arms when viewed in the Milky Way. In this paper, we study the time evolution of GMFs in a high-resolution section of a spiral galaxy simulation, and their link with spiral arm GMCs and star formation, over a period of 11 Myr. The GMFs generally survive the inter-arm passage, although they are subject to a number of processes (e.g. star formation, stellar feedback and differential rotation) that can break the giant filamentary structure into smaller sections. The GMFs are not gravitationally bound clouds as a whole, but are, to some extent, confined by external pressure. Once they reach the spiral arms, the GMFs tend to evolve into more substructured spiral arm GMCs, suggesting that GMFs may be precursors to arm GMCs. Here, they become incorporated into the more complex and almost continuum molecular medium that makes up the gaseous spiral arm. Instead of retaining a clear filamentary shape, their shapes are distorted both by their climbing up the spiral potential and their interaction with the gas within the spiral arm. The GMFs do tend to become aligned with the spiral arms just before they enter them (when they reach the minimum of the spiral potential), which could account for the observations of GMFs in the Milky Way.

  11. Why do species vary in their rate of molecular evolution?

    PubMed Central

    Bromham, Lindell

    2009-01-01

    Despite hopes that the processes of molecular evolution would be simple, clock-like and essentially universal, variation in the rate of molecular evolution is manifest at all levels of biological organization. Furthermore, it has become clear that rate variation has a systematic component: rate of molecular evolution can vary consistently with species body size, population dynamics, lifestyle and location. This suggests that the rate of molecular evolution should be considered part of life-history variation between species, which must be taken into account when interpreting DNA sequence differences between lineages. Uncovering the causes and correlates of rate variation may allow the development of new biologically motivated models of molecular evolution that may improve bioinformatic and phylogenetic analyses. PMID:19364710

  12. Why do species vary in their rate of molecular evolution?

    PubMed

    Bromham, Lindell

    2009-06-23

    Despite hopes that the processes of molecular evolution would be simple, clock-like and essentially universal, variation in the rate of molecular evolution is manifest at all levels of biological organization. Furthermore, it has become clear that rate variation has a systematic component: rate of molecular evolution can vary consistently with species body size, population dynamics, lifestyle and location. This suggests that the rate of molecular evolution should be considered part of life-history variation between species, which must be taken into account when interpreting DNA sequence differences between lineages. Uncovering the causes and correlates of rate variation may allow the development of new biologically motivated models of molecular evolution that may improve bioinformatic and phylogenetic analyses.

  13. 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

  14. Directionality of evolution at molecular and organismic levels.

    PubMed

    Livshits, M A; Volkenstein, M V

    1991-01-01

    The molecular evolution theories of Eigen and Kimura are compared and their difference is explained. In terms of Eigen's theory for the evolution of macromolecules, the selection of genotypes occurs directly. The physical meaning of the neutral theory is the degeneracy of the correlation between a phenotype and a genotype at the molecular level. A model theory of evolution on a fitness landscape is proposed. The theory shows that the constraints of selection determined by the structure and dynamics of previous evolution stages increases its rate strongly.

  15. 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

  16. Molecular musings in microbial ecology and evolution.

    PubMed

    Case, Rebecca J; Boucher, Yan

    2011-11-10

    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

  17. Elements for the Development of a Darwinian Scheme Leading to Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Baladrón, Carlos

    2015-10-01

    A subquantum theory is examined in which a fundamental system has been characterized as the association of a particle with a continuous trajectory in real space and a classical probabilistic Turing machine defined on an informational space. The particle transfers information to the machine, and this steers the particle by means of self-interaction. In a certain sense, the associated Turing machine might be considered a generalization of the pilot wave function of Bohmian mechanics. The data processing capability entailed by the Turing machine makes the particle a generalized Darwinian system on which natural selection may operate. Darwinian evolution acting on the informational space should then drive the particle from random behaviour purportedly associated to an initial blank state to a possible evolutionarily stable strategy (ESS). Three regulating principles that plausibly encode an ESS are stated. The derivation of the postulates of quantum mechanics is discussed assuming that the behaviour of systems is governed by the three regulating principles. The theory also enables, within the generalized Darwinian framework, a natural characterization of entanglement through the local interaction between the Turing machines of the subsystems. Some possible future experimental and computational tests of the theory are outlined. The central aim of this scheme is to explore the possibility that generalized Darwinian natural selection might induce the emergence of quantum mechanics and its weird features from a real and local underlying description of particles supplemented with a Turing machine on an informational space, since those systems presenting quantum behaviour seem to be the most robust at a microscopic level.

  18. 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'.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. Galaxy chemical evolution models: the role of molecular gas formation

    NASA Astrophysics Data System (ADS)

    Mollá, Mercedes; Díaz, Ángeles I.; Ascasibar, Yago; Gibson, Brad K.

    2017-06-01

    In our classical grid of multiphase chemical evolution models, star formation in the disc occurs in two steps: first, molecular gas forms, and then stars are created by cloud-cloud collisions or interactions of massive stars with the surrounding molecular clouds. The formation of both molecular clouds and stars are treated through the use of free parameters we refer to as efficiencies. In this work, we modify the formation of molecular clouds based on several new prescriptions existing in the literature, and we compare the results obtained for a chemical evolution model of the Milky Way Galaxy regarding the evolution of the Solar region, the radial structure of the Galactic disc and the ratio between the diffuse and molecular components, H i/H2. Our results show that the six prescriptions we have tested reproduce fairly consistent most of the observed trends, differing mostly in their predictions for the (poorly constrained) outskirts of the Milky Way and the evolution in time of its radial structure. Among them, the model proposed by Ascasibar et al. (in preparation), where the conversion of diffuse gas into molecular clouds depends on the local stellar and gas densities as well as on the gas metallicity, seems to provide the best overall match to the observed data.

  8. 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.

  9. 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.

  10. Molecular evolution of the vertebrate mechanosensory cell and ear

    PubMed Central

    Fritzsch, Bernd; Beisel, Kirk W.; Pauley, Sarah; Soukup, Garrett

    2014-01-01

    The molecular basis of mechanosensation, mechanosensory cell development and mechanosensory organ development is reviewed with an emphasis on its evolution. In contrast to eye evolution and development, which apparently modified a genetic program through intercalation of genes between the master control genes on the top (Pax6, Eya1, Six1) of the hierarchy and the structural genes (rhodopsin) at the bottom, the as yet molecularly unknown mechanosensory channel precludes such a firm conclusion for mechanosensors. However, recent years have seen the identification of several structural genes which are involved in mechanosensory tethering and several transcription factors controlling mechanosensory cell and organ development; these warrant the interpretation of available data in very much the same fashion as for eye evolution: molecular homology combined with potential morphological parallelism. This assertion of molecular homology is strongly supported by recent findings of a highly conserved set of microRNAs that appear to be associated with mechanosensory cell development across phyla. The conservation of transcription factors and their regulators fits very well to the known or presumed mechanosensory specializations which can be mostly grouped as variations of a common cellular theme. Given the widespread distribution of the molecular ability to form mechanosensory cells, it comes as no surprise that structurally different mechanosensory organs evolved in different phyla, presenting a variation of a common theme specified by a conserved set of transcription factors in their cellular development. Within vertebrates and arthropods, some mechanosensory organs evolved into auditory organs, greatly increasing sensitivity to sound through modifications of accessory structures to direct sound to the specific sensory epithelia. However, while great attention has been paid to the evolution of these accessory structures in vertebrate fossils, comparatively less attention has

  11. Cellular heterogeneity and molecular evolution in cancer.

    PubMed

    Almendro, Vanessa; Marusyk, Andriy; Polyak, Kornelia

    2013-01-24

    Intratumor heterogeneity represents a major obstacle to effective cancer treatment and personalized medicine. However, investigators are now elucidating intratumor heterogeneity at the single-cell level due to improvements in technologies. Better understanding of the composition of tumors, and monitoring changes in cell populations during disease progression and treatment, will improve cancer diagnosis and therapeutic design. Measurements of intratumor heterogeneity may also be used as biomarkers to predict the risk of progression and therapeutic resistance. We summarize important considerations related to intratumor heterogeneity during tumor evolution. We also discuss experimental approaches that are commonly used to infer intratumor heterogeneity and describe how these methodologies can be translated into clinical practice.

  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. 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.

  14. 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.

  15. 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. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  16. Fish rhabdoviruses: molecular epidemiology and evolution.

    PubMed

    Hoffmann, B; Beer, M; Schütze, H; Mettenleiter, T C

    2005-01-01

    Rhabdoviruses may cause serious diseases in wild and farmed fish. Within the Rhabdoviridae six genera have been established: Ephemerovirus, Cytorhabdovirus, Nucleorhabdovirus, Lyssavirus, Vesiculovirus, and Novirhabdovirus. Viruses that infect fish are official or tentative members of the genera Vesiculovirus and Novirhabdovirus, or are listed as unassigned rhabdoviruses. In this report, we summarize and discuss published and our own unpublished data on the molecular epidemiology and phylogeography of fish rhabdoviruses including intrapopulational differences and subgrouping of fish rhabdoviruses, in particular the species spring viremia of carp virus (SVCV), infectious hematopoietic necrosis virus (IHNV) and viral hemorrhagic septicemia virus (VHSV).

  17. Molecular evolution of GPCRs: Ghrelin/ghrelin receptors.

    PubMed

    Kaiya, Hiroyuki; Kangawa, Kenji; Miyazato, Mikiya

    2014-06-01

    After the discovery in 1996 of the GH secretagogue-receptor type-1a (GHS-R1a) as an orphan G-protein coupled receptor, many research groups attempted to identify the endogenous ligand. Finally, Kojima and colleagues successfully isolated the peptide ligand from rat stomach extracts, determined its structure, and named it ghrelin. The GHS-R1a is now accepted to be the ghrelin receptor. The existence of the ghrelin system has been demonstrated in many animal classes through biochemical and molecular biological strategies as well as through genome projects. Our work, focused on identifying the ghrelin receptor and its ligand ghrelin in laboratory animals, particularly nonmammalian vertebrates, has provided new insights into the molecular evolution of the ghrelin receptor. In mammals, it is assumed that the ghrelin receptor evolution is in line with the plate tectonics theory. In contrast, the evolution of the ghrelin receptor in nonmammalian vertebrates differs from that of mammals: multiplicity of the ghrelin receptor isoforms is observed in nonmammalian vertebrates only. This multiplicity is due to genome duplication and polyploidization events that particularly occurred in Teleostei. Furthermore, it is likely that the evolution of the ghrelin receptor is distinct from that of its ligand, ghrelin, because only one ghrelin isoform has been detected in all species examined so far. In this review, we summarize current knowledge related to the molecular evolution of the ghrelin receptor in mammalian and nonmammalian vertebrates. © 2014 Society for Endocrinology.

  18. 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…

  19. 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…

  20. 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

  1. 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.

  2. 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

  3. 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

  4. [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.

  5. Climbing the social ladder: the molecular evolution of sociality.

    PubMed

    Rehan, Sandra M; Toth, Amy L

    2015-07-01

    Genomic tools are allowing us to dissect the roles of genes and genetic architecture in social evolution, and eusocial insects are excellent models. Numerous hypotheses for molecular evolution of eusociality have been proposed, ranging from regulatory shifts in 'old' genes to rapid evolution of 'new' genes. A broad model to explain this major transition in evolution has been lacking. We provide a synthetic framework centered on the idea that different evolutionary processes dominate during different transitional stages, beginning with changes in gene regulation and culminating in novel genes later on. By considering multiple mechanisms as we 'climb the social ladder', we can test whether the transitions from solitary to simple sociality to complex sociality represent incremental changes or genetic revolutions. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Compensatory vs. pseudocompensatory evolution in molecular and developmental interactions.

    PubMed

    Haag, Eric S

    2007-01-01

    The evolution of molecules, developmental circuits, and new species are all characterized by the accumulation of incompatibilities between ancestors and descendants. When specific interactions between components are necessary at any of these levels, this requires compensatory coevolution. Theoretical treatments of compensatory evolution that only consider the endpoints predict that it should be rare because intermediate states are deleterious. However, empirical data suggest that compensatory evolution is common at all levels of molecular interaction. A general solution to this paradox is provided by plausible neutral or nearly neutral intermediates that possess informational redundancy. These intermediates provide an evolutionary path between coadapted allelic combinations. Although they allow incompatible end points to evolve, at no point was a deleterious mutation ever in need of compensation. As a result, what appears to be compensatory evolution may often actually be "pseudocompensatory." Both theoretical and empirical studies indicate that pseudocompensation can speed the evolution of intergenic incompatibility, especially when driven by adaptation. However, under strong stabilizing selection the rate of pseudocompensatory evolution is still significant. Important examples of this process at work discussed here include the evolution of rRNA secondary structures, intra- and inter-protein interactions, and developmental genetic pathways. Future empirical work in this area should focus on comparing the details of intra- and intergenic interactions in closely related organisms.

  7. 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

  8. 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.

  9. Medicine in the 21st century: towards a Darwinian medical epistemology.

    PubMed

    Román-Franco, Angel A

    2009-12-01

    In this review we reflect upon the new science of Darwinian medicine. It is a tenet of modern biology that evolutionary theory as proposed by Charles Darwin and further refined via the new synthesis is the common thread that ties all of biological inquiry into a coherent whole. This review aims at making clear how evolution by natural selection is relevant to medicine. A set of pertinent examples linking Homo sapiens sapiens' present disease conditions to its evolution during the Late Pleistocene and Holocene epochs are discussed. The review concludes with observations as to the epistemological value of evolutionary theory as a heuristic tool for articulating a medical paradigm in accord with modern biology.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. Molecular mechanisms of dominance evolution in Müllerian mimicry.

    PubMed

    Llaurens, V; Joron, M; Billiard, S

    2015-12-01

    Natural selection acting on dominance between adaptive alleles at polymorphic loci can be sufficiently strong for dominance to evolve. However, the molecular mechanisms underlying such evolution are generally unknown. Here, using Müllerian mimicry as a case-study for adaptive morphological variation, we present a theoretical analysis of the invasion of dominance modifiers altering gene expression through different molecular mechanisms. Toxic species involved in Müllerian mimicry exhibit warning coloration, and converge morphologically with other toxic species of the local community, due to positive frequency-dependent selection acting on these colorations. Polymorphism in warning coloration may be maintained by migration-selection balance with fine scale spatial heterogeneity. We modeled a dominance modifier locus altering the expression of the warning coloration locus, targeting one or several alleles, acting in cis or trans, and either enhancing or repressing expression. We confirmed that dominance could evolve when balanced polymorphism was maintained at the color locus. Dominance evolution could result from modifiers enhancing one allele specifically, irrespective of their linkage with the targeted locus. Nonspecific enhancers could also persist in populations, at frequencies tightly depending on their linkage with the targeted locus. Altogether, our results identify which mechanisms of expression alteration could lead to dominance evolution in polymorphic mimicry. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  16. 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. Copyright © 2010 Elsevier Ltd. All rights reserved.

  17. 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.

  18. 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.

  19. 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

  20. Widespread convergence in toxin resistance by predictable molecular evolution.

    PubMed

    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

    2015-09-22

    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.

  1. 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.

  2. Molecular masers as tracers of early stellar evolution

    NASA Astrophysics Data System (ADS)

    Strel'Nitskii, V. S.

    The discovery, observation, and interpretation of molecular masers in regions of active star formation are discussed. OH masers noted in these regions are the product of the disintegration of dense molecular envelopes surrounding compact H-II regions of young OB stars, and they typically have densities of about 10 to the 6th/cu cm and temperatures of about 100 K. H2O masers are connected with still earlier stages of stellar evolution, and are located closer to their parent stars than the OH sources. Strong CH3OH 2.5-cm masers are closely associated with OH masers.

  3. Darwinian selection on a selfing locus.

    PubMed

    Shimizu, Kentaro K; Cork, Jennifer M; Caicedo, Ana L; Mays, Charlotte A; Moore, Richard C; Olsen, Kenneth M; Ruzsa, Stephanie; Coop, Graham; Bustamante, Carlos D; Awadalla, Philip; Purugganan, Michael D

    2004-12-17

    The shift to self-pollination is one of the most prevalent evolutionary transitions in flowering plants. In the selfing plant Arabidopsis thaliana, pseudogenes at the SCR and SRK self-incompatibility loci are believed to underlie the evolution of self-fertilization. Positive directional selection has driven the evolutionary fixation of pseudogene alleles of SCR, leading to substantially reduced nucleotide variation. Coalescent simulations indicate that this adaptive event may have occurred very recently and is possibly associated with the post-Pleistocene expansion of A. thaliana from glacial refugia. This suggests that ancillary morphological innovations associated with self-pollination can evolve rapidly after the inactivation of the self-incompatibility response.

