WorldWideScience

Sample records for understand evolutionary trees

  1. Evaluating Two Approaches to Helping College Students Understand Evolutionary Trees through Diagramming Tasks

    Science.gov (United States)

    Perry, Judy; Meir, Eli; Herron, Jon C.; Maruca, Susan; Stal, Derek

    2008-01-01

    To understand evolutionary theory, students must be able to understand and use evolutionary trees and their underlying concepts. Active, hands-on curricula relevant to macroevolution can be challenging to implement across large college-level classes where textbook learning is the norm. We evaluated two approaches to helping students learn…

  2. Tree Contractions and Evolutionary Trees

    OpenAIRE

    Kao, Ming-Yang

    2001-01-01

    An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of species. An agreement subtree of two evolutionary trees is an evolutionary tree which is also a topological subtree of the two given trees. We give an algorithm to determine the largest possible number of leaves in any agreement subtree of two trees T_1 and ...

  3. How to Identify and Interpret Evolutionary Tree Diagrams

    Science.gov (United States)

    Kong, Yi; Anderson, Trevor; Pelaez, Nancy

    2016-01-01

    Evolutionary trees are key tools for modern biology and are commonly portrayed in textbooks to promote learning about biological evolution. However, many people have difficulty in understanding what evolutionary trees are meant to portray. In fact, some ideas that current professional biologists depict with evolutionary trees are neither clearly…

  4. QDist—Quartet Distance Between Evolutionary Trees

    DEFF Research Database (Denmark)

    Mailund; Pedersen, Christian N. Storm

    2004-01-01

    QDist is a program for computing the quartet distance between two unrooted evolutionary trees, i.e. the number of quartet topology differences between the two trees, where a quartet topology is the topological subtree induced by four species. The implementation is based on an algorithm with running...... time O(n log² n), which makes it practical to compare large trees....

  5. BEAST: Bayesian evolutionary analysis by sampling trees.

    Science.gov (United States)

    Drummond, Alexei J; Rambaut, Andrew

    2007-11-08

    The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

  6. BEAST: Bayesian evolutionary analysis by sampling trees

    Directory of Open Access Journals (Sweden)

    Drummond Alexei J

    2007-11-01

    Full Text Available Abstract Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. Conclusion BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

  7. Dynamic Ising model: reconstruction of evolutionary trees

    International Nuclear Information System (INIS)

    De Oliveira, P M C

    2013-01-01

    An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. ‘Species’ here is a general denomination for biological species, spoken languages or any other entity which evolves through heredity. From the N currently alive species within a clade, distances are measured through pairwise comparisons made by geneticists, linguists, etc. The larger is such a distance that, for a pair of species, the older is their last common ancestor. The aim is to reconstruct the previously unknown bifurcations, i.e. the whole clade, from knowledge of the N(N − 1)/2 quoted distances, which are taken for granted. A mechanical method is presented and its applicability is discussed. (paper)

  8. Undergraduate Students’ Initial Ability in Understanding Phylogenetic Tree

    Science.gov (United States)

    Sa'adah, S.; Hidayat, T.; Sudargo, Fransisca

    2017-04-01

    The Phylogenetic tree is a visual representation depicts a hypothesis about the evolutionary relationship among taxa. Evolutionary experts use this representation to evaluate the evidence for evolution. The phylogenetic tree is currently growing for many disciplines in biology. Consequently, learning about the phylogenetic tree has become an important part of biological education and an interesting area of biology education research. Skill to understanding and reasoning of the phylogenetic tree, (called tree thinking) is an important skill for biology students. However, research showed many students have difficulty in interpreting, constructing, and comparing among the phylogenetic tree, as well as experiencing a misconception in the understanding of the phylogenetic tree. Students are often not taught how to reason about evolutionary relationship depicted in the diagram. Students are also not provided with information about the underlying theory and process of phylogenetic. This study aims to investigate the initial ability of undergraduate students in understanding and reasoning of the phylogenetic tree. The research method is the descriptive method. Students are given multiple choice questions and an essay that representative by tree thinking elements. Each correct answer made percentages. Each student is also given questionnaires. The results showed that the undergraduate students’ initial ability in understanding and reasoning phylogenetic tree is low. Many students are not able to answer questions about the phylogenetic tree. Only 19 % undergraduate student who answered correctly on indicator evaluate the evolutionary relationship among taxa, 25% undergraduate student who answered correctly on indicator applying concepts of the clade, 17% undergraduate student who answered correctly on indicator determines the character evolution, and only a few undergraduate student who can construct the phylogenetic tree.