  4. Biogeographic, molecular evolution, and diversification patterns in Neotropical plants

    NASA Astrophysics Data System (ADS)

    Smith, S. A.; Dick, C. W.

    2014-12-01

    Neotropical plants demonstrate a phenomenal range of ecological and morphological diversity. We will explore the phylogenetic and biogeographic patterns of a group of Neotropical plants and how these patterns relate to the geological history of the area. This includes the timing and location of biological exchange between areas. Neotropical plants also demonstrate repeated examples of rapid speciation and diversification. We will examine these evolutionary patterns and how they relate to molecular evolution.

  5. [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.

  6. Multiple explanations in Darwinian evolutionary theory.

    PubMed

    Bock, Walter J

    2010-03-01

    Variational evolutionary theory as advocated by Darwin is not a single theory, but a bundle of related but independent theories, namely: (a) variational evolution; (b) gradualism rather than large leaps; (c) processes of phyletic evolution and of speciation; (d) causes for the formation of varying individuals in populations and for the action of selective agents; and (e) all organisms evolved from a common ancestor. The first four are nomological-deductive explanations and the fifth is historical-narrative. Therefore evolutionary theory must be divided into nomological and historical theories which are both testable against objective empirical observations. To be scientific, historical evolutionary theories must be based on well corroborated nomological theories, both evolutionary and functional. Nomological and general historical evolutionary theories are well tested and must be considered as strongly corroborated scientific theories. Opponents of evolutionary theory are concerned only with historical evolutionary theories, having little interest in nomological theory. Yet given a well corroborated nomological evolutionary theory, historical evolutionary theories follow automatically. If understood correctly, both forms of evolutionary theories stand on their own as corroborated scientific theories and should not be labeled as facts.

  7. 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

  8. 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

  9. Molecular Evolution of the Testis TAFs of Drosophila

    PubMed Central

    Davis, Jerel C.; Lenkov, Kapa; Bolival, Benjamin; Fuller, Margaret T.; Petrov, Dmitri A.

    2009-01-01

    The basal transcription machinery is responsible for initiating transcription at core promoters. During metazoan evolution, its components have expanded in number and diversified to increase the complexity of transcriptional regulation in tissues and developmental stages. To explore the evolutionary events and forces underlying this diversification, we analyzed the evolution of the Drosophila testis TAFs (TBP-associated factors), paralogs of TAFs from the basal transcription factor TFIID that are essential for normal transcription during spermatogenesis of a large set of specific genes involved in terminal differentiation of male gametes. There are five testis-specific TAFs in Drosophila, each expressed only in primary spermatocytes and each a paralog of a different generally expressed TFIID subunit. An examination of the presence of paralogs across taxa as well as molecular clock dating indicates that all five testis TAFs likely arose within a span of ∼38 My 63–250 Ma by independent duplication events from their generally expressed paralogs. Furthermore, the evolution of the testis TAFs has been rapid, with apparent further accelerations in multiple Drosophila lineages. Analysis of between-species divergence and intraspecies polymorphism indicates that the major forces of evolution on these genes have been reduced purifying selection, pervasive positive selection, and coevolution. Other genes that exhibit similar patterns of evolution in the Drosophila lineages are also characterized by enriched expression in the testis, suggesting that the pervasive positive selection acting on the tTAFs is likely to be related to their expression in the testis. PMID:19244474

  10. 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

  11. Social molecular pathways and the evolution of bee societies

    PubMed Central

    Bloch, Guy; Grozinger, Christina M.

    2011-01-01

    Bees provide an excellent model with which to study the neuronal and molecular modifications associated with the evolution of sociality because relatively closely related species differ profoundly in social behaviour, from solitary to highly social. The recent development of powerful genomic tools and resources has set the stage for studying the social behaviour of bees in molecular terms. We review ‘ground plan’ and ‘genetic toolkit’ models which hypothesize that discrete pathways or sets of genes that regulate fundamental behavioural and physiological processes in solitary species have been co-opted to regulate complex social behaviours in social species. We further develop these models and propose that these conserved pathways and genes may be incorporated into ‘social pathways’, which consist of relatively independent modules involved in social signal detection, integration and processing within the nervous and endocrine systems, and subsequent behavioural outputs. Modifications within modules or in their connections result in the evolution of novel behavioural patterns. We describe how the evolution of pheromonal regulation of social pathways may lead to the expression of behaviour under new social contexts, and review plasticity in circadian rhythms as an example for a social pathway with a modular structure. PMID:21690132

  12. Molecular evolution of haemagglutinin (H) gene in measles virus

    PubMed Central

    Kimura, Hirokazu; Saitoh, Mika; Kobayashi, Miho; Ishii, Haruyuki; Saraya, Takeshi; Kurai, Daisuke; Tsukagoshi, Hiroyuki; Shirabe, Komei; Nishina, Atsuyoshi; Kozawa, Kunihisa; Kuroda, Makoto; Takeuchi, Fumihiko; Sekizuka, Tsuyoshi; Minakami, Hisanori; Ryo, Akihide; Takeda, Makoto

    2015-01-01

    We studied the molecular evolution of the haemagglutinin (H) gene (full length) in all genotypes (24 genotypes, 297 strains) of measles virus (MeV). The gene’s evolutionary timescale was estimated by the Bayesian Markov chain Monte Carlo (MCMC) method. We also analysed positive selection sites. The MCMC tree indicated that the MeV H gene diverged from the rinderpest virus (same genus) about 250 years ago and that 24 MeV genotypes formed 3 lineages dating back to a 1915 ancestor (95% highest posterior density [HPD] 1882–1941) with relatively rapid evolution (mean rate: 9.02 × 10−4 substitutions/site/year). The 3 lineages diverged in 1915 (lineage 1, 95% HPD 1882–1941), 1954 (lineage 2, 95% HPD 1937–1969), and 1940 (lineage 3, 95% HPD 1927–1952). These 24 genotypes may have diverged and emerged between the 1940s and 1990s. Selective pressure analysis identified many negative selection sites on the H protein but only a few positive selection sites, suggesting strongly operated structural and/or functional constraint of changes on the H protein. Based on the molecular evolution of H gene, an ancestor MeV of the 24 genotypes emerged about 100 years ago and the structure of H protein has been well conserved. PMID:26130388

  13. 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.

  14. 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.

  15. Carbonic anhydrase and the molecular evolution of C4 photosynthesis.

    PubMed

    Ludwig, Martha

    2012-01-01

    C(4) photosynthesis, a biochemical CO(2)-concentrating mechanism (CCM), evolved more than 60 times within the angiosperms from C(3) ancestors. The genus Flaveria, which contains species demonstrating C(3), C(3)-C(4), C(4)-like or C(4) photosynthesis, is a model for examining the molecular evolution of the C(4) pathway. Work with carbonic anhydrase (CA), and C(3) and C(4) Flaveria congeners has added significantly to the understanding of this process. The C(4) form of CA3, a β-CA, which catalyses the first reaction in the C(4) pathway by hydrating atmospheric CO(2) to bicarbonate in the cytosol of mesophyll cells (mcs), evolved from a chloroplastic C(3) ancestor. The molecular modifications to the ancestral CA3 gene included the loss of the sequence encoding the chloroplast transit peptide, and mutations in regulatory regions that resulted in high levels of expression in the C(4) mesophyll. Analyses of the CA3 proteins and regulatory elements from Flaveria photosynthetic intermediates indicated C(4) biochemistry very likely evolved in a specific, stepwise manner in this genus. The details of the mechanisms involved in the molecular evolution of other C(4) plant β-CAs are unknown; however, comparative genetics indicate gene duplication and neofunctionalization played significant roles as they did in Flaveria. © 2011 Blackwell Publishing Ltd.

  16. 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.

  17. 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.

  18. A Tale of Two Crocoducks: Creationist Misuses of Molecular Evolution

    NASA Astrophysics Data System (ADS)

    Hofmann, James R.

    2014-10-01

    Although some creationist objections to evolutionary biology are simplistic and thus are easily refuted, when more technical arguments become widespread it is important for science educators to explain the relevant science in a straightforward manner. An interesting case study is provided by misguided allegations about how cytochrome c data pertain to molecular evolution. The most common of these misrepresentations bears a striking similarity to a particularly glaring misunderstanding of what should be expected of a transitional form in a fossil sequence. Although evangelist Kirk Cameron's ridiculous injunction of a hypothetical `crocoduck' as an example of a potential transitional form is frequently invoked to illustrate the ignorance of many critics of evolutionary science, a strikingly analogous argument was applied to cytochrome c data by biochemist Michael Denton in 1985. The details of this analogy are worth exploring to clarify the fallacy of the widely circulated molecular argument.

  19. Sexual selection and the molecular evolution of ADAM proteins.

    PubMed

    Finn, Scott; Civetta, Alberto

    2010-09-01

    Rapid evolution has been identified for many reproductive genes and recent studies have combined phylogenetic tests and information on species mating systems to test sexual selection. Here we examined the molecular evolution of the ADAM gene family, a diverse group of 35 proteins capable of adhesion to and cleavage of other proteins, using sequence data from 25 mammalian genes. Out of the 25 genes analyzed, all those expressed in male reproductive tissue showed evidence of positive selection. Positively selected amino acids within the protein adhesion domain were only found in sperm surface ADAM proteins (ADAMs 1, 2, 3, 4, and 32) suggesting selection driven by male x female interactions. We tested heterogeneity in rates of evolution of the adhesion domain of ADAM proteins by using sequence data from Hominidae and macaques. The use of the branch and branch-site models (PAML) showed evidence of higher d (N)/d (S) and/or positive selection linked to branches experiencing high postmating selective pressures (chimpanzee and macaque) for Adams 2, 18, and 23. Moreover, we found consistent higher proportion of nonsynonymous relative to synonymous and noncoding sequence substitutions in chimpanzee and/or macaque only for Adams 2, 18, and 23. Our results suggest that lineage-specific sexual selection bouts might have driven the evolution of the adhesion sperm protein surface domains of ADAMs 2 and 18 in primates. Adams 2 and 18 are localized in chromosome 8 of primates and adjacent to each other, so their evolution might have also been influenced by their common genome localization.

  20. New evidence for the Darwinian hypothesis of heterostyly: breeding systems and pollinators in Narcissus sect. Apodanthi.

    PubMed

    Pérez-Barrales, Rocio; Vargas, Pablo; Arroyo, Juan

    2006-01-01

    Here we analysed the role played by breeding systems and pollinators in the evolution of heterostyly by testing whether evolution towards heterostyly is associated with style polymorphism and changes in pollinator proficiency or breeding system variation (Darwinian hypothesis). We studied pollinators, pollen-transfer efficiency, and incompatibility systems in all seven species of Narcissus sect. Apodanthi for which we also obtained chloroplast DNA (cpDNA) sequences from three spacers to infer phylogenetic relationships. Five species are self-incompatible and within-morph cross-compatible. Heterostylous (Narcissus albimarginatus) and style-dimorphic (Narcissus cuatrecasasii) species that have a high degree of reciprocity in stigma and anther height are primarily pollinated by solitary bees. The style-monomorphic species (Narcissus watieri) and the style-dimorphic species with the least stigma-anther reciprocity (Narcissus rupicola) are both self-compatible and pollinated by butterflies, moths and hover flies. Phylogenetic reconstruction of character transitions indicates that the shift from style dimorphism to distyly is associated with a shift to bee pollination. Pollination by lepidopterans and flies is associated with stable style dimorphism and monomorphism. Evolution and maintenance of style polymorphisms in this group of species are independent of incompatibility systems. Taken together, our results strongly support the pollinator-based model for evolution of heterostyly and style length polymorphisms in general.

  1. Toward the Darwinian transition: Switching between distributed and speciated states in a simple model of early life

    NASA Astrophysics Data System (ADS)

    Arnoldt, Hinrich; Strogatz, Steven H.; Timme, Marc

    2015-11-01

    It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer (HGT). At a certain point, however, life made a transition to the modern era of individuality and vertical descent. Here we present a minimal model for stochastic processes potentially contributing to this hypothesized "Darwinian transition." The model suggests that HGT-dominated dynamics may have been intermittently interrupted by selection-driven processes during which genotypes became fitter and decreased their inclination toward HGT. Stochastic switching in the population dynamics with three-point (hypernetwork) interactions may have destabilized the HGT-dominated collective state and essentially contributed to the emergence of vertical descent and the first well-defined species in early evolution. A systematic nonlinear analysis of the stochastic model dynamics covering key features of evolutionary processes (such as selection, mutation, drift and HGT) supports this view. Our findings thus suggest a viable direction out of early collective evolution, potentially enabling the start of individuality and vertical Darwinian evolution.

  2. 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. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. Molecular origins of rapid and continuous morphological evolution.

    PubMed

    Fondon, John W; Garner, Harold R

    2004-12-28

    Mutations in cis-regulatory sequences have been implicated as being the predominant source of variation in morphological evolution. We offer a hypothesis that gene-associated tandem repeat expansions and contractions are a major source of phenotypic variation in evolution. Here, we describe a comparative genomic study of repetitive elements in developmental genes of 92 breeds of dogs. We find evidence for selection for divergence at coding repeat loci in the form of both elevated purity and extensive length polymorphism among different breeds. Variations in the number of repeats in the coding regions of the Alx-4 (aristaless-like 4) and Runx-2 (runt-related transcription factor 2) genes were quantitatively associated with significant differences in limb and skull morphology. We identified similar repeat length variation in the coding repeats of Runx-2, Twist, and Dlx-2 in several other species. The high frequency and incremental effects of repeat length mutations provide molecular explanations for swift, yet topologically conservative morphological evolution.

  9. [Molecular evidence of regression in evolution of metazoa].

    PubMed

    Aleshin, V V; Petrov, N B

    2002-01-01

    Molecular data permit to construct phylogenetic trees independently of morphological characters. It allows to consider their evolution without the frames of a priori hypothesis of regularities of morphological evolution and independently of palaeontological data. Cladistic analysis of elements of secondary structure of varible areas V7 and V2 in 18S rRNA with different Protozoa as "external" groups shows that Bilateria + Cnidaria are monophyletic, Ctenophora and Porifera are early derivatives of Metazoa, Trichoplax (Placozoa) is a form related to Cnidaria, while Rhombozoa, Orthonectida and Myxozoa were branched within Bilateria. Morphological reduction with losses of any organs and tissues took place many times in early evolution of Metazoa and Bilateria not only in parasitic species. It occurred both at early and late stages of embryonic development and differentiation. Two alternative scenario of morphological degeneration in Trichoplax and the way of their testing are suggested. The similarity of Ctenophora and Calcarea is discussed. Meridional or oblique position of the third cleavage furrow of ovule can be considered as an evidence of their origin from common ancestor.

  10. 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. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. 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

  12. 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

  13. 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.

  14. 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. Published by Elsevier B.V.

  15. The predictability of molecular evolution during functional innovation.

    PubMed

    Blank, Diana; Wolf, Luise; Ackermann, Martin; Silander, Olin K

    2014-02-25

    Determining the molecular changes that give rise to functional innovations is a major unresolved problem in biology. The paucity of examples has served as a significant hindrance in furthering our understanding of this process. Here we used experimental evolution with the bacterium Escherichia coli to quantify the molecular changes underlying functional innovation in 68 independent instances ranging over 22 different metabolic functions. Using whole-genome sequencing, we show that the relative contribution of regulatory and structural mutations depends on the cellular context of the metabolic function. In addition, we find that regulatory mutations affect genes that act in pathways relevant to the novel function, whereas structural mutations affect genes that act in unrelated pathways. Finally, we use population genetic modeling to show that the relative contributions of regulatory and structural mutations during functional innovation may be affected by population size. These results provide a predictive framework for the molecular basis of evolutionary innovation, which is essential for anticipating future evolutionary trajectories in the face of rapid environmental change.