  9. Evolutionary approaches to understanding sleep.

    Science.gov (United States)

    Lee Kavanau, J

    2005-04-01

    A major controversy over REM sleep's role in memory processing may owe to inadequate allowances for the highly conservative nature of evolutionary adaptations. The controversy hinges on whether NREM sleep, alone, retains primitive memory processing capabilities. The selective pressure for primitive sleep, is thought to have been the need to obviate conflicts between enormous neural processing requirements of complex visual analysis and split-second control of movements, on the one hand, and memory processing, on the other. The most efficient memory processing during mammalian and avian sleep appears to be a two-step process: synapses in individual component circuits of events are reinforced primarily by slow brain waves during NREM sleep, with the reinforced components temporally bound by fast waves, and manifested as dreams, during REM sleep. This dual action could account for partitioning of sleep periods into multiple NREM-REM cycles. It is proposed that in the absence of REM sleep, all needed memory processing can be accomplished by NREM sleep, alone, though less efficiently. Many symptoms of fatal familial insomnia are attributed to subnormal nightly reinforcement of brain circuitry because of almost total loss of sleep, and compensatory responses thereto during waking. During this disorder, sensory circuitry seemingly is spared by virtue of its supernormal reinforcement during almost continuous waking. Contrariwise, sparing of an adult's 'higher faculties' in encephalitis lethargica appears to owe to supernormal circuit reinforcement during almost continuous sleep.

  10. The Complexity of Constructing Evolutionary Trees Using Experiments

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Fagerberg, Rolf; Pedersen, Christian N.S.

    2001-01-01

    We present tight upper and lower bounds for the problem of constructing evolutionary trees in the experiment model. We describe an algorithm which constructs an evolutionary tree of n species in time O(nd logd n) using at most n⌈d/2⌉(log2⌈d/2⌉-1 n+O(1)) experiments for d > 2, and at most n(log n...

  11. Reconstructing evolutionary trees in parallel for massive sequences.

    Science.gov (United States)

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

    2017-12-14

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

  12. A Beta-splitting model for evolutionary trees.

    Science.gov (United States)

    Sainudiin, Raazesh; Véber, Amandine

    2016-05-01

    In this article, we construct a generalization of the Blum-François Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric shares of diversification rates (or diversification 'potential') between two sister species in an evolutionarily interpretable manner, as well as the addition of extinction to the model in a natural way. We describe the incremental evolutionary construction of a tree with n leaves by splitting or freezing extant lineages through the generating, organizing and deleting processes. We then give the probability of any (binary rooted) tree under this model with no extinction, at several resolutions: ranked planar trees giving asymmetric roles to the first and second offspring species of a given species and keeping track of the order of the speciation events occurring during the creation of the tree, unranked planar trees, ranked non-planar trees and finally (unranked non-planar) trees. We also describe a continuous-time equivalent of the generating, organizing and deleting processes where tree topology and branch lengths are jointly modelled and provide code in SageMath/Python for these algorithms.

  13. Evolutionary heritage influences amazon tree ecology

    NARCIS (Netherlands)

    Souza, De Fernanda Coelho; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J.W.; Chave, Jerome; Galbraith, David R.; Gonzalez, Gabriela Lopez; Mendoza, Abel Monteagudo; Toby Pennington, R.; Poorter, Lourens; Arets, E.J.M.M.; Boot, Rene G.A.; Meer, van der Peter J.

    2016-01-01

    Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of

  14. Assessing and Improving Student Understanding of Tree-Thinking

    Science.gov (United States)

    Kummer, Tyler A.

    Evolution is the unifying theory of biology. The importance of understanding evolution by those who study the origins, diversification and diversity life cannot be overstated. Because of its importance, in addition to a scientific study of evolution, many researchers have spent time studying the acceptance and the teaching of evolution. Phylogenetic Systematics is the field of study developed to understand the evolutionary history of organisms, traits, and genes. Tree-thinking is the term by which we identify concepts related to the evolutionary history of organisms. It is vital that those who undertake a study of biology be able to understand and interpret what information these phylogenies are meant to convey. In this project, we evaluated the current impact a traditional study of biology has on the misconceptions students hold by assessing tree-thinking in freshman biology students to those nearing the end of their studies. We found that the impact of studying biology was varied with some misconceptions changing significantly while others persisted. Despite the importance of tree-thinking no appropriately developed concept inventory exists to measure student understanding of these important concepts. We developed a concept inventory capable of filling this important need and provide evidence to support its use among undergraduate students. Finally, we developed and modified activities as well as courses based on best practices to improve teaching and learning of tree-thinking and organismal diversity. We accomplished this by focusing on two key questions. First, how do we best introduce students to tree-thinking and second does tree-thinking as a course theme enhance student understanding of not only tree-thinking but also organismal diversity. We found important evidence suggesting that introducing students to tree-thinking via building evolutionary trees was less successful than introducing the concept via tree interpretation and may have in fact introduced or

  15. Tapping the woodpecker tree for evolutionary insight.

    Science.gov (United States)

    Shakya, Subir B; Fuchs, Jérôme; Pons, Jean-Marc; Sheldon, Frederick H

    2017-11-01

    Molecular phylogenetic studies of woodpeckers (Picidae) have generally focused on relationships within specific clades or have sampled sparsely across the family. We compared DNA sequences of six loci from 203 of the 217 recognized species of woodpeckers to construct a comprehensive tree of intrafamilial relationships. We recovered many known, but also numerous unknown, relationships among clades and species. We found, for example, that the three picine tribes are related as follows (Picini, (Campephilini, Melanerpini)) and that the genus Dinopium is paraphyletic. We used the tree to analyze rates of diversification and biogeographic patterns within the family. Diversification rate increased on two occasions during woodpecker history. We also tested diversification rates between temperate and tropical species but found no significant difference. Biogeographic analysis supported an Old World origin of the family and identified at least six independent cases of New World-Old World sister relationships. In light of the tree, we discuss how convergence, mimicry, and potential cases of hybridization have complicated woodpecker taxonomy. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Hierarchical classification with a competitive evolutionary neural tree.

    Science.gov (United States)

    Adams, R G.; Butchart, K; Davey, N

    1999-04-01

    A new, dynamic, tree structured network, the Competitive Evolutionary Neural Tree (CENT) is introduced. The network is able to provide a hierarchical classification of unlabelled data sets. The main advantage that the CENT offers over other hierarchical competitive networks is its ability to self determine the number, and structure, of the competitive nodes in the network, without the need for externally set parameters. The network produces stable classificatory structures by halting its growth using locally calculated heuristics. The results of network simulations are presented over a range of data sets, including Anderson's IRIS data set. The CENT network demonstrates its ability to produce a representative hierarchical structure to classify a broad range of data sets.

  17. Calibrating the Tree of Life: fossils, molecules and evolutionary timescales.

    Science.gov (United States)

    Forest, Félix

    2009-10-01

    Molecular dating has gained ever-increasing interest since the molecular clock hypothesis was proposed in the 1960s. Molecular dating provides detailed temporal frameworks for divergence events in phylogenetic trees, allowing diverse evolutionary questions to be addressed. The key aspect of the molecular clock hypothesis, namely that differences in DNA or protein sequence between two species are proportional to the time elapsed since they diverged, was soon shown to be untenable. Other approaches were proposed to take into account rate heterogeneity among lineages, but the calibration process, by which relative times are transformed into absolute ages, has received little attention until recently. New methods have now been proposed to resolve potential sources of error associated with the calibration of phylogenetic trees, particularly those involving use of the fossil record. The use of the fossil record as a source of independent information in the calibration process is the main focus of this paper; other sources of calibration information are also discussed. Particularly error-prone aspects of fossil calibration are identified, such as fossil dating, the phylogenetic placement of the fossil and the incompleteness of the fossil record. Methods proposed to tackle one or more of these potential error sources are discussed (e.g. fossil cross-validation, prior distribution of calibration points and confidence intervals on the fossil record). In conclusion, the fossil record remains the most reliable source of information for the calibration of phylogenetic trees, although associated assumptions and potential bias must be taken into account.