  16. The consuming instinct. What Darwinian consumption reveals about human nature.

    PubMed

    Saad, Gad

    2013-01-01

    Editor's note: In this engaging talk given last February on a particularly cold and blustery day at Texas Tech University, Professor Gad Saad of Concordia University discusses his work in the area of evolutionary consumption. In making the case for understanding consumerism from a Darwinian perspective, Saad addresses several key tenets from his books The Consuming Instinct (1) and The Evolutionary Bases of Consumption. (2) In particular, Saad argues that: (1) many consumption acts can be mapped onto four key Darwinian modules (survival, mating, kin selection, and reciprocal altruism); and, (2) cultural products such as song lyrics and movie plotlines are fossils of the human mind that highlight a shared, biologically based human nature. In this wide-ranging inquiry, Saad summarizes several of his other empirical works, including the effects of conspicuous consumption on men's testosterone levels (3) and how the ovulatory cycle in the human female influences consumption. (4) Overall, Professor Saad contends that an infusion of evolutionary and biologically based perspectives into the discipline of consumer behavior and related government regulatory policies yields myriad benefits, notably greater consilience, more effective practices, an ethos of interdisciplinarity, and methodological pluralism.

  17. Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

    PubMed Central

    2017-01-01

    Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. PMID:28637852

  18. Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.

    PubMed

    Warnock, Rachel C M; Yang, Ziheng; Donoghue, Philip C J

    2017-06-28

    Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. © 2017 The Authors.

  19. 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.

  20. Molecular evolution of mitochondrial introns in the liverwort Marchantia polymorpha.

    PubMed

    Ohyama, Kanji; Takemura, Miho

    2008-01-01

    We here describe in detail the characterization and molecular evolution of group II introns in the mitochondrial genome of the liverwort Marchantia polymorpha. We find that 18 introns of the 25 group II introns can be assigned by their similarities to six clusters, indicating an intra-genomic propagation of one ancestral intron each into the respective clusters in the liverwort mitochondrial genome. Interestingly, the intra-genomic propagation of some of these introns occurred only after the evolutionary separation of the bryophytes from the other clades of plants. Finally we report that the maturase-like sequences in the liverwort group II introns have further evolved by horizontal and independent transposition and substitution by analogous sequences from other fungal introns.

  1. 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.

  2. 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.

  3. Bio++: efficient extensible libraries and tools for computational molecular evolution.

    PubMed

    Guéguen, Laurent; Gaillard, Sylvain; Boussau, Bastien; Gouy, Manolo; Groussin, Mathieu; Rochette, Nicolas C; Bigot, Thomas; Fournier, David; Pouyet, Fanny; Cahais, Vincent; Bernard, Aurélien; Scornavacca, Céline; Nabholz, Benoît; Haudry, Annabelle; Dachary, Loïc; Galtier, Nicolas; Belkhir, Khalid; Dutheil, Julien Y

    2013-08-01

    Efficient algorithms and programs for the analysis of the ever-growing amount of biological sequence data are strongly needed in the genomics era. The pace at which new data and methodologies are generated calls for the use of pre-existing, optimized-yet extensible-code, typically distributed as libraries or packages. This motivated the Bio++ project, aiming at developing a set of C++ libraries for sequence analysis, phylogenetics, population genetics, and molecular evolution. The main attractiveness of Bio++ is the extensibility and reusability of its components through its object-oriented design, without compromising the computer-efficiency of the underlying methods. We present here the second major release of the libraries, which provides an extended set of classes and methods. These extensions notably provide built-in access to sequence databases and new data structures for handling and manipulating sequences from the omics era, such as multiple genome alignments and sequencing reads libraries. More complex models of sequence evolution, such as mixture models and generic n-tuples alphabets, are also included.

  4. 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.

  5. 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.

  6. 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.

  7. Molecular cytogenetic and genomic insights into chromosomal evolution

    PubMed Central

    Ruiz-Herrera, A; Farré, M; Robinson, T J

    2012-01-01

    This review summarizes aspects of the extensive literature on the patterns and processes underpinning chromosomal evolution in vertebrates and especially placental mammals. It highlights the growing synergy between molecular cytogenetics and comparative genomics, particularly with respect to fully or partially sequenced genomes, and provides novel insights into changes in chromosome number and structure across deep division of the vertebrate tree of life. The examination of basal numbers in the deeper branches of the vertebrate tree suggest a haploid (n) chromosome number of 10–13 in an ancestral vertebrate, with modest increases in tetrapods and amniotes most probably by chromosomal fissioning. Information drawn largely from cross-species chromosome painting in the data-dense Placentalia permits the confident reconstruction of an ancestral karyotype comprising n=23 chromosomes that is similarly retained in Boreoeutheria. Using in silico genome-wide scans that include the newly released frog genome we show that of the nine ancient syntenies detected in conserved karyotypes of extant placentals (thought likely to reflect the structure of ancestral chromosomes), the human syntenic segmental associations 3p/21, 4pq/8p, 7a/16p, 14/15, 12qt/22q and 12pq/22qt predate the divergence of tetrapods. These findings underscore the enhanced quality of ancestral reconstructions based on the integrative molecular cytogenetic and comparative genomic approaches that collectively highlight a pattern of conserved syntenic associations that extends back ∼360 million years ago. PMID:22108627

  8. 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

  9. 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.

  10. 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

  11. 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

  12. Molecular evolution of the polyamine oxidase gene family in Metazoa.

    PubMed

    Polticelli, Fabio; Salvi, Daniele; Mariottini, Paolo; Amendola, Roberto; Cervelli, Manuela

    2012-06-20

    the SMOs and APAOs from vertebrates. The two vertebrate monophyletic clades clustered strictly mirroring the organismal phylogeny of fishes, amphibians, reptiles, birds, and mammals. Evidences from comparative genomic analysis, structural evolution and functional divergence in a phylogenetic framework across Metazoa suggested an evolutionary scenario where the ancestor PAO coding sequence, present in invertebrates as an orthologous gene, has been duplicated in the vertebrate branch to originate the paralogous SMO and APAO genes. A further genome evolution event concerns the SMO gene of placental, but not marsupial and monotremate, mammals which increased its functional variation following an alternative splicing (AS) mechanism. In this study the explicit integration in a phylogenomic framework of phylogenetic tree construction, structure prediction, and biochemical function data/prediction, allowed inferring the molecular evolutionary history of the PAO gene family and to disambiguate paralogous genes related by duplication event (SMO and APAO) and orthologous genes related by speciation events (PAOs, SMOs/APAOs). Further, while in vertebrates experimental data corroborate SMO and APAO molecular function predictions, in invertebrates the finding of a supported phylogenetic clusters of insect PAOs and the co-occurrence of two PAO variants in the amphioxus urgently claim the need for future structure-function studies.

  13. Molecular evolution of the polyamine oxidase gene family in Metazoa

    PubMed Central

    2012-01-01

    , respectively, all the SMOs and APAOs from vertebrates. The two vertebrate monophyletic clades clustered strictly mirroring the organismal phylogeny of fishes, amphibians, reptiles, birds, and mammals. Evidences from comparative genomic analysis, structural evolution and functional divergence in a phylogenetic framework across Metazoa suggested an evolutionary scenario where the ancestor PAO coding sequence, present in invertebrates as an orthologous gene, has been duplicated in the vertebrate branch to originate the paralogous SMO and APAO genes. A further genome evolution event concerns the SMO gene of placental, but not marsupial and monotremate, mammals which increased its functional variation following an alternative splicing (AS) mechanism. Conclusions In this study the explicit integration in a phylogenomic framework of phylogenetic tree construction, structure prediction, and biochemical function data/prediction, allowed inferring the molecular evolutionary history of the PAO gene family and to disambiguate paralogous genes related by duplication event (SMO and APAO) and orthologous genes related by speciation events (PAOs, SMOs/APAOs). Further, while in vertebrates experimental data corroborate SMO and APAO molecular function predictions, in invertebrates the finding of a supported phylogenetic clusters of insect PAOs and the co-occurrence of two PAO variants in the amphioxus urgently claim the need for future structure-function studies. PMID:22716069

  14. 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

  15. 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.

  16. 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.

  17. Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda (Crustacea).

    PubMed

    Tinn, Oive; Oakley, Todd H

    2008-07-01

    Dating evolutionary origins of taxa is essential for understanding rates and timing of evolutionary events, often inciting intense debate when molecular estimates differ from first fossil appearances. For numerous reasons, ostracods present a challenging case study of rates of evolution and congruence of fossil and molecular divergence time estimates. On the one hand, ostracods have one of the densest fossil records of any metazoan group. However, taxonomy of fossil ostracods is controversial, owing at least in part to homoplasy of carapaces, the most commonly fossilized part. In addition, rates of evolution are variable in ostracods. Here, we report evidence of extreme variation in the rate of molecular evolution in different ostracod groups. This rate is significantly elevated in Halocyprid ostracods, a widespread planktonic group, consistent with previous observations that planktonic groups show elevated rates of molecular evolution. At the same time, the rate of molecular evolution is slow in the lineage leading to Manawa staceyi, a relict species that we estimate diverged approximately 500 million years ago from its closest known living relative. We also report multiple cases of significant incongruence between fossil and molecular estimates of divergence times in Ostracoda. Although relaxed clock methods improve the congruence of fossil and molecular divergence estimates over strict clock models, incongruence is present regardless of method. We hypothesize that this observed incongruence is driven largely by problems with taxonomy of fossil Ostracoda. Our results illustrate the difficulty in consistently estimating lineage divergence times, even in the presence of a voluminous fossil record.

  18. Molecular evolution and functional divergence of Vibrio cholerae.

    PubMed

    Das, Bhabatosh; Pazhani, Gururaja P; Sarkar, Anirban; Mukhopadhyay, Asish K; Nair, G Balakrish; Ramamurthy, Thandavarayan

    2016-10-01

    The purpose of this review is to synopsize and highlight the recent subtle genetic changes in cholera causing toxigenic Vibrio cholerae with special reference to their virulence, integrating and conjugative elements and toxin-antitoxin systems. It is not intended to cover issues on the whole genome sequence and epidemiology of cholera. Analyses have been made using major published works on genetic changes associated with potential virulence, integrating and conjugative elements and toxin-antitoxin systems of toxigenic V. cholerae. During the course of evolution, V. cholerae strains show evidence of genetic selection for the expression of additional virulence, better survival in the environment, colonization ability and antimicrobial resistance. Some of the critical modifications that occurred at the molecular level include CTXϕ genome, cholera toxin B-subunit, integrating and conjugative elements and toxin-antitoxin systems. Frequent changes in the genome of V. cholerae appear to be an ongoing dynamic process that is assisting the pathogen to subtly change during or after epidemics of cholera. Cholera is a reemerging public health problem. Continued basic research is important to understand the changing dynamics of bacterial virulence, survival strategies and disease pathogenesis for efficient therapeutic intervention and to abort transmission of the disease.

  19. Molecular evolution of the EGF-CFC protein family.

    PubMed

    Ravisankar, V; Singh, Taran P; Manoj, Narayanan

    2011-08-15

    The epidermal growth factor-Cripto-1/FRL-1/Cryptic (EGF-CFC) proteins, characterized by the highly conserved EGF and CFC domains, are extracellular membrane associated growth factor-like glycoproteins. These proteins are essential components of the Nodal signaling pathway during early vertebrate embryogenesis. Homologs of the EGF-CFC family have also been implicated in tumorigenesis in humans. Yet, little is known about the mode of molecular evolution in this family. Here we investigate the origin, extent of conservation and evolutionary relationships of EGF-CFC proteins across the metazoa. The results suggest that the first appearance of the EGF-CFC gene occurred in the ancestor of the deuterostomes. Phylogenetic analysis supports the classification of the family into distinct subfamilies that appear to have evolved through lineage-specific duplication and divergence. Site-specific analyses of evolutionary rate shifts between the two major mammalian paralogous subfamilies, Cripto and Cryptic, reveal critical amino acid sites that may account for the observed functional divergence. Furthermore, estimates of functional divergence suggest that rapid change of evolutionary rates at sites located mainly in the CFC domain may contribute towards distinct functional properties of the two paralogs. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. 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.

  1. Microstructure evolution of polycrystalline silicon by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Chen, Xiao; Ding, Jianning; Jiang, Cunhua; Liu, Zunfeng; Yuan, Ningyi

    2017-06-01

    Polycrystalline silicon is the dominant material in solar cells and plays an important role in photovoltaic industry. It is important for not only the conventional production of silicon ingots but also the direct growth of silicon wafers to control crystallization for obtaining the desired polycrystalline silicon. To the best of our knowledge, few studies have systematically reported about the effects of crystalline planes on the solidification behavior of liquid silicon and the analysis of the microstructural features of the polysilicon structure. In this study, molecular dynamics simulations were employed to investigate the solidification and microstructure evolution of polysilicon, with focus on the effects of the seed distribution and cooling rate on the growth of polycrystalline silicon. The (110), (111), and (112) planes were extruded by the (100) plane and formed the inclusion shape. The crystallization of silicon consisted of diamond-type structures is relatively high at a low cooling rate. The simulations provide substantial information regarding microstructures and serve as guidance for the growth of polycrystalline silicon.

  2. Molecular evolution of neuropeptides in the genus Drosophila

    PubMed Central

    Wegener, Christian; Gorbashov, Anton

    2008-01-01

    Background Neuropeptides comprise the most diverse group of neuronal signaling molecules. They often occur as multiple sequence-related copies within single precursors (the prepropeptides). These multiple sequence-related copies have not arisen by gene duplication, and it is debated whether they are mutually redundant or serve specific functions. The fully sequenced genomes of 12 Drosophila species provide a unique opportunity to study the molecular evolution of neuropeptides. Results We data-mined the 12 Drosophila genomes for homologs of neuropeptide genes identified in Drosophila melanogaster. We then predicted peptide precursors and the neuropeptidome, and biochemically identified about half of the predicted peptides by direct mass spectrometric profiling of neuroendocrine tissue in four species covering main phylogenetic lines of Drosophila. We found that all species have an identical neuropeptidome and peptide hormone complement. Calculation of amino acid distances showed that ortholog peptide copies are highly sequence-conserved between species, whereas the observed sequence variability between peptide copies within single precursors must have occurred prior to the divergence of the Drosophila species. Conclusion We provide a first genomic and chemical characterization of fruit fly neuropeptides outside D. melanogaster. Our results suggest that neuropeptides including multiple peptide copies are under stabilizing selection, which suggests that multiple peptide copies are functionally important and not dispensable. The last common ancestor of Drosophila obviously had a set of neuropeptides and peptide hormones identical to that of modern fruit flies. This is remarkable, since drosophilid flies have adapted to very different environments. PMID:18717992

  3. Molecular evolution of shark and other vertebrate DNases I.

    PubMed

    Yasuda, Toshihiro; Iida, Reiko; Ueki, Misuzu; Kominato, Yoshihiko; Nakajima, Tamiko; Takeshita, Haruo; Kobayashi, Takanori; Kishi, Koichiro

    2004-11-01

    We purified pancreatic deoxyribonuclease I (DNase I) from the shark Heterodontus japonicus using three-step column chromatography. Although its enzymatic properties resembled those of other vertebrate DNases I, shark DNase I was unique in being a basic protein. Full-length cDNAs encoding the DNases I of two shark species, H. japonicus and Triakis scyllia, were constructed from their total pancreatic RNAs using RACE. Nucleotide sequence analyses revealed two structural alterations unique to shark enzymes: substitution of two Cys residues at positions 101 and 104 (which are well conserved in all other vertebrate DNases I) and insertion of an additional Thr or Asn residue into an essential Ca(2+)-binding site. Site-directed mutagenesis of shark DNase I indicated that both of these alterations reduced the stability of the enzyme. When the signal sequence region of human DNase I (which has a high alpha-helical structure content) was replaced with its amphibian, fish and shark counterparts (which have low alpha-helical structure contents), the activity expressed by the chimeric mutant constructs in transfected mammalian cells was approximately half that of the wild-type enzyme. In contrast, substitution of the human signal sequence region into the amphibian, fish and shark enzymes produced higher activity compared with the wild-types. The vertebrate DNase I family may have acquired high stability and effective expression of the enzyme protein through structural alterations in both the mature protein and its signal sequence regions during molecular evolution.

  4. Molecular Evolution of the Sorghum Maturity Gene Ma3

    PubMed Central

    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. PMID:25961888

  5. 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

  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. 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.