  18. Performance Analysis of Evolutionary Algorithms for Steiner Tree Problems.

    Science.gov (United States)

    Lai, Xinsheng; Zhou, Yuren; Xia, Xiaoyun; Zhang, Qingfu

    2017-01-01

    The Steiner tree problem (STP) aims to determine some Steiner nodes such that the minimum spanning tree over these Steiner nodes and a given set of special nodes has the minimum weight, which is NP-hard. STP includes several important cases. The Steiner tree problem in graphs (GSTP) is one of them. Many heuristics have been proposed for STP, and some of them have proved to be performance guarantee approximation algorithms for this problem. Since evolutionary algorithms (EAs) are general and popular randomized heuristics, it is significant to investigate the performance of EAs for STP. Several empirical investigations have shown that EAs are efficient for STP. However, up to now, there is no theoretical work on the performance of EAs for STP. In this article, we reveal that the (1+1) EA achieves 3/2-approximation ratio for STP in a special class of quasi-bipartite graphs in expected runtime [Formula: see text], where [Formula: see text], [Formula: see text], and [Formula: see text] are, respectively, the number of Steiner nodes, the number of special nodes, and the largest weight among all edges in the input graph. We also show that the (1+1) EA is better than two other heuristics on two GSTP instances, and the (1+1) EA may be inefficient on a constructed GSTP instance.

  19. Impact of gene family evolutionary histories on phylogenetic species tree inference by gene tree parsimony.

    Science.gov (United States)

    Shi, Tao

    2016-03-01

    Complicated history of gene duplication and loss brings challenge to molecular phylogenetic inference, especially in deep phylogenies. However, phylogenomic approaches, such as gene tree parsimony (GTP), show advantage over some other approaches in its ability to use gene families with duplications. GTP searches the 'optimal' species tree by minimizing the total cost of biological events such as duplications, but accuracy of GTP and phylogenetic signal in the context of different gene families with distinct histories of duplication and loss are unclear. To evaluate how different evolutionary properties of different gene families can impact on species tree inference, 3900 gene families from seven angiosperms encompassing a wide range of gene content, lineage-specific expansions and contractions were analyzed. It was found that the gene content and total duplication number in a gene family strongly influence species tree inference accuracy, with the highest accuracy achieved at either very low or very high gene content (or duplication number) and lowest accuracy centered in intermediate gene content (or duplication number), as the relationship can fit a binomial regression. Besides, for gene families of similar level of average gene content, those with relatively higher lineage-specific expansion or duplication rates tend to show lower accuracy. Additional correlation tests support that high accuracy for those gene families with large gene content may rely on abundant ancestral copies to provide many subtrees to resolve conflicts, whereas high accuracy for single or low copy gene families are just subject to sequence substitution per se. Very low accuracy reached by gene families of intermediate gene content or duplication number can be due to insufficient subtrees to resolve the conflicts from loss of alternative copies. As these evolutionary properties can significantly influence species tree accuracy, I discussed the potential weighting of the duplication cost by

  20. How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity.

    Science.gov (United States)

    Franklin, Oskar; Palmroth, Sari; Näsholm, Torgny

    2014-11-01

    Tree breeding and biotechnology can enhance forest productivity and help alleviate the rising pressure on forests from climate change and human exploitation. While many physiological processes and genes are targeted in search of genetically improved tree productivity, an overarching principle to guide this search is missing. Here, we propose a method to identify the traits that can be modified to enhance productivity, based on the differences between trees shaped by natural selection and 'improved' trees with traits optimized for productivity. We developed a tractable model of plant growth and survival to explore such potential modifications under a range of environmental conditions, from non-water limited to severely drought-limited sites. We show how key traits are controlled by a trade-off between productivity and survival, and that productivity can be increased at the expense of long-term survival by reducing isohydric behavior (stomatal regulation of leaf water potential) and allocation to defense against pests compared with native trees. In contrast, at dry sites occupied by naturally drought-resistant trees, the model suggests a better strategy may be to select trees with slightly lower wood density than the native trees and to augment isohydric behavior and allocation to defense. Thus, which traits to modify, and in which direction, depend on the original tree species or genotype, the growth environment and wood-quality versus volume production preferences. In contrast to this need for customization of drought and pest resistances, consistent large gains in productivity for all genotypes can be obtained if root traits can be altered to reduce competition for water and nutrients. Our approach illustrates the potential of using eco-evolutionary theory and modeling to guide plant breeding and genetic technology in selecting target traits in the quest for higher forest productivity. © The Author 2014. Published by Oxford University Press. All rights reserved

  1. Incorporating tree-thinking and evolutionary time scale into developmental biology.

    Science.gov (United States)

    Kuraku, Shigehiro; Feiner, Nathalie; Keeley, Sean D; Hara, Yuichiro

    2016-01-01

    Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as "cryptic pan-vertebrate genes", are introduced as examples. © 2016 Japanese Society of Developmental Biologists.