  8. 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.

  9. Cognitive phylogenies, the Darwinian logic of descent, and the inadequacy of cladistic thinking.

    PubMed

    Theofanopoulou, Constantina; Boeckx, Cedric

    2015-01-01

    There has been a reappraisal of phylogenetic issues in cognitive science, as reconstructing cognitive phylogenies has been considered a key for unveiling the cognitive novelties that set the stage for what makes humans special. In our opinion, the studies made until now have approached cognitive phylogenies in a non-optimal way, and we wish to both highlight their problems, drawing on recent considerations in philosophy of biology. The inadequacy of current visions on cognitive phylogenies stems from the influence of the traditional "linear cladograms," according to which every seemingly new or more sophisticated feature of a cognitive mechanism, viewed as a novelty, is represented as a node on top of the old and shared elements. We claim that this kind of cladograms does not succeed in depicting the complexity with which traits are distributed across species and, furthermore, that the labels of the nodes of these traditional representational systems fail to capture the "tinkering" nature of evolution. We argue that if we are to conceive of cognitive mechanisms in a multi-dimensional, bottom-up perspective, in accordance with the Darwinian logic of descent, we should rather focus on decomposing these mechanisms into lower-level, generic functions, which have the additional advantage of being implementable in neural matter, which ultimately produces cognition. Doing so renders current constructions of cognitive phylogenies otiose.

  10. Molecular evolution of the crustacean hyperglycemic hormone family in ecdysozoans

    PubMed Central

    2010-01-01

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

  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. 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

  14. 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.

  15. 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.

  16. Choosing the right molecular genetic markers for studying biodiversity: from molecular evolution to practical aspects.

    PubMed

    Chenuil, Anne; Anne, Chenuil

    2006-05-01

    The use of molecular genetic markers (MGMs) has become widespread among evolutionary biologists, and the methods of analysis of genetic data improve rapidly, yet an organized framework in which scientists can work is lacking. Elements of molecular evolution are summarized to explain the origin of variation at the DNA level, its measures, and the relationships linking genetic variability to the biological parameters of the studied organisms. MGM are defined by two components: the DNA region(s) screened, and the technique used to reveal its variation. Criteria of choice belong to three categories: (1) the level of variability, (2) the nature of the information (e.g. dominance vs. codominance, ploidy, ... ) which must be determined according to the biological question and (3) some practical criteria which mainly depend on the equipment of the laboratory and experience of the scientist. A three-step procedure is proposed for drawing up MGMs suitable to answer given biological questions, and compiled data are organized to guide the choice at each step: (1) choice, determined by the biological question, of the level of variability and of the criteria of the nature of information, (2) choice of the DNA region and (3) choice of the technique.

  17. [The coast of Northeast Brazil as a Darwinian scientific object: the explorations of John Casper Branner, 1899-1911].

    PubMed

    de Oliveira, Almir Leal

    2014-01-01

    John Casper Branner, a US geologist, had a long history of research in Brazil. The article analyzes his exploration of the geology of the coast of Northeast Brazil during the Branner-Agassiz (1899) and Stanford (1911) expeditions. In the findings from both voyages, Branner characterized the geomorphology of sedimentary basins, sandstone reefs, and coral reefs from a Darwinian evolutionary perspective, blending natural history's model of field research with the practices of modern biology and dynamic geology. He based his interpretation of the evolution of the geological formation on physical and chemical factors. Zoological studies identified the place of evolutionary variation and adaptations of isolated marine species as an auxiliary factor in natural selection.

  18. 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".

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. MEvoLib v1.0: the first molecular evolution library for Python.

    PubMed

    Álvarez-Jarreta, Jorge; Ruiz-Pesini, Eduardo

    2016-10-28

    Molecular evolution studies involve many different hard computational problems solved, in most cases, with heuristic algorithms that provide a nearly optimal solution. Hence, diverse software tools exist for the different stages involved in a molecular evolution workflow. We present MEvoLib, the first molecular evolution library for Python, providing a framework to work with different tools and methods involved in the common tasks of molecular evolution workflows. In contrast with already existing bioinformatics libraries, MEvoLib is focused on the stages involved in molecular evolution studies, enclosing the set of tools with a common purpose in a single high-level interface with fast access to their frequent parameterizations. The gene clustering from partial or complete sequences has been improved with a new method that integrates accessible external information (e.g. GenBank's features data). Moreover, MEvoLib adjusts the fetching process from NCBI databases to optimize the download bandwidth usage. In addition, it has been implemented using parallelization techniques to cope with even large-case scenarios. MEvoLib is the first library for Python designed to facilitate molecular evolution researches both for expert and novel users. Its unique interface for each common task comprises several tools with their most used parameterizations. It has also included a method to take advantage of biological knowledge to improve the gene partition of sequence datasets. Additionally, its implementation incorporates parallelization techniques to enhance computational costs when handling very large input datasets.

  4. 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

  5. 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.

  6. 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.

  7. 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…

  8. 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…

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

    PubMed

    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.

  10. 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

  11. 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. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  12. 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.

  13. "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)

  14. 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.

  15. 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.

  16. "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)

  17. Evolutionary relationships, interisland biogeography, and molecular evolution in the Hawaiian violets (Viola: Violaceae).

    PubMed

    Havran, J Christopher; Sytsma, Kenneth J; Ballard, Harvey E

    2009-11-01

    The endemic Hawaiian flora offers remarkable opportunities to study the patterns of plant morphological and molecular evolution. The Hawaiian violets are a monophyletic lineage of nine taxa distributed across six main islands of the Hawaiian archipelago. To describe the evolutionary relationships, biogeography, and molecular evolution rates of the Hawaiian violets, we conducted a phylogenetic study using nuclear rDNA internal transcribed spacer sequences from specimens of each species. Parsimony, maximum likelihood (ML), and Bayesian inference reconstructions of island colonization and radiation strongly suggest that the Hawaiian violets first colonized the Maui Nui Complex, quickly radiated to Kaua'i and O'ahu, and recently dispersed to Hawai'i. The lineage consists of "wet" and "dry" clades restricted to distinct precipitation regimes. The ML and Bayesian inference reconstructions of shifts in habitat, habit, and leaf shape indicate that ecologically analogous taxa have undergone parallel evolution in leaf morphology and habit. This parallel evolution correlates with shifts to specialized habitats. Relative rate tests showed that woody and herbaceous sister species possess equal molecular evolution rates. The incongruity of molecular evolution rates in taxa on younger islands suggests that these rates may not be determined by growth form (or lifespan) alone, but may be influenced by complex dispersal events.

  18. 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

  19. 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.

  20. Molecular evolution of a Drosophila homolog of human BRCA2.

    PubMed

    Bennett, Sarah M; Noor, Mohamed A F

    2009-11-01

    The human cancer susceptibility gene, BRCA2, functions in double-strand break repair by homologous recombination, and it appears to function via interaction of a repetitive region ("BRC repeats") with RAD-51. A putatively simpler homolog, dmbrca2, was identified in Drosophila melanogaster recently and also affects mitotic and meiotic double-strand break repair. In this study, we examined patterns of repeat variation both within Drosophila pseudoobscura and among available Drosophila genome sequences. We identified extensive variation within and among closely related Drosophila species in BRC repeat number, to the extent that variation within this genus recapitulates the extent of variation found across the entire animal kingdom. We describe patterns of evolution across species by documenting recent repeat expansions (sometimes in tandem arrays) and homogenizations within available genome sequences. Overall, we have documented patterns and modes of evolution in a new model system of a gene which is important to human health.

  1. Evolution and Molecular Control of Hybrid Incompatibility in Plants.

    PubMed

    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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Genetic Diversity and Molecular Evolution of Chinese Waxy Maize Germplasm

    PubMed Central

    Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun

    2013-01-01

    Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection. PMID:23818949

  9. Functional divergence of the brain-size regulating gene MCPH1 during primate evolution and the origin of humans.

    PubMed

    Shi, Lei; Li, Ming; Lin, Qiang; Qi, Xuebin; Su, Bing

    2013-05-22

    One of the key genes that regulate human brain size, MCPH1 has evolved under strong Darwinian positive selection during the evolution of primates. During this evolution, the divergence of MCPH1 protein sequences among primates may have caused functional changes that contribute to brain enlargement. To test this hypothesis, we used co-immunoprecipitation and reporter gene assays to examine the activating and repressing effects of MCPH1 on a set of its down-stream genes and then compared the functional outcomes of a series of mutant MCPH1 proteins that carry mutations at the human- and great-ape-specific sites. The results demonstrate that the regulatory effects of human MCPH1 and rhesus macaque MCPH1 are different in three of eight down-stream genes tested (p73, cyclinE1 and p14ARF), suggesting a functional divergence of MCPH1 between human and non-human primates. Further analyses of the mutant MCPH1 proteins indicated that most of the human-specific mutations could change the regulatory effects on the down-stream genes. A similar result was also observed for one of the four great-ape-specific mutations. Collectively, we propose that during primate evolution in general and human evolution in particular, the divergence of MCPH1 protein sequences under Darwinian positive selection led to functional modifications, providing a possible molecular mechanism of how MCPH1 contributed to brain enlargement during primate evolution and human origin.

  10. Functional divergence of the brain-size regulating gene MCPH1 during primate evolution and the origin of humans

    PubMed Central

    2013-01-01

    Background One of the key genes that regulate human brain size, MCPH1 has evolved under strong Darwinian positive selection during the evolution of primates. During this evolution, the divergence of MCPH1 protein sequences among primates may have caused functional changes that contribute to brain enlargement. Results To test this hypothesis, we used co-immunoprecipitation and reporter gene assays to examine the activating and repressing effects of MCPH1 on a set of its down-stream genes and then compared the functional outcomes of a series of mutant MCPH1 proteins that carry mutations at the human- and great-ape-specific sites. The results demonstrate that the regulatory effects of human MCPH1 and rhesus macaque MCPH1 are different in three of eight down-stream genes tested (p73, cyclinE1 and p14ARF), suggesting a functional divergence of MCPH1 between human and non-human primates. Further analyses of the mutant MCPH1 proteins indicated that most of the human-specific mutations could change the regulatory effects on the down-stream genes. A similar result was also observed for one of the four great-ape-specific mutations. Conclusions Collectively, we propose that during primate evolution in general and human evolution in particular, the divergence of MCPH1 protein sequences under Darwinian positive selection led to functional modifications, providing a possible molecular mechanism of how MCPH1 contributed to brain enlargement during primate evolution and human origin. PMID:23697381

  11. 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.

  12. 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.

  13. Luria-Delbrück, revisited: the classic experiment does not rule out Lamarckian evolution

    NASA Astrophysics Data System (ADS)

    Holmes, Caroline M.; Ghafari, Mahan; Abbas, Anzar; Saravanan, Varun; Nemenman, Ilya

    2017-10-01

    We re-examined data from the classic Luria-Delbrück fluctuation experiment, which is often credited with establishing a Darwinian basis for evolution. We argue that, for the Lamarckian model of evolution to be ruled out by the experiment, the experiment must favor pure Darwinian evolution over both the Lamarckian model and a model that allows both Darwinian and Lamarckian mechanisms (as would happen for bacteria with CRISPR-Cas immunity). Analysis of the combined model was not performed in the original 1943 paper. The Luria-Delbrück paper also did not consider the possibility of neither model fitting the experiment. Using Bayesian model selection, we find that the Luria-Delbrück experiment, indeed, favors the Darwinian evolution over purely Lamarckian. However, our analysis does not rule out the combined model, and hence cannot rule out Lamarckian contributions to the evolutionary dynamics.

  14. Luria-Delbrück, revisited: the classic experiment does not rule out Lamarckian evolution.

    PubMed

    Holmes, Caroline M; Ghafari, Mahan; Abbas, Anzar; Saravanan, Varun; Nemenman, Ilya

    2017-08-21

    We re-examined data from the classic Luria-Delbrück fluctuation experiment, which is often credited with establishing a Darwinian basis for evolution. We argue that, for the Lamarckian model of evolution to be ruled out by the experiment, the experiment must favor pure Darwinian evolution over both the Lamarckian model and a model that allows both Darwinian and Lamarckian mechanisms (as would happen for bacteria with CRISPR-Cas immunity). Analysis of the combined model was not performed in the original 1943 paper. The Luria-Delbrück paper also did not consider the possibility of neither model fitting the experiment. Using Bayesian model selection, we find that the Luria-Delbrück experiment, indeed, favors the Darwinian evolution over purely Lamarckian. However, our analysis does not rule out the combined model, and hence cannot rule out Lamarckian contributions to the evolutionary dynamics.

  15. More genes underwent positive selection in chimpanzee evolution than in human evolution

    PubMed Central

    Bakewell, Margaret A.; Shi, Peng; Zhang, Jianzhi

    2007-01-01

    Observations of numerous dramatic and presumably adaptive phenotypic modifications during human evolution prompt the common belief that more genes have undergone positive Darwinian selection in the human lineage than in the chimpanzee lineage since their evolutionary divergence 6–7 million years ago. Here, we test this hypothesis by analyzing nearly 14,000 genes of humans and chimps. To ensure an accurate and unbiased comparison, we select a proper outgroup, avoid sequencing errors, and verify statistical methods. Our results show that the number of positively selected genes is substantially smaller in humans than in chimps, despite a generally higher nonsynonymous substitution rate in humans. These observations are explainable by the reduced efficacy of natural selection in humans because of their smaller long-term effective population size but refute the anthropocentric view that a grand enhancement in Darwinian selection underlies human origins. Although human and chimp positively selected genes have different molecular functions and participate in different biological processes, the differences do not ostensibly correspond to the widely assumed adaptations of these species, suggesting how little is currently known about which traits have been under positive selection. Our analysis of the identified positively selected genes lends support to the association between human Mendelian diseases and past adaptations but provides no evidence for either the chromosomal speciation hypothesis or the widespread brain-gene acceleration hypothesis of human origins. PMID:17449636

  16. 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.

  17. A Simple, General Result for the Variance of Substitution Number in Molecular Evolution.

    PubMed

    Houchmandzadeh, Bahram; Vallade, Marcel

    2016-07-01

    The number of substitutions (of nucleotides, amino acids, etc.) that take place during the evolution of a sequence is a stochastic variable of fundamental importance in the field of molecular evolution. Although the mean number of substitutions during molecular evolution of a sequence can be estimated for a given substitution model, no simple solution exists for the variance of this random variable. We show in this article that the computation of the variance is as simple as that of the mean number of substitutions for both short and long times. Apart from its fundamental importance, this result can be used to investigate the dispersion index R, that is, the ratio of the variance to the mean substitution number, which is of prime importance in the neutral theory of molecular evolution. By investigating large classes of substitution models, we demonstrate that although [Formula: see text], to obtain R significantly larger than unity necessitates in general additional hypotheses on the structure of the substitution model. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

    PubMed Central

    Shi, Fei; Qin, Song; Wang, Yin-Chu

    2011-01-01

    Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions. PMID:21904470

  19. Molecular Evolution of the TET Gene Family in Mammals.

    PubMed

    Akahori, Hiromichi; Guindon, Stéphane; Yoshizaki, Sumio; Muto, Yoshinori

    2015-12-01

    Ten-eleven translocation (TET) proteins, a family of Fe(2+)- and 2-oxoglutarate-dependent dioxygenases, are involved in DNA demethylation. They also help regulate various cellular functions. Three TET paralogs have been identified (TET1, TET2, and TET3) in humans. This study focuses on the evolution of mammalian TET genes. Distinct patterns in TET1 and TET2 vs. TET3 were revealed by codon-based tests of positive selection. Results indicate that TET1 and TET2 genes have experienced positive selection more frequently than TET3 gene, and that the majority of codon sites evolved under strong negative selection. These findings imply that the selective pressure on TET3 may have been relaxed in several lineages during the course of evolution. Our analysis of convergent amino acid substitutions also supports the different evolutionary dynamics among TET gene subfamily members. All of the five amino acid sites that are inferred to have evolved under positive selection in the catalytic domain of TET2 are localized at the protein's outer surface. The adaptive changes of these positively selected amino acid sites could be associated with dynamic interactions between other TET-interacting proteins, and positive selection thus appears to shift the regulatory scheme of TET enzyme function.

  20. 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

  1. Time Evolution of the Giant Molecular Cloud Mass Functions across Galactic Disks

    NASA Astrophysics Data System (ADS)

    Kobayashi, Masato I. N.; Inutsuka, Shu-Ichiro; Kobayashi, Hiroshi; Hasegawa, Kenji

    2017-01-01

    We formulate and conduct the time-integration of time evolution equation for the giant molecular cloud mass function (GMCMF) including the cloud-cloud collision (CCC) effect. Our results show that the CCC effect is only limited in the massive-end of the GMCMF and indicate that future high resolution and sensitivity radio observations may constrain giant molecular cloud (GMC) timescales by observing the GMCMF slope in the lower mass regime.

  2. 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.

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

    PubMed Central

    Ao, P.

    2011-01-01

    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. PMID:21949462

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

    NASA Astrophysics Data System (ADS)

    Ao, P.

    2008-05-01

    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.

  5. The driving force for molecular evolution of translation

    PubMed Central

    NOLLER, HARRY F.

    2004-01-01

    It is widely argued that protein synthesis evolved out of an RNA world, in which catalytic and other biological functions now carried out by proteins were performed by RNAs. However, it is not clear what selective advantage would have provided the driving force for evolution of a primitive translation apparatus, because of the unlikelihood that rudimentary polypeptides would have contributed sufficiently useful biological functions. Here, I suggest that the availability of even simple peptides could have significantly enlarged the otherwise limited structure space of RNA. In other words, translation initially evolved not to create a protein world, but to extend the structural, and therefore the functional, capabilities of the RNA world. Observed examples of substantial structural rearrangements in RNA that are induced by binding of peptides and other small molecules support this possibility. PMID:15547132

  6. Molecular networks and the evolution of human cognitive specializations.

    PubMed

    Fontenot, Miles; Konopka, Genevieve

    2014-12-01

    Inroads into elucidating the origins of human cognitive specializations have taken many forms, including genetic, genomic, anatomical, and behavioral assays that typically compare humans to non-human primates. While the integration of all of these approaches is essential for ultimately understanding human cognition, here, we review the usefulness of coexpression network analysis for specifically addressing this question. An increasing number of studies have incorporated coexpression networks into brain expression studies comparing species, disease versus control tissue, brain regions, or developmental time periods. A clearer picture has emerged of the key genes driving brain evolution, as well as the developmental and regional contributions of gene expression patterns important for normal brain development and those misregulated in cognitive diseases. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Molecular evolution of peste des petits ruminants virus.

    PubMed

    Muniraju, Murali; Munir, Muhammad; Parthiban, AravindhBabu R; Banyard, Ashley C; Bao, Jingyue; Wang, Zhiliang; Ayebazibwe, Chrisostom; Ayelet, Gelagay; El Harrak, Mehdi; Mahapatra, Mana; Libeau, Geneviève; Batten, Carrie; Parida, Satya

    2014-12-01

    Despite safe and efficacious vaccines against peste des petits ruminants virus (PPRV), this virus has emerged as the cause of a highly contagious disease with serious economic consequences for small ruminant agriculture across Asia, the Middle East, and Africa. We used complete and partial genome sequences of all 4 lineages of the virus to investigate evolutionary and epidemiologic dynamics of PPRV. A Bayesian phylogenetic analysis of all PPRV lineages mapped the time to most recent common ancestor and initial divergence of PPRV to a lineage III isolate at the beginning of 20th century. A phylogeographic approach estimated the probability for root location of an ancestral PPRV and individual lineages as being Nigeria for PPRV, Senegal for lineage I, Nigeria/Ghana for lineage II, Sudan for lineage III, and India for lineage IV. Substitution rates are critical parameters for understanding virus evolution because restrictions in genetic variation can lead to lower adaptability and pathogenicity.

  8. Molecular Evolution of Peste des Petits Ruminants Virus

    PubMed Central

    Muniraju, Murali; Munir, Muhammad; Parthiban, AravindhBabu R.; Banyard, Ashley C.; Bao, Jingyue; Wang, Zhiliang; Ayebazibwe, Chrisostom; Ayelet, Gelagay; El Harrak, Mehdi; Mahapatra, Mana; Libeau, Geneviève; Batten, Carrie

    2014-01-01

    Despite safe and efficacious vaccines against peste des petits ruminants virus (PPRV), this virus has emerged as the cause of a highly contagious disease with serious economic consequences for small ruminant agriculture across Asia, the Middle East, and Africa. We used complete and partial genome sequences of all 4 lineages of the virus to investigate evolutionary and epidemiologic dynamics of PPRV. A Bayesian phylogenetic analysis of all PPRV lineages mapped the time to most recent common ancestor and initial divergence of PPRV to a lineage III isolate at the beginning of 20th century. A phylogeographic approach estimated the probability for root location of an ancestral PPRV and individual lineages as being Nigeria for PPRV, Senegal for lineage I, Nigeria/Ghana for lineage II, Sudan for lineage III, and India for lineage IV. Substitution rates are critical parameters for understanding virus evolution because restrictions in genetic variation can lead to lower adaptability and pathogenicity. PMID:25418782

  9. 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.

  10. Molecular Imaging and Contrast Agent Database (MICAD): Evolution and Progress

    PubMed Central

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

    2011-01-01

    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 >1000 agents in MICAD is provided in a chapter format and can be accessed through PubMed. Lists containing >4250 unique MI probes and CAs published in peer-reviewed journals and agents approved by the United States Food and Drug Administration (FDA) as well as a CSV 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, preclinical 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 PMID:21989943

  11. 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.

  12. The rate of DNA evolution: effects of body size and temperature on the molecular clock.

    PubMed

    Gillooly, James F; Allen, Andrew P; West, Geoffrey B; Brown, James H

    2005-01-04

    Observations that rates of molecular evolution vary widely within and among lineages have cast doubts on the existence of a single "molecular clock." Differences in the timing of evolutionary events estimated from genetic and fossil evidence have raised further questions about the accuracy of molecular clocks. Here, we present a model of nucleotide substitution that combines theory on metabolic rate with the now-classic neutral theory of molecular evolution. The model quantitatively predicts rate heterogeneity and may reconcile differences in molecular- and fossil-estimated dates of evolutionary events. Model predictions are supported by extensive data from mitochondrial and nuclear genomes. By accounting for the effects of body size and temperature on metabolic rate, this model explains heterogeneity in rates of nucleotide substitution in different genes, taxa, and thermal environments. This model also suggests that there is indeed a single molecular clock, as originally proposed by Zuckerkandl and Pauling [Zuckerkandl, E. & Pauling, L. (1965) in Evolving Genes and Proteins, eds. Bryson, V. & Vogel, H. J. (Academic, New York), pp. 97-166], but that it "ticks" at a constant substitution rate per unit of mass-specific metabolic energy rather than per unit of time. This model therefore links energy flux and genetic change. More generally, the model suggests that body size and temperature combine to control the overall rate of evolution through their effects on metabolism.

  13. The chemokine and chemokine receptor superfamilies and their molecular evolution

    PubMed Central

    Zlotnik, Albert; Yoshie, Osamu; Nomiyama, Hisayuki

    2006-01-01

    The human chemokine superfamily currently includes at least 46 ligands, which bind to 18 functionally signaling G-protein-coupled receptors and two decoy or scavenger receptors. The chemokine ligands probably comprise one of the first completely known molecular superfamilies. The genomic organization of the chemokine ligand genes and a comparison of their sequences between species shows that tandem gene duplication has taken place independently in the mouse and human lineages of some chemokine families. This means that care needs to be taken when extrapolating experimental results on some chemokines from mouse to human. PMID:17201934

  14. [Molecular biology and prostate cancer: evolution or revolution?].

    PubMed

    Molinié, Vincent; Beuzeboc, Philippe; Mahjoub, Wafa K

    2008-10-01

    The identification of fusion genes provides new insights into the initial mechanisms of molecular events implicated in the tumorigenesis of prostate cancer. The presence of TEMPRSS2-ETS fusion in up to half of all human prostate cancers makes it perhaps the most common genetic rearrangement in human epithelial tumors. Some data suggest that TMPRSS2-ERG fusion prostate cancers have a more aggressive phenotype which may affect cancer progression and outcome in localized tumors treated with prostatectomy. This discovery should pave the way towards future targeted therapies.

  15. 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.

  16. 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.

  17. Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants

    PubMed Central

    Li, Zhen; Van de Peer, Yves; Ingvarsson, Pär K.

    2017-01-01

    Abstract The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes. PMID:28333233

  18. Molecular phylogenetic evidence for the evolution of specialization in anemonefishes.

    PubMed Central

    Elliott, J K; Lougheed, S C; Bateman, B; McPhee, L K; Boag, P T

    1999-01-01

    Anemonefishes (genera: Amphiprion and Premnas; family Pomacentridae) are a group of 28 species of coral reef fishes that are found in obligate symbiosis with large tropical sea anemones. A phylogenetic hypothesis based on morphological analyses of this group suggests that the ancestral anemonefish was a generalist with similar morphology to other pomacentrids, and that it gave rise to other anemonefish species that were more specialized for living with particular species of host anemones. To test this hypothesis we constructed a molecular phylogeny for the anemonefishes by sequencing 1140 base pairs of the cytochrome b gene and 522 base pairs of the 16S rRNA gene for six species of anemonefishes (representatives of all subgenera and species complexes) and two other pomacentrid species. Three methods of phylogenetic analysis all strongly supported the conclusion that anemonefishes are a monophyletic group. The molecular phylogeny differs from the tree based on morphological data in that the two species of specialized anemonefishes (Premnas biaculeatus and Amphiprion ocellaris) were assigned to a basal position within the clade, and the extreme host generalist (Amphiprion clarkii) to a more derived position. Thus, the initial anemonefish ancestors were probably host specialists and subsequent speciation events led to a combination of generalist and specialist groups. Further phylogenetic studies of additional anemonefish species are required to substantiate this hypothesis. PMID:10331288

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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. © 2013 by The International Union of Biochemistry and Molecular Biology.

  7. 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

  8. 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. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Decoding the molecular evolution of human cognition using comparative genomics.

    PubMed

    Usui, Noriyoshi; Co, Marissa; Konopka, Genevieve

    2014-01-01

    Identification of genetic and molecular factors responsible for the specialized cognitive abilities of humans is expected to provide important insights into the mechanisms responsible for disorders of cognition such as autism, schizophrenia and Alzheimer's disease. Here, we discuss the use of comparative genomics for identifying salient genes and gene networks that may underlie cognition. We focus on the comparison of human and non-human primate brain gene expression and the utility of building gene coexpression networks for prioritizing hundreds of genes that differ in expression among the species queried. We also discuss the importance of and methods for functional studies of the individual genes identified. Together, this integration of comparative genomics with cellular and animal models should provide improved systems for developing effective therapeutics for disorders of cognition. © 2014 S. Karger AG, Basel.

  10. Molecular systematics and evolution of Regina and the thamnophiine snakes.

    PubMed

    Alfaro, M E; Arnold, S J

    2001-12-01

    Snakes of the tribe Thamnophiini represent an ecologically important component of the herpetofauna in a range of habitats across North America. Thamnophiines are the best-studied colubrids, yet little is known of their systematic relationships. A molecular phylogenetic study of 32 thamnophiine species using three complete mitochondrial genes (cytochrome b, NADH dehydrogenase subunit 2, and 12S ribosomal DNA) recovered a well-supported phylogeny with three major clades: a garter snake group, a water snake group, and a novel semifossorial group. The historically contentious genus Regina, which contains the crayfish-eating snakes, is polyphyletic. The phylogeographic pattern of Thamnophis is consistent with an hypothesis of at least one invasion of northern North America from Mexico.

  11. Decoding the molecular evolution of human cognition using comparative genomics

    PubMed Central

    Usui, Noriyoshi; Co, Marissa; Konopka, Genevieve

    2014-01-01

    Identification of genetic and molecular factors responsible for the specialized cognitive abilities of humans is expected to provide important insights into the mechanisms responsible for disorders of cognition such as autism, schizophrenia, and Alzheimer’s disease. Here, we discuss the use of comparative genomics for identifying salient genes and gene networks that may underlie cognition. We focus on the comparison of human and non-human primate brain gene expression and the utility of building gene co-expression networks for prioritizing hundreds of genes that differ in expression among the species queried. We also discuss the importance and methods for functional studies of individual genes identified. Together, this integration of comparative genomics with cellular and animal models should provide improved systems for developing effective therapeutics for disorders of cognition. PMID:25247723

  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. 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

  15. 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.

  16. Molecular evolution of PKD2 gene family in mammals.

    PubMed

    Ye, Chun; Sun, Huan; Guo, Wenhu; Wei, Yuquan; Zhou, Qin

    2009-09-01

    PKD2 gene encodes a critical cation channel protein that plays important roles in various developmental processes and is usually evolutionarily conserved. In the present study, we analyzed the evolutionary patterns of PKD2 and its homologous genes (PKD2L1, PKD2L2) from nine mammalian species. In this study, we demonstrated the orthologs of PKD2 gene family evolved under a dominant purifying selection force. Our results in combination with the reported evidences from functional researches suggested the entire PKD2 gene family are conserved and perform essential biological roles during mammalian evolution. In rodents, PKD2 gene family members appeared to have evolved more rapidly than other mammalian lineages, probably resulting from relaxation of purifying selection. However, positive selection imposed on synonymous sites also potentially contributed to this case. For the paralogs, our results implied that PKD2L2 genes evolved under a weaker purifying selection constraint than PKD2 and PKD2L1 genes. Interestingly, some loop regions of transmembrane domain of PKD2L2 exhibited higher P (N)/P (S) ratios than expected, suggesting these regions are more functional divergent in organisms and worthy of special attention.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  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. Phylogeography and Molecular Evolution of Potato virus Y

    PubMed Central

    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 (PVYO, PVYN and PVYC) 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. PMID:22655074

  3. 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.

  4. [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.

  5. Molecular evolution of the capsid gene in human norovirus genogroup II

    PubMed Central

    Kobayashi, Miho; Matsushima, Yuki; Motoya, Takumi; Sakon, Naomi; Shigemoto, Naoki; Okamoto-Nakagawa, Reiko; Nishimura, Koichi; Yamashita, Yasutaka; Kuroda, Makoto; Saruki, Nobuhiro; Ryo, Akihide; Saraya, Takeshi; Morita, Yukio; Shirabe, Komei; Ishikawa, Mariko; Takahashi, Tomoko; Shinomiya, Hiroto; Okabe, Nobuhiko; Nagasawa, Koo; Suzuki, Yoshiyuki; Katayama, Kazuhiko; Kimura, Hirokazu

    2016-01-01

    Capsid protein of norovirus genogroup II (GII) plays crucial roles in host infection. Although studies on capsid gene evolution have been conducted for a few genotypes of norovirus, the molecular evolution of norovirus GII is not well understood. Here we report the molecular evolution of all GII genotypes, using various bioinformatics techniques. The time-scaled phylogenetic tree showed that the present GII strains diverged from GIV around 1630CE at a high evolutionary rate (around 10−3 substitutions/site/year), resulting in three lineages. The GII capsid gene had large pairwise distances (maximum > 0.39). The effective population sizes of the present GII strains were large (>102) for about 400 years. Positive (20) and negative (over 450) selection sites were estimated. Moreover, some linear and conformational B-cell epitopes were found in the deduced GII capsid protein. These results suggested that norovirus GII strains rapidly evolved with high divergence and adaptation to humans. PMID:27384324

  6. 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.

  7. 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.

  8. Distribution and Molecular Evolution of Bacillus anthracis Genotypes in Namibia

    PubMed Central

    Beyer, Wolfgang; Bellan, Steve; Eberle, Gisela; Ganz, Holly H.; Getz, Wayne M.; Haumacher, Renate; Hilss, Karen A.; Kilian, Werner; Lazak, Judith; Turner, Wendy C.; Turnbull, Peter C. B.