  2. Understanding search trees via statistical physics

    Indian Academy of Sciences (India)

    ary search tree model (where stands for the number of branches of the search tree), an important problem for data storage in computer science, using a variety of statistical physics techniques that allow us to obtain exact asymptotic results.

  3. Understanding of evolutionary genomics of invasive species of rice

    Science.gov (United States)

    Red rice is an aggressive, weedy form of cultivated rice (Oryza sativa) that infests crop fields and is a primary factor limiting rice productivity in the U.S. and worldwide. As the weedy relative of a genomic model species, red rice is a model for understanding the genetic and evolutionary mechani...

  4. An Evolutionary Framework for Understanding the Origin of Eukaryotes.

    Science.gov (United States)

    Blackstone, Neil W

    2016-04-27

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

  5. An Evolutionary Framework for Understanding the Origin of Eukaryotes

    Directory of Open Access Journals (Sweden)

    Neil W. Blackstone

    2016-04-01

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

  6. Evolutionary trees and the rise of modern primatology: the forgotten contribution of St. George Mivart.

    Science.gov (United States)

    Bigoni, Francesca; Barsanti, Giulio

    2011-01-01

    The modern concept of the tree of life originated as a popular, iconic synthesis of the Darwinian evolutionary theory of descent by modification even if Darwin's own trees were hypothetical and abstract. It is generally thought that Ernst Haeckel in 1866 was the first to publish a true evolutionary tree which showed actual taxa. It is apparently forgotten that St. George Mivart beginning in 1865 made significant contributions to the development of evolutionary based trees of life which dealt with primate evolution, including human phylogeny. His trees were built on the most extensive sets of original data published up to that time, and were clearly articulated as working hypotheses. Mivart's trees were surprisingly modern for appearance and for content. Not only are most taxonomic names still in use today, but also many of the issues he raised are still under discussion in current scientific literature. The history of biology and especially that of primatology in the 19th century can benefit from a more thorough knowledge of how the image of the tree was used in scientific writings, especially after Darwin in the context of the theory of evolution by descent from common ancestors. A reappraisal of Mivart's scientific achievements is necessary to better establish the origins and the development not only of evolutionary trees but of modern primatology. The history of primatology, a discipline that is fundamental for investigating the place of humans in nature, would also benefit from a reappraisal of Mivart's role in Victorian biology.

  7. Reasoning about Evolution's Grand Patterns: College Students' Understanding of the Tree of Life

    Science.gov (United States)

    Novick, Laura R.; Catley, Kefyn M.

    2013-01-01

    Tree thinking involves using cladograms, hierarchical diagrams depicting the evolutionary history of a set of taxa, to reason about evolutionary relationships and support inferences. Tree thinking is indispensable in modern science. College students' tree-thinking skills were investigated using tree (much more common in professional biology) and…

  8. Understanding search trees via statistical physics

    Indian Academy of Sciences (India)

    Abstract. We study the random m-ary search tree model (where m stands for the number of branches of the search tree), an important problem for data storage in computer science, using a variety of statistical physics techniques that allow us to obtain exact asymptotic results. In particular, we show that the probability ...

  9. Potential for evolutionary responses to climate change - evidence from tree populations.

    Science.gov (United States)

    Alberto, Florian J; Aitken, Sally N; Alía, Ricardo; González-Martínez, Santiago C; Hänninen, Heikki; Kremer, Antoine; Lefèvre, François; Lenormand, Thomas; Yeaman, Sam; Whetten, Ross; Savolainen, Outi

    2013-06-01

    Evolutionary responses are required for tree populations to be able to track climate change. Results of 250 years of common garden experiments show that most forest trees have evolved local adaptation, as evidenced by the adaptive differentiation of populations in quantitative traits, reflecting environmental conditions of population origins. On the basis of the patterns of quantitative variation for 19 adaptation-related traits studied in 59 tree species (mostly temperate and boreal species from the Northern hemisphere), we found that genetic differentiation between populations and clinal variation along environmental gradients were very common (respectively, 90% and 78% of cases). Thus, responding to climate change will likely require that the quantitative traits of populations again match their environments. We examine what kind of information is needed for evaluating the potential to respond, and what information is already available. We review the genetic models related to selection responses, and what is known currently about the genetic basis of the traits. We address special problems to be found at the range margins, and highlight the need for more modeling to understand specific issues at southern and northern margins. We need new common garden experiments for less known species. For extensively studied species, new experiments are needed outside the current ranges. Improving genomic information will allow better prediction of responses. Competitive and other interactions within species and interactions between species deserve more consideration. Despite the long generation times, the strong background in quantitative genetics and growing genomic resources make forest trees useful species for climate change research. The greatest adaptive response is expected when populations are large, have high genetic variability, selection is strong, and there is ecological opportunity for establishment of better adapted genotypes. © 2013 Blackwell Publishing Ltd.