    2012-01-01

    The recent development of genetic markers for Bacillus anthracis has made it possible to monitor the spread and distribution of this pathogen during and between anthrax outbreaks. In Namibia, anthrax outbreaks occur annually in the Etosha National Park (ENP) and on private game and livestock farms. We genotyped 384 B. anthracis isolates collected between 1983–2010 to identify the possible epidemiological correlations of anthrax outbreaks within and outside the ENP and to analyze genetic relationships between isolates from domestic and wild animals. The isolates came from 20 animal species and from the environment and were genotyped using a 31-marker multi-locus-VNTR-analysis (MLVA) and, in part, by twelve single nucleotide polymorphism (SNP) markers and four single nucleotide repeat (SNR) markers. A total of 37 genotypes (GT) were identified by MLVA, belonging to four SNP-groups. All GTs belonged to the A-branch in the cluster- and SNP-analyses. Thirteen GTs were found only outside the ENP, 18 only within the ENP and 6 both inside and outside. Genetic distances between isolates increased with increasing time between isolations. However, genetic distance between isolates at the beginning and end of the study period was relatively small, indicating that while the majority of GTs were only found sporadically, three genetically close GTs, accounting for more than four fifths of all the ENP isolates, appeared dominant throughout the study period. Genetic distances among isolates were significantly greater for isolates from different host species, but this effect was small, suggesting that while species-specific ecological factors may affect exposure processes, transmission cycles in different host species are still highly interrelated. The MLVA data were further used to establish a model of the probable evolution of GTs within the endemic region of the ENP. SNR-analysis was helpful in correlating an isolate with its source but did not elucidate epidemiological

  9. 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.

  10. 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

  11. The rapid evolution of molecular genetic diagnostics in neuromuscular diseases.

    PubMed

    Volk, Alexander E; Kubisch, Christian

    2017-10-01

    The development of massively parallel sequencing (MPS) has revolutionized molecular genetic diagnostics in monogenic disorders. The present review gives a brief overview of different MPS-based approaches used in clinical diagnostics of neuromuscular disorders (NMDs) and highlights their advantages and limitations. MPS-based approaches like gene panel sequencing, (whole) exome sequencing, (whole) genome sequencing, and RNA sequencing have been used to identify the genetic cause in NMDs. Although gene panel sequencing has evolved as a standard test for heterogeneous diseases, it is still debated, mainly because of financial issues and unsolved problems of variant interpretation, whether genome sequencing (and to a lesser extent also exome sequencing) of single patients can already be regarded as routine diagnostics. However, it has been shown that the inclusion of parents and additional family members often leads to a substantial increase in the diagnostic yield in exome-wide/genome-wide MPS approaches. In addition, MPS-based RNA sequencing just enters the research and diagnostic scene. Next-generation sequencing increasingly enables the detection of the genetic cause in highly heterogeneous diseases like NMDs in an efficient and affordable way. Gene panel sequencing and family-based exome sequencing have been proven as potent and cost-efficient diagnostic tools. Although clinical validation and interpretation of genome sequencing is still challenging, diagnostic RNA sequencing represents a promising tool to bypass some hurdles of diagnostics using genomic DNA.

  12. 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.

  13. 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.

  14. 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

  15. 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.

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

    PubMed Central

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

    2009-01-01

    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. PMID:19289848

  17. 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.

  18. Edward Hitchcock's pre-Darwinian (1840) "tree of life".

    PubMed

    Archibald, J David

    2009-01-01

    The "tree of life" iconography, representing the history of life, dates from at least the latter half of the 18th century, but evolution as the mechanism providing this bifurcating history of life did not appear until the early 19th century. There was also a shift from the straight line, scala naturae view of change in nature to a more bifurcating or tree-like view. Throughout the 19th century authors presented tree-like diagrams, some regarding the Deity as the mechanism of change while others argued for evolution. Straight-line or anagenetic evolution and bifurcating or cladogenetic evolution are known in biology today, but are often misrepresented in popular culture, especially with anagenesis being confounded with scala naturae. Although well known in the mid 19th century, the geologist Edward Hitchcock has been forgotten as an early, if not the first author to publish a paleontologically based "tree of life" beginning in 1840 in the first edition of his popular general geology text Elementary Geology. At least 31 editions were published and those between 1840 and 1859 had this "paleontological chart" showing two trees, one for fossil and living plants and another for animals set within a context of geological time. Although the chart did not vary in later editions, the text explaining the chart did change to reflect newer ideas in paleontology and geology. Whereas Lamarck, Chambers, Bronn, Darwin, and Haeckel saw some form of transmutation as the mechanism that created their "trees of life," Hitchcock, like his contemporaries Agassiz and Miller, who also produced "trees of life," saw a deity as the agent of change. Through each edition of his book Hitchcock denounced the newer transmutationist hypotheses of Lamarck, then Chambers, and finally Darwin in an 1860 edition that no longer presented his tree-like "paleontological chart."

  19. 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.

  20. Protein engineering of conger eel galectins by tracing of molecular evolution using probable ancestral mutants

    PubMed Central

    2010-01-01

    Background Conger eel galectins, congerin I (ConI) and congerin II (ConII), show the different molecular characteristics resulting from accelerating evolution. We recently reconstructed a probable ancestral form of congerins, Con-anc. It showed properties similar to those of ConII in terms of thermostability and carbohydrate recognition specificity, although it shares a higher sequence similarity with ConI than ConII. Results In this study, we have focused on the different amino acid residues between Con-anc and ConI, and have performed the protein engineering of Con-anc through site-directed mutagenesis, followed by the molecular evolution analysis of the mutants. This approach revealed the functional importance of loop structures of congerins: (1) N- and C-terminal and loop 5 regions that are involved in conferring a high thermostability to ConI; (2) loops 3, 5, and 6 that are responsible for stronger binding of ConI to most sugars; and (3) loops 5 and 6, and Thr38 residue in loop 3 contribute the specificity of ConI toward lacto-N-fucopentaose-containing sugars. Conclusions Thus, this methodology, with tracing of the molecular evolution using ancestral mutants, is a powerful tool for the analysis of not only the molecular evolutionary process, but also the structural elements of a protein responsible for its various functions. PMID:20152053

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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].

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

    PubMed

    Cai, James J; Smith, David K; Xia, Xuhua; Yuen, Kwok-Yung

    2005-03-22

    MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454

  11. 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.

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

    PubMed Central

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

    2006-01-01

    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 (Nav1.4a) 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. PMID:16505358

  13. Punctualism, non-adaptationism, neutralism and evolution.

    PubMed

    Volkenstein, M V

    1987-01-01

    In its further development the theory of evolution will incorporate molecular biology, synergetics and the theory of information. Using a simple model it is shown that speciation can be similar to phase transition. This is a thermodynamical statement which does not say anything concerning the sharpness and kinetic features of transition. Hence there is no contradiction between punctuated equilibrium and phyletic gradualism. The notion of punctualism can be used in the sense of phase transition. Evolution is directional because of constraints of natural selection due to the structure of organisms already existing and to the possible pathways of development. Correspondingly many characters are non-adaptative. Not only are the structures of proteins important for speciation but also the exact answers to the questions: "how much", "where" and "when"? These answers can be obtained as the results of regulation of genes, particularly of homeiotic regulation. The basis features of the structure of proteins are considered and the sense of the neutral theory is discussed in connection with degeneracy of correlation between the primary structure of a protein, its spatial structure and biological function. Informational aspects of evolution are discussed. Punctualism, non-adaptationism and neutralism form the triad of internally connected features of evolution. The Darwinian theory preserves its fundamental significance.

  14. 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.

  15. 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

  16. 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.

  17. Evolution before genes

    PubMed Central

    2012-01-01

    Background Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. However, this is exactly the kind of scheme we propose for how Darwinian evolution could have occurred prior to template replication. Results We cannot confirm previous claims that autocatalytic sets of organic polymer molecules could undergo evolution in any interesting sense by themselves. While we and others have previously imagined inhibition would result in selectability, we found that it produced multiple attractors in an autocatalytic set that cannot be selected for. Instead, we discovered that if general conditions are satisfied, the accumulation of adaptations in chemical reaction networks can occur. These conditions are the existence of rare reactions producing viable cores (analogous to a genotype), that sustains a molecular periphery (analogous to a phenotype). Conclusions We conclude that only when a chemical reaction network consists of many such viable cores, can it be evolvable. When many cores are enclosed in a compartment there is competition between cores within the same compartment, and when there are many compartments, there is between-compartment competition due to the phenotypic effects of cores and their periphery at the compartment level. Acquisition of cores by rare chemical events, and loss of cores at division, allows macromutation, limited heredity and selectability, thus explaining how a poor man's natural selection could have operated prior to genetic templates. This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur. Reviewers This article was reviewed by William Martin and Eugene Koonin. PMID:22221860

  18. Evolution before genes.

    PubMed

    Vasas, Vera; Fernando, Chrisantha; Santos, Mauro; Kauffman, Stuart; Szathmáry, Eörs

    2012-01-05

    Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. However, this is exactly the kind of scheme we propose for how Darwinian evolution could have occurred prior to template replication. We cannot confirm previous claims that autocatalytic sets of organic polymer molecules could undergo evolution in any interesting sense by themselves. While we and others have previously imagined inhibition would result in selectability, we found that it produced multiple attractors in an autocatalytic set that cannot be selected for. Instead, we discovered that if general conditions are satisfied, the accumulation of adaptations in chemical reaction networks can occur. These conditions are the existence of rare reactions producing viable cores (analogous to a genotype), that sustains a molecular periphery (analogous to a phenotype). We conclude that only when a chemical reaction network consists of many such viable cores, can it be evolvable. When many cores are enclosed in a compartment there is competition between cores within the same compartment, and when there are many compartments, there is between-compartment competition due to the phenotypic effects of cores and their periphery at the compartment level. Acquisition of cores by rare chemical events, and loss of cores at division, allows macromutation, limited heredity and selectability, thus explaining how a poor man's natural selection could have operated prior to genetic templates. This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur.

  19. Re"CYC"ling molecular regulators in the evolution and development of flower symmetry.

    PubMed

    Spencer, Victoria; Kim, Minsung

    2017-08-31

    Flower forms are both highly diverse and multifaceted. As well as varying in colour, size, organ number, and much more, flowers show different types of symmetry. Floral symmetry can be grouped into three main categories: asymmetry, bilateral symmetry and radial symmetry, characterised by zero, one, and multiple planes of symmetry, respectively. This review will first explore floral symmetry from a classical morphological view, then from a modern molecular perspective. The recent molecular work on symmetry in monocots and eudicots will be discussed, followed by an in-depth discussion into the evolution of CYC genes, particularly in the capitulum of the sunflower family (Asteraceae). Whilst recent studies on non-model species are helping to bring new light to this field, more species coverage is required to understand how traits such as bilateral symmetry have evolved so many times, and whether the same molecular regulators were recruited for this function. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. 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

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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)

  7. 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)

  8. 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…

  9. 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…

  10. 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…

  11. Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species.

    PubMed

    Mosquera-Rendón, Jeanneth; Rada-Bravo, Ana M; Cárdenas-Brito, Sonia; Corredor, Mauricio; Restrepo-Pineda, Eliana; Benítez-Páez, Alfonso

    2016-01-12

    Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains. The P. aeruginosa pangenome was estimated to contain more than 16,000 non-redundant genes, and approximately 15 % of these constituted the core genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P. aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of P. aeruginosa clinical isolates. We report the unprecedented pangenome characterization of P. aeruginosa on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein

  12. 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.

  13. 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.

  14. The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms.

    PubMed

    Tiley, George P; Burleigh, J Gordon; Burleigh, Gordon

    2015-09-16

    Although homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC biased gene conversion, contribute to complex histories of gene duplication and loss through tandem duplication, and enhance purifying selection on genes. Therefore, variation in recombination rate across species may explain some of the variation in genomic architecture as well as rates of molecular evolution. We used phylogenetic comparative methods to investigate the evolution of global meiotic recombination rate in angiosperms and its effects on genome architecture and selection at the molecular level using genetic maps and genome sequences from thirty angiosperm species. Recombination rate is negatively correlated with genome size, which is likely caused by the removal of LTR retrotransposons. After correcting recombination rates for euchromatin content, we also found an association between global recombination rate and average gene family size. This suggests a role for recombination in the preservation of duplicate genes or expansion of gene families. An analysis of the correlation between the ratio of nonsynonymous to synonymous substitution rates (dN/dS) and recombination rate in 3748 genes indicates that higher recombination rates are associated with an increased efficacy of purifying selection, suggesting that global recombination rates affect variation in rates of molecular evolution across distantly related angiosperm species, not just between populations. We also identified shifts in dN/dS for recombination proteins that are associated with shifts in global recombination rate across our sample of angiosperms. Although our analyses only reveal correlations, not mechanisms, and do not include potential covariates of recombination rate, like effective

  15. 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.

  16. Metabolite toxicity determines the pace of molecular evolution within microbial populations.

    PubMed

    Lilja, Elin E; Johnson, David R

    2017-02-14

    The production of toxic metabolites has shaped the spatial and temporal arrangement of metabolic processes within microbial cells. While diverse solutions to mitigate metabolite toxicity have evolved, less is known about how evolution itself is affected by metabolite toxicity. We hypothesized that the pace of molecular evolution should increase as metabolite toxicity increases. At least two mechanisms could cause this. First, metabolite toxicity could increase the mutation rate. Second, metabolite toxicity could increase the number of available mutations with large beneficial effects that selection could act upon (e.g., mutations that provide tolerance to toxicity), which consequently would increase the rate at which those mutations increase in frequency. We tested this hypothesis by experimentally evolving the bacterium Pseudomonas stutzeri under denitrifying conditions. The metabolite nitrite accumulates during denitrification and has pH-dependent toxic effects, which allowed us to evolve P. stutzeri at different magnitudes of nitrite toxicity. We demonstrate that increased nitrite toxicity results in an increased pace of molecular evolution. We further demonstrate that this increase is generally due to an increased number of available mutations with large beneficial effects and not to an increased mutation rate. Our results demonstrate that the production of toxic metabolites can have important impacts on the evolutionary processes of microbial cells. Given the ubiquity of toxic metabolites, they could also have implications for understanding the evolutionary histories of biological organisms.

  17. Molecular evolution of GYPC: evidence for recent structural innovation and positive selection in humans.

    PubMed

    Wilder, Jason A; Hewett, Elizabeth K; Gansner, Meredith E

    2009-12-01

    GYPC encodes two erythrocyte surface sialoglycoproteins in humans, glycophorin C and glycophorin D (GPC and GPD), via initiation of translation at two start codons on a single transcript. The malaria-causing parasite Plasmodium falciparum uses GPC as a means of invasion into the human red blood cell. Here, we examine the molecular evolution of GYPC among the Hominoidea (Greater and Lesser Apes) and also the pattern of polymorphism at the locus in a global human sample. We find an excess of nonsynonymous divergence among species that appears to be caused solely by accelerated evolution of GYPC in the human lineage. Moreover, we find that the ability of GYPC to encode both GPC and GPD is a uniquely human trait, caused by the evolution of the GPC start codon in the human lineage. The pattern of polymorphism among humans is consistent with a hitchhiking event at the locus, suggesting that positive natural selection affected GYPC in the relatively recent past. Because GPC is exploited by P. falciparum for invasion of the red blood cell, we hypothesize that selection for evasion of P. falciparum has caused accelerated evolution of GYPC in humans (relative to other primates) and that this positive selection has continued to act in the recent evolution of our species. These data suggest that malaria has played a powerful role in shaping molecules on the surface of the human red blood cell. In addition, our examination of GYPC reveals a novel mechanism of protein evolution: co-option of untranslated region (UTR) sequence following the formation of a new start codon. In the case of human GYPC, the ancestral protein (GPD) continues to be produced through leaky translation. Because leaky translation is a widespread phenomenon among genes and organisms, we suggest that co-option of UTR sequence may be an important source of protein innovation.

  18. 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.

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

    PubMed Central

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

    2009-01-01

    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 endothermy1–3. 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 ventricles4–7? We examined 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 precursors8,9. 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. PMID:19727199

  20. Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi.

    PubMed Central

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

    2000-01-01

    The von Willebrand factor (vWF) gene has been used to understand the origin and timing of Rodentia evolution in the context of placental phylogeny vWF exon 28 sequences of 15 rodent families and eight non-rodent eutherian clades are analysed with two different molecular dating methods (uniform clock on a linearized tree; quartet dating). Three main conclusions are drawn from the study of this nuclear exon. First, Ctenodactylidae (gundis) and Hystricognathi (e.g. porcupines, guinea-pigs, chinchillas) robustly cluster together in a newly recognized clade, named 'Ctenohystrica'. The Sciurognathi monophyly is subsequently rejected. Pedetidae (springhares) is an independent and early diverging rodent lineage, suggesting a convergent evolution of the multiserial enamel of rodent incisors. Second, molecular date estimates are here more influenced by accuracy and choice of the palaeontological temporal references used to calibrate the molecular clock than by either characters analysed (nucleotides versus amino acids) or species sampling. The caviomorph radiation at 31 million years (Myr) and the pig porpoise split at 63 Myr appear to be reciprocally compatible dates. Third, during the radiation of Rodentia, at least three lineages (Gliridae, Sciuroidea and Ctenohystrica) emerged close to the Cretaceous-Tertiary boundary, and their common ancestor separated from other placental orders in the Late Cretaceous. PMID:10722222

  1. 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.

  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. Understanding the reaction of nuclear graphite with molecular oxygen: Kinetics, transport, and structural evolution

    DOE PAGES

    Kane, Joshua J.; Contescu, Cristian I.; Smith, Rebecca E.; ...

    2017-06-08

    A thorough understanding of oxidation is important when considering the health and integrity of graphite components in graphite reactors. For the next generation of graphite reactors, HTGRs specifically, an unlikely air ingress has been deemed significant enough to have made its way into the licensing applications of many international licensing bodies. While a substantial body of literature exists on nuclear graphite oxidation in the presence of molecular oxygen and significant efforts have been made to characterize oxidation kinetics of various grades, the value of existing information is somewhat limited. Often, multiple competing processes, including reaction kinetics, mass transfer, and microstructuralmore » evolution, are lumped together into a single rate expression that limits the ability to translate this information to different conditions. This article reviews the reaction of graphite with molecular oxygen in terms of the reaction kinetics, gas transport, and microstructural evolution of graphite. It also presents the foundations of a model for the graphite-molecular oxygen reaction system that is kinetically independent of graphite grade, and is capable of describing both the bulk and local oxidation rates under a wide range of conditions applicable to air-ingress.« less

  4. Evolution of the C4 photosynthetic pathway: events at the cellular and molecular levels.

    PubMed

    Ludwig, Martha

    2013-11-01

    The biochemistry and leaf anatomy of plants using C4 photosynthesis promote the concentration of atmospheric CO2 in leaf tissue that leads to improvements in growth and yield of C4 plants over C3 species in hot, dry, high light, and/or saline environments. C4 plants like maize and sugarcane are significant food, fodder, and bioenergy crops. The C4 photosynthetic pathway is an excellent example of convergent evolution, having evolved in multiple independent lineages of land plants from ancestors employing C3 photosynthesis. In addition to C3 and C4 species, some plant lineages contain closely related C3-C4 intermediate species that demonstrate leaf anatomical, biochemical, and physiological characteristics between those of C3 plants and species using C4 photosynthesis. These groups of plants have been extremely useful in dissecting the modifications to leaf anatomy and molecular biology, which led to the evolution of C4 photosynthesis. It is now clear that great variation exists in C4 leaf anatomy, and diverse molecular mechanisms underlie C4 biochemistry and physiology. However, all these different paths have led to the same destination-the expression of a C4 CO2 concentrating mechanism. Further identification of C4 leaf anatomical traits and molecular biological components, and understanding how they are controlled and assembled will not only allow for additional insights into evolutionary convergence, but also contribute to sustainable food and bioenergy production strategies.

  5. Hepatitis C virus molecular evolution: Transmission, disease progression and antiviral therapy

    PubMed Central

    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

    2014-01-01

    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. PMID:25473152

  6. 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.

  7. 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.

  8. Molecular evolution of arthropod color vision deduced from multiple opsin genes of jumping spiders.

    PubMed

    Koyanagi, Mitsumasa; Nagata, Takashi; Katoh, Kazutaka; Yamashita, Shigeki; Tokunaga, Fumio

    2008-02-01

    Among terrestrial animals, only vertebrates and arthropods possess wavelength-discrimination ability, so-called "color vision". For color vision to exist, multiple opsins which encode visual pigments sensitive to different wavelengths of light are required. While the molecular evolution of opsins in vertebrates has been well investigated, that in arthropods remains to be elucidated. This is mainly due to poor information about the opsin genes of non-insect arthropods. To obtain an overview of the evolution of color vision in Arthropoda, we isolated three kinds of opsins, Rh1, Rh2, and Rh3, from two jumping spider species, Hasarius adansoni and Plexippus paykulli. These spiders belong to Chelicerata, one of the most distant groups from Hexapoda (insects), and have color vision as do insects. Phylogenetic analyses of jumping spider opsins revealed a birth and death process of color vision evolution in the arthropod lineage. Phylogenetic positions of jumping spider opsins revealed that at least three opsins had already existed before the Chelicerata-Pancrustacea split. In addition, sequence comparison between jumping spider Rh3 and the shorter wavelength-sensitive opsins of insects predicted that an opsin of the ancestral arthropod had the lysine residue responsible for UV sensitivity. These results strongly suggest that the ancestral arthropod had at least trichromatic vision with a UV pigment and two visible pigments. Thereafter, in each pancrustacean and chelicerate lineage, the opsin repertoire was reconstructed by gene losses, gene duplications, and function-altering amino acid substitutions, leading to evolution of color vision.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  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. Patterns of molecular evolution and predicted function in thaumatin-like proteins of Populus trichocarpa.

    PubMed

    Zhao, Jia Ping; Su, Xiao Hua

    2010-09-01

    Some pathogenesis-related proteins (PR proteins) are subject to positive selection, while others are under negative selection. Here, we report the patterns of molecular evolution in thaumatin-like protein (TLP, PR5 protein) genes of Populus trichocarpa. Signs of positive selection were found in 20 out of 55 Populus TLPs using the likelihood ratio test and ML-based Bayesian methods. Due to the connection between the acidic cleft and the antifungal activity, the secondary structure and three-dimensional structure analyses predicted antifungal activity beta-1,3-glucanase activities in these TLPs. Moreover, the coincidence with variable basic sites in the acidic cleft and positively selected sites suggested that fungal diseases may have been the main environmental stress that drove rapid adaptive evolution in Populus.

  15. Molecular evolution and recombination in gender-associated mitochondrial DNAs of the Manila clam Tapes philippinarum.

    PubMed Central

    Passamonti, Marco; Boore, Jeffrey L; Scali, Valerio

    2003-01-01

    Doubly uniparental inheritance (DUI) provides an intriguing system for addressing aspects of molecular evolution and intermolecular recombination of mitochondrial DNA. For this reason, a large sequence analysis has been performed on Tapes philippinarum (Bivalvia, Veneridae), which has mitochondrial DNA heteroplasmy that is consistent with a DUI. The sequences of a 9.2-kb region (containing 29 genes) from 9 individuals and the sequences of a single gene from another 44 individuals are analyzed. Comparisons suggest that the two sex-related mitochondrial genomes do not experience a neutral pattern of divergence and that selection may act with varying strength on different genes. This pattern of evolution may be related to the long, separate history of M and F genomes within their tissue-specific "arenas." Moreover, our data suggest that recombinants, although occurring in soma, may seldom be transmitted to progeny in T. philippinarum. PMID:12807780

  16. 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.

  17. 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.

  18. 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.

  19. Evolution of the Toxoglossa Venom Apparatus as Inferred by Molecular Phylogeny of the Terebridae

    PubMed Central

    Puillandre, Nicolas; Terryn, Yves; Cruaud, Corinne; Olivera, Baldomero; Bouchet, Philippe

    2009-01-01

    Toxoglossate marine gastropods, traditionally assigned to the families Conidae, Terebridae, and Turridae, are one of the most populous animal groups that use venom to capture their prey. These marine animals are generally characterized by a venom apparatus that consists of a muscular venom bulb and a tubular venom gland. The toxoglossan radula, often compared with a hypodermic needle for its use as a conduit to inject toxins into prey, is considered a major anatomical breakthrough that assisted in the successful initial radiation of these animals in the Cretaceous and early Tertiary. The pharmacological success of toxins from cone snails has made this group a star among biochemists and neuroscientists, but very little is known about toxins from the other Toxoglossa, and the phylogeny of these families is largely in doubt. Here we report the first molecular phylogeny for the Terebridae and use the results to infer the evolution of the venom apparatus for this group. Our findings indicate that most of the genera of terebrids are polyphyletic, and one species (“Terebra” (s.l.) jungi) is the sister group to all other terebrids. Molecular analyses combined with mapping of venom apparatus morphology indicate that the Terebridae have lost the venom apparatus at least twice during their evolution. Species in the genera Terebra and Hastula have the typical venom apparatus found in most toxoglossate gastropods, but all other terebrid species do not. For venomous organisms, the dual analysis of molecular phylogeny and toxin function is an instructive combination for unraveling the larger questions of phylogeny and speciation. The results presented here suggest a paradigm shift in the current understanding of terebrid evolution, while presenting a road map for discovering novel terebrid toxins, a largely unexplored resource for biomedical research and potential therapeutic drug development. PMID:18840603

  20. Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis

    PubMed Central

    Goubet, Pauline M.; Bergès, Hélène; Bellec, Arnaud; Prat, Elisa; Helmstetter, Nicolas; Mangenot, Sophie; Gallina, Sophie; Holl, Anne-Catherine; Fobis-Loisy, Isabelle; Vekemans, Xavier; Castric, Vincent

    2012-01-01

    Self-incompatibility has been considered by geneticists a model system for reproductive biology and balancing selection, but our understanding of the genetic basis and evolution of this molecular lock-and-key system has remained limited by the extreme level of sequence divergence among haplotypes, resulting in a lack of appropriate genomic sequences. In this study, we report and analyze the full sequence of eleven distinct haplotypes of the self-incompatibility locus (S-locus) in two closely related Arabidopsis species, obtained from individual BAC libraries. We use this extensive dataset to highlight sharply contrasted patterns of molecular evolution of each of the two genes controlling self-incompatibility themselves, as well as of the genomic region surrounding them. We find strong collinearity of the flanking regions among haplotypes on each side of the S-locus together with high levels of sequence similarity. In contrast, the S-locus region itself shows spectacularly deep gene genealogies, high variability in size and gene organization, as well as complete absence of sequence similarity in intergenic sequences and striking accumulation of transposable elements. Of particular interest, we demonstrate that dominant and recessive S-haplotypes experience sharply contrasted patterns of molecular evolution. Indeed, dominant haplotypes exhibit larger size and a much higher density of transposable elements, being matched only by that in the centromere. Overall, these properties highlight that the S-locus presents many striking similarities with other regions involved in the determination of mating-types, such as sex chromosomes in animals or in plants, or the mating-type locus in fungi and green algae. PMID:22457631

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

    PubMed

    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. (c) 2010 American Institute of Physics.

  2. 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.

  3. Evolution of the Toxoglossa venom apparatus as inferred by molecular phylogeny of the Terebridae.

    PubMed

    Holford, Mandë; Puillandre, Nicolas; Terryn, Yves; Cruaud, Corinne; Olivera, Baldomero; Bouchet, Philippe

    2009-01-01

    Toxoglossate marine gastropods, traditionally assigned to the families Conidae, Terebridae, and Turridae, are one of the most populous animal groups that use venom to capture their prey. These marine animals are generally characterized by a venom apparatus that consists of a muscular venom bulb and a tubular venom gland. The toxoglossan radula, often compared with a hypodermic needle for its use as a conduit to inject toxins into prey, is considered a major anatomical breakthrough that assisted in the successful initial radiation of these animals in the Cretaceous and early Tertiary. The pharmacological success of toxins from cone snails has made this group a star among biochemists and neuroscientists, but very little is known about toxins from the other Toxoglossa, and the phylogeny of these families is largely in doubt. Here we report the first molecular phylogeny for the Terebridae and use the results to infer the evolution of the venom apparatus for this group. Our findings indicate that most of the genera of terebrids are polyphyletic, and one species ("Terebra" (s.l.) jungi) is the sister group to all other terebrids. Molecular analyses combined with mapping of venom apparatus morphology indicate that the Terebridae have lost the venom apparatus at least twice during their evolution. Species in the genera Terebra and Hastula have the typical venom apparatus found in most toxoglossate gastropods, but all other terebrid species do not. For venomous organisms, the dual analysis of molecular phylogeny and toxin function is an instructive combination for unraveling the larger questions of phylogeny and speciation. The results presented here suggest a paradigm shift in the current understanding of terebrid evolution, while presenting a road map for discovering novel terebrid toxins, a largely unexplored resource for biomedical research and potential therapeutic drug development.

  4. 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.

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

    PubMed Central

    Fedor, Anna; de Vladar, Harold P.; Szathmáry, Eörs

    2017-01-01

    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

  6. Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer.

    PubMed

    Dienstmann, Rodrigo; Vermeulen, Louis; Guinney, Justin; Kopetz, Scott; Tejpar, Sabine; Tabernero, Josep

    2017-02-01

    Critical driver genomic events in colorectal cancer have been shown to affect the response to targeted agents that were initially developed under the 'one gene, one drug' paradigm of precision medicine. Our current knowledge of the complexity of the cancer genome, clonal evolution patterns under treatment pressure and pharmacodynamic effects of target inhibition support the transition from a one gene, one drug approach to a 'multi-gene, multi-drug' model when making therapeutic decisions. Better characterization of the transcriptomic subtypes of colorectal cancer, encompassing tumour, stromal and immune components, has revealed convergent pathway dependencies that mandate a 'multi-molecular' perspective for the development of therapies to treat this disease.

  7. 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.

  8. Determination of proton transfer rate constants using Ab initio, molecular dynamics and density matrix evolution calculations.

    PubMed

    van der Spoel, D; Berendsen, H J

    1996-01-01

    In this work we give an overview of the methodologies required to compute the rate of proton transfer in hydrogen bonded systems in solution. Using ab initio or density functional methods we determine proton potentials of a truncated system as a function of proton-donor proton-acceptor distance as well as nonbonding parameters. By classical molecular dynamics we evaluate a swarm of proton potentials with the proton fixed in the reactant well. The rate of proton transfer is calculated perturbatively using the Density Matrix Evolution (DME) method, going beyond the Born Oppenheimer approximation. The method is illustrated by two examples: hydrogen malonate and the active center of HIV-1 protease.

  9. 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.

  10. Evolution of shear banding flows in metallic glasses characterized by molecular dynamics

    SciTech Connect

    Yao, Li; Luan, Yingwei

    2016-06-21

    To reveal the evolution of shear banding flows, one-dimensional nanostructure metallic glass composites have been studied with molecular dynamics. The inherent size determines the initial thickness of shear bands, and the subsequent broadening can be restricted to some extent. The vortex-like flows evoke the atomic motion perpendicular to the shear plane, which accelerates the interatomic diffusion. The reduction of local strain rate causes the flow softening for monolithic Cu-Zr glass, but the participation of Cu-atoms in the shear banding flow gradually leads to the shear hardening for the composites.

  11. 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.