  10. Calculating the probability of multitaxon evolutionary trees: bootstrappers Gambit.

    OpenAIRE

    Lake, J A

    1995-01-01

    The reconstruction of multitaxon trees from molecular sequences is confounded by the variety of algorithms and criteria used to evaluate trees, making it difficult to compare the results of different analyses. A global method of multitaxon phylogenetic reconstruction described here, Bootstrappers Gambit, can be used with any four-taxon algorithm, including distance, maximum likelihood, and parsimony methods. It incorporates a Bayesian-Jeffreys'-bootstrap analysis to provide a uniform probabil...

  11. Understanding search trees via statistical physics

    Indian Academy of Sciences (India)

    Other applications of statistical physics (networks, traffic flows, algorithmic problems, econophysics, astrophysical applications, etc.) ... of branches of the search tree), an important problem for data storage in computer science, using a variety of statistical physics techniques that allow us to obtain exact asymptotic results.

  12. ImmTree: Database of evolutionary relationships of genes and proteins in the human immune system

    Science.gov (United States)

    Ortutay, Csaba; Siermala, Markku; Vihinen, Mauno

    2007-01-01

    Background The immune system, which is a complex machinery, is based on the highly coordinated expression of a wide array of genes and proteins. The evolutionary history of the human immune system is not well characterised. Although several studies related to the development and evolution of immunological processes have been published, a full-scale genome-based analysis is still missing. A database focused on the evolutionary relationships of immune related genes would contribute to and facilitate research on immunology and evolutionary biology. Results An Internet resource called ImmTree was constructed for studying the evolution and evolutionary trees of the human immune system. ImmTree contains information about orthologs in 80 species collected from the HomoloGene, OrthoMCL and EGO databases. In addition to phylogenetic trees, the service provides data for the comparison of human-mouse ortholog pairs, including synonymous and non-synonymous mutation rates, Z values, and Ka/Ks quotients. A versatile search engine allows complex queries from the database. Currently, data is available for 847 human immune system related genes and proteins. Conclusion ImmTree provides a unique data set of genes and proteins from the human immune system, their phylogenetics, and information for comparisons of human-mouse ortholog pairs, synonymous and non-synonymous mutation rates, as well as other statistical information. PMID:17376226

  13. Fixed Parameter Evolutionary Algorithms and Maximum Leaf Spanning Trees: A Matter of Mutations

    DEFF Research Database (Denmark)

    Kratsch, Stefan; Lehre, Per Kristian; Neumann, Frank

    2011-01-01

    Evolutionary algorithms have been shown to be very successful for a wide range of NP-hard combinatorial optimization problems. We investigate the NP-hard problem of computing a spanning tree that has a maximal number of leaves by evolutionary algorithms in the context of fixed parameter...... tractability (FPT) where the maximum number of leaves is the parameter under consideration. Our results show that simple evolutionary algorithms working with an edge-set encoding are confronted with local optima whose size of the inferior neighborhood grows with the value of an optimal solution. Investigating...

  14. A Cooperative Co-Evolutionary Genetic Algorithm for Tree Scoring and Ancestral Genome Inference.

    Science.gov (United States)

    Gao, Nan; Zhang, Yan; Feng, Bing; Tang, Jijun

    2015-01-01

    Recent advances of technology have made it easy to obtain and compare whole genomes. Rearrangements of genomes through operations such as reversals and transpositions are rare events that enable researchers to reconstruct deep evolutionary history among species. Some of the popular methods need to search a large tree space for the best scored tree, thus it is desirable to have a fast and accurate method that can score a given tree efficiently. During the tree scoring procedure, the genomic structures of internal tree nodes are also provided, which provide important information for inferring ancestral genomes and for modeling the evolutionary processes. However, computing tree scores and ancestral genomes are very difficult and a lot of researchers have to rely on heuristic methods which have various disadvantages. In this paper, we describe the first genetic algorithm for tree scoring and ancestor inference, which uses a fitness function considering co-evolution, adopts different initial seeding methods to initialize the first population pool, and utilizes a sorting-based approach to realize evolution. Our extensive experiments show that compared with other existing algorithms, this new method is more accurate and can infer ancestral genomes that are much closer to the true ancestors.