  12. Evolution of the circumstellar atomic and molecular envelopes around evolved stars

    NASA Astrophysics Data System (ADS)

    Fong, David Ken

    2003-09-01

    The asymptotic giant branch (AGB) mass loss history of stars is recorded in the structure of their circumstellar envelope (CSE). For the more evolved protoplanetary nebula (PPN) and planetary nebula (PN) phases, the CSE also chronicles its interaction with fast winds and photodissociating/photoionizing radiation. Most AGB stars lose mass in spherically symmetric outflows, whereas PNe are largely axisymmetric. To investigate the physical properties of these winds and the processes that shape the CSE prior to the PN stage, the neutral atomic and molecular gas are probed. Here we present observations of the atomic and molecular components of the CSE for objects at different epochs of evolution. Far-infrared (FIR) spectra were taken for 24 evolved stars, including the line emission of [O I], [C II], [Si I], [Si II], [S I], [Fe I], [Fe II], and [Ne II]. Atomic emission was found only in those sources where Teff ≥ 10000 K. With higher T eff the number of detectable lines increase as well as the intensity of the emission, which imply that these atomic lines originate from photodissociation regions (PDRs). The line measurements agree reasonably well with intensities predicted by PDR models. Shock models, however, do not compare well with the observed line intensities. The kinematics of the atomic gas are comparable to the molecular expansion velocities, expected for cooling lines associated with circumstellar PDRs. PDR mass estimates ranging from ˜0.01 1.3 M⊙ were derived from the [C II] 158 μm line emission. Half of these objects were selected for a complementary, study of the molecular gas component. In the 12CO J = 1 → 0 imaging survey, high resolution maps of their full molecular envelopes are presented. A variety of different nebular morphologies and kinematic structures were encountered. For the PPNe and PN, the neutral molecular envelopes are compared with images taken at optical, near-IR, and mid-IR wavelengths. These trace the different components of the

  13. Molecular anions in circumstellar envelopes, interstellar clouds and planetary atmospheres: quantum dynamics of formation and evolution

    NASA Astrophysics Data System (ADS)

    Carelli, Fabio

    2012-09-01

    For decades astronomers and astrophysicists believed that only positively charged ions were worthy of relevance in drawing the networks for possible chemical reactions in the interstellar medium, as well as in modeling the physical conditions in most of astrophysical environments. Thus, molecular negative ions received minor attention until their possible existence was observationally confirmed (discovery of the first interstellar anion, C6H-), about thirty years after the first physically reasonable proposal on their actual detection was theoretically surmised by E.Herbst. In an astrophysical context, their role should be then found in their involvement in the charge balance as well as in the chemical evolution of the considered environment: depending on their amount and on the global gas density, in fact, the possible evolutive scenario could be susceptible of marked variations on the estimated time needed for reaching the steady state, their presence having thus also important repercussions on the final chemical composition of a given environment. The main reasons that originally motivated us to undertake the present work, were at least two. First of all, we intended to demonstrate the importance of resonances in forming molecular anions in different astrophysical environments. Secondly, we were attracted by the possibility of investigating the occurrence of radiationless paths like intramolecular vibrational redistributions to account for the dissipation of the extra energy initially carried by the impinging electron. Accordingly, the present PhD represents a theoretical/computational work which deals with an area placed at the boundary between (molecular) astrophysics, quantum collision thery, and theoretical chemistry. The three molecular species whose behaviour under low-energy electron collisions will be discussed are: the ortho-benzyne, the coronene and the carbon nitride.

  14. 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.

  15. Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria.

    PubMed

    Kuo, Chih-Horng; Ochman, Howard

    2009-09-29

    Because bacteria do not have a robust fossil record, attempts to infer the timing of events in their evolutionary history requires comparisons of molecular sequences. This use of molecular clocks is based on the assumptions that substitution rates for homologous genes or sites are fairly constant through time and across taxa. Violation of these conditions can lead to erroneous inferences and result in estimates that are off by orders of magnitude. In this study, we examine the consistency of substitution rates among a set of conserved genes in diverse bacterial lineages, and address the questions regarding the validity of molecular dating. By examining the evolution of 16S rRNA gene in obligate endosymbionts, which can be calibrated by the fossil record of their hosts, we found that the rates are consistent within a clade but varied widely across different bacterial lineages. Genome-wide estimates of nonsynonymous and synonymous substitutions suggest that these two measures are highly variable in their rates across bacterial taxa. Genetic drift plays a fundamental role in determining the accumulation of substitutions in 16S rRNA genes and at nonsynonymous sites. Moreover, divergence estimates based on a set of universally conserved protein-coding genes also exhibit low correspondence to those based on 16S rRNA genes. Our results document a wide range of substitution rates across genes and bacterial taxa. This high level of variation cautions against the assumption of a universal molecular clock for inferring divergence times in bacteria. However, by applying relative-rate tests to homologous genes, it is possible to derive reliable local clocks that can be used to calibrate bacterial evolution. This article was reviewed by Adam Eyre-Walker, Simonetta Gribaldo and Tal Pupko (nominated by Dan Graur).

  16. 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

  17. 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.

  18. 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

  19. Some thoughts on evolution.

    PubMed

    Conyers, R A; Fazzalari, N L

    1980-01-01

    The sparsity of transitional forms and the abrupt appearance of higher taxa in the fossil record are enigmas for the neo-Darwinian theory of evolution. If the cell is considered to be a steady state system then mutations affecting non-regulatory proteins will have far less effect on the steady state than mutations affecting regulatory proteins. This latter type of mutation, when expressed in multicellular biological systems, is a sufficient explanation for the discontinuities observed between species. Such a mechanism, however, has its own implications for any theory of evolution.

  20. 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

  1. 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.

  2. 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.

  3. Molecular evolution of the clustered MIC-3 multigene family of Gossypium species.

    PubMed

    Buriev, Zabardast T; Saha, Sukumar; Shermatov, Shukhrat E; Jenkins, Johnie N; Abdukarimov, Abdusattor; Stelly, David M; Abdurakhmonov, Ibrokhim Y

    2011-12-01

    The Gossypium MIC-3 (Meloidogyne Induced Cotton-3) gene family is of great interest for molecular evolutionary studies because of its uniqueness to Gossypium species, multi-gene content, clustered localization, and root-knot nematode resistance-associated features. Molecular evolution of the MIC-3 gene family was studied in 15 tetraploid and diploid Gossypium genotypes that collectively represent seven phylogenetically distinct genomes. Synonymous (d(S)) and non-synonymous (d(N)) nucleotide substitution rates suggest that the second of the two exons of the MIC-3 genes has been under strong positive selection pressure, while the first exon has been under strong purifying selection to preserve function. Based on nucleotide substitution rates, we conclude that MIC-3 genes are evolving by a birth-and-death process and that a 'gene amplification' mechanism has helped to retain all duplicate copies, which best fits with the "bait and switch" model of R-gene evolution. The data indicate MIC-3 gene duplication events occurred at various rates, once per 1 million years (MY) in the allotetraploids, once per ~2 MY in the A/F genome clade, and once per ~8 MY in the D-genome clade. Variations in the MIC-3 gene family seem to reflect evolutionary selection for increased functional stability, while also expanding the capacity to develop novel "switch" pockets for responding to diverse pests and pathogens. Such evolutionary roles are congruent with the hypothesis that members of this unique resistance gene family provide fitness advantages in Gossypium.

  4. 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

  5. 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.

  6. Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry.

    PubMed

    Anisimova, Maria

    2015-05-01

    Today computational molecular evolution is a vibrant research field that benefits from the availability of large and complex new generation sequencing data - ranging from full genomes and proteomes to microbiomes, metabolomes and epigenomes. The grounds for this progress were established long before the discovery of the DNA structure. Specifically, Darwin's theory of evolution by means of natural selection not only remains relevant today, but also provides a solid basis for computational research with a variety of applications. But a long-term progress in biology was ensured by the mathematical sciences, as exemplified by Sir R. Fisher in early 20th century. Now this is true more than ever: The data size and its complexity require biologists to work in close collaboration with experts in computational sciences, modeling and statistics. Natural selection drives function conservation and adaptation to emerging pathogens or new environments; selection plays key role in immune and resistance systems. Here I focus on computational methods for evaluating selection in molecular sequences, and argue that they have a high potential for applications. Pharma and biotech industries can successfully use this potential, and should take the initiative to enhance their research and development with state of the art bioinformatics approaches. This review provides a quick guide to the current computational approaches that apply the evolutionary principles of natural selection to real life problems - from drug target validation, vaccine design and protein engineering to applications in agriculture, ecology and conservation.

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. Contribution of recombination and selection to molecular evolution of Citrus tristeza virus.

    PubMed

    Martín, Susana; Sambade, Adrián; Rubio, Luis; Vives, María C; Moya, Patricia; Guerri, José; Elena, Santiago F; Moreno, Pedro

    2009-06-01

    The genetic variation of Citrus tristeza virus (CTV) was analysed by comparing the predominant sequence variants in seven genomic regions (p33, p65, p61, p18, p13, p20 and p23) of 18 pathogenically distinct isolates from seven different countries. Analyses of the selective constraints acting on each codon suggest that most regions were under purifying selection. Phylogenetic analysis shows diverse patterns of molecular evolution for different genomic regions. A first clade composed of isolates that are genetically close to the reference mild isolates T385 or T30 was inferred from all genomic regions. A second clade, mostly comprising virulent isolates, was defined from regions p33, p65, p13 and p23. For regions p65, p61, p18, p13 and p23, a third clade that mostly included South American isolates could not be related to any reference genotype. Phylogenetic relationships among isolates did not reflect their geographical origin, suggesting significant gene flow between geographically distant areas. Incongruent phylogenetic trees for different genomic regions suggested recombination events, an extreme that was supported by several recombination-detecting methods. A phylogenetic network incorporating the effect of recombination showed an explosive radiation pattern for the evolution of some isolates and also grouped isolates by virulence. Taken together, the above results suggest that negative selection, gene flow, sequence recombination and virulence may be important factors driving CTV evolution.

  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. © 2015 John Wiley & Sons Ltd.

  15. 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. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

  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. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

  17. 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.

  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. 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.

  20. 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

  1. Molecular evolution of globin genes in Gymnotiform electric fishes: relation to hypoxia tolerance.

    PubMed

    Tian, Ran; Losilla, Mauricio; Lu, Ying; Yang, Guang; Zakon, Harold

    2017-02-13

    Nocturnally active gymnotiform weakly electric fish generate electric signals for communication and navigation, which can be energetically taxing. These fish mainly inhabit the Amazon basin, where some species prefer well-oxygenated waters and others live in oxygen-poor, stagnant habitats. The latter species show morphological, physiological, and behavioral adaptations for hypoxia-tolerance. However, there have been no studies of hypoxia tolerance on the molecular level. Globins are classic respiratory proteins. They function principally in oxygen-binding and -delivery in various tissues and organs. Here, we investigate the molecular evolution of alpha and beta hemoglobins, myoglobin, and neuroglobin in 12 gymnotiforms compared with other teleost fish. The present study identified positively selected sites (PSS) on hemoglobin (Hb) and myoglobin (Mb) genes using different maximum likelihood (ML) methods; some PSS fall in structurally important protein regions. This evidence for the positive selection of globin genes suggests that the adaptive evolution of these genes has helped to enhance the capacity for oxygen storage and transport. Interestingly, a substitution of a Cys at a key site in the obligate air-breathing electric eel (Electrophorus electricus) is predicted to enhance oxygen storage of Mb and contribute to NO delivery during hypoxia. A parallel Cys substitution was also noted in an air-breathing African electric fish (Gymnarchus niloticus). Moreover, the expected pattern under normoxic conditions of high expression of myoglobin in heart and neuroglobin in the brain in two hypoxia-tolerant species suggests that the main effect of selection on these globin genes is on their sequence rather than their basal expression patterns. Results indicate a clear signature of positive selection in the globin genes of most hypoxia-tolerant gymnotiform fishes, which are obligate or facultative air breathers. These findings highlight the critical role of globin genes in

  2. 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'.

  3. Phylogenetic Analysis and Molecular Evolution Patterns in the MIR482-MIR1448 Polycistron of Populus L

    PubMed Central

    Zhao, Jia-Ping; Diao, Shu; Zhang, Bing-Yu; Niu, Bao-Qing; Wang, Qing-Ling; Wan, Xian-Chong; Luo, You-Qing

    2012-01-01

    The microRNAs (miRNAs) miR482 and miR1448 are disease resistance-related miRNAs; the former is ubiquitously distributed in seed plants whereas the latter has only been reported in Populus trichocarpa. The precursor and mature sequences of poplar miR1448 are highly homologous to those of poplar miR482, and these two miRNAs are located in one transcript as a polycistron. Therefore, we hypothesized that the MIR1448 gene may have evolved from the MIR482 gene in poplar. However, the molecular evolution patterns of this process remain unclear. In this study, utilizing cloning and Blast analysis in NCBI ESTs and whole-genome shotgun contigs (WGS) dataset, we determined that the MIR482-MIR1448 polycistron is a family-specific clustered miRNA in Salicaceae. Moreover, phylogenetic analysis illustrated that MIR1448 is the product of a tandem duplication event from MIR482. Nucleotide substitution analysis revealed that both MIR482 and MIR1448 have more rapid evolution ratios than ribosomal DNA (rDNA) genes, and that compensatory mutations that occurred in the stem region of the secondary structure were the main mechanisms that drove the evolution of these MIRNA genes. Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the “duplicated MIR482” evolve to MIR1448. We propose a novel miRNA-target pairing pattern called the “frameshift targeted mechanism” to explain the gain of target genes by miR1448. The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse. PMID:23094096

  4. Temporal dynamics of intrahost molecular evolution for a plant RNA virus.

    PubMed

    Cuevas, José M; Willemsen, Anouk; Hillung, Julia; Zwart, Mark P; Elena, Santiago F

    2015-05-01

    Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host pepper were phenotypically characterized and genetically analyzed. Temporal and compartmental variabilities of TEV populations were quantified using high throughput Illumina sequencing and population genetic approaches. Of the two viral phenotypic traits measured, virulence increased in the novel host but decreased in the original one, and viral load decreased in both hosts, though to a lesser extent in the novel one. Dynamics of population genetic diversity were also markedly different among hosts. Population heterozygosity increased in the ancestral host, with a dominance of synonymous mutations fixed, whereas it did not change or even decreased in the new host, with an excess of nonsynonymous mutations. All together, these observations suggest that directional selection is the dominant evolutionary force in TEV populations evolving in a novel host whereas either diversifying selection or random genetic drift may play a fundamental role in the natural host. To better understand these evolutionary dynamics, we developed a computer simulation model that incorporates the effects of mutation, selection, and drift. Upon parameterization with empirical data from previous studies, model predictions matched the observed patterns, thus reinforcing our idea that the empirical patterns of mutation accumulation represent adaptive evolution. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution.

    PubMed

    Xia, Xuhua

    2013-07-01

    Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20 standard sequence formats including MEGA, NEXUS, PHYLIP, GenBank, and the new NeXML format for interoperability, 2) motif characterization and discovery functions such as position weight matrix and Gibbs sampler, 3) descriptive genomic analysis tools with improved versions of codon adaptation index, effective number of codons, protein isoelectric point profiling, RNA and protein secondary structure prediction and calculation of minimum folding energy, and genomic skew plots with optimized window size, 4) molecular phylogenetics including sequence alignment, testing substitution saturation, distance-based, maximum parsimony, and maximum-likelihood methods for tree reconstructions, testing the molecular clock hypothesis with either a phylogeny or with relative-rate tests, dating gene duplication and speciation events, choosing the best-fit substitution models, and estimating rate heterogeneity over sites, 5) phylogeny-based comparative methods for continuous and discrete variables, and 6) graphic functions including secondary structure display, optimized skew plot, hydrophobicity plot, and many other plots of amino acid properties along a protein sequence, tree display and drawing by dragging nodes to each other, and visual searching of the maximum parsimony tree. DAMBE features a graphic, user-friendly, and intuitive interface and is freely available from http://dambe.bio.uottawa.ca (last accessed April 16, 2013).

  6. Molecular evolution of anthocyanin pigmentation genes following losses of flower color.

    PubMed

    Ho, Winnie W; Smith, Stacey D

    2016-05-10

    Phenotypic transitions, such as trait gain or loss, are predicted to carry evolutionary consequences for the genes that control their development. For example, trait losses can result in molecular decay of the pathways underlying the trait. Focusing on the Iochrominae clade (Solanaceae), we examine how repeated losses of floral anthocyanin pigmentation associated with flower color transitions have affected the molecular evolution of three anthocyanin pathway genes (Chi, F3h, and Dfr). We recovered intact coding regions for the three genes in all of the lineages that have lost floral pigmentation, suggesting that molecular decay is not associated with these flower color transitions. However, two of the three genes (Chi, F3h) show significantly elevated dN/dS ratios in lineages without floral pigmentation. Maximum likelihood analyses suggest that this increase is due to relaxed constraint on anthocyanin genes in the unpigmented lineages as opposed to positive selection. Despite the increase, the values for dN/dS in both pigmented and unpigmented lineages were consistent overall with purifying selection acting on these loci. The broad conservation of anthocyanin pathway genes across lineages with and without floral anthocyanins is consistent with the growing consensus that losses of pigmentation are largely achieved by changes in gene expression as opposed to structural mutations. Moreover, this conservation maintains the potential for regain of flower color, and indicates that evolutionary losses of floral pigmentation may be readily reversible.

  7. 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.

  8. 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

  9. 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

  10. Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems

    PubMed Central

    Ruiz-Mirazo, Kepa; Briones, Carlos

    2017-01-01

    In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided. PMID:28446711

  11. Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems.

    PubMed