  15. Barking up the right tree: Understanding local attitudes towards dogs ...

    African Journals Online (AJOL)

    Barking up the right tree: Understanding local attitudes towards dogs in villages surrounding Ranomafana National Park, Madagascar can benefit applied conservation. Kim Valenta, Joseph A Gettinger-Larson, Colin A Chapman, Zachary J Farris ...

  16. The tree as evolutionary icon: TREE in the Natural History Museum, London.

    Science.gov (United States)

    Hellström, Nils Petter

    2011-01-01

    As part of the Darwin celebrations in 2009, the Natural History Museum in London unveiled TREE, the first contemporary artwork to win a permanent place in the Museum. While the artist claimed that the inspiration for TREE came from Darwin's famous notebook sketch of branching evolution, sometimes referred to as his "tree of life" drawing, this article emphasises the apparent incongruity between Darwin's sketch and the artist's design -- best explained by other, complementary sources of inspiration. In the context of the Museum's active participation in struggles over science and religion, the effect of the new artwork is contradictory. TREE celebrates Darwinian evolutionism, but it resonates with deep-rooted, mythological traditions of tree symbolism to do so. This complicates the status of the Museum space as one of disinterested, secular science, but it also contributes, with or without the intentions of the Museum's management, to consolidate two sometimes conflicting strains within the Museum's history. TREE celebrates human effort, secular science and reason -- but it also evokes long-standing mythological traditions to inspire reverence and remind us of our humble place in the world.

  17. Architecture of an antagonistic tree/fungus network: the asymmetric influence of past evolutionary history.

    Science.gov (United States)

    Vacher, Corinne; Piou, Dominique; Desprez-Loustau, Marie-Laure

    2008-03-05

    Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions. Based on a long-term (1972-2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns. Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependent on recent ecological processes.

  18. Playing Multi-Action Adversarial Games: Online Evolutionary Planning versus Tree Search

    DEFF Research Database (Denmark)

    Justesen, Niels; Mahlmann, Tobias; Risi, Sebastian

    2017-01-01

    We address the problem of playing turn-based multi-action adversarial games, which include many strategy games with extremely high branching factors as players take multiple actions each turn. This leads to the breakdown of standard tree search methods, including Monte Carlo Tree Search (MCTS......), as they become unable to reach a sufficient depth in the game tree. In this paper, we introduce Online Evolutionary Planning (OEP) to address this challenge, which searches for combinations of actions to perform during a single turn guided by a fitness function that evaluates the quality of a particular state....... We compare OEP to different MCTS variations that constrain the exploration to deal with the high branching factor in the turn-based multi-action game Hero Academy. While the constrained MCTS variations outperform the vanilla MCTS implementation by a large margin, OEP is able to search the space...

  19. The Use of Evolutionary Approaches to Understand Single Cell Genomes

    Directory of Open Access Journals (Sweden)

    Haiwei eLuo

    2015-03-01

    Full Text Available The vast majority of environmental bacteria and archaea remain uncultivated, yet their genome sequences are rapidly becoming available through single cell sequencing technologies. Reconstructing metabolism is one common way to make use of genome sequences of ecologically important bacteria, but molecular evolutionary analysis is another approach that, while currently underused, can reveal important insights into the function of these uncultivated microbes in nature. Because genome sequences from single cells are often incomplete, metabolic reconstruction based on genome content can be compromised. However, this problem does not necessarily impede the use of phylogenomic and population genomic approaches that are based on patterns of polymorphisms and substitutions at nucleotide and amino acid sites. These approaches explore how various evolutionary forces act to assemble genetic diversity within and between lineages. In this mini-review, I present examples illustrating the benefits of analyzing single cell genomes using evolutionary approaches.

  20. Cosmic phylogeny: reconstructing the chemical history of the solar neighbourhood with an evolutionary tree

    Science.gov (United States)

    Jofré, Paula; Das, Payel; Bertranpetit, Jaume; Foley, Robert

    2017-05-01

    Using 17 chemical elements as a proxy for stellar DNA, we present a full phylogenetic study of stars in the solar neighbourhood. This entails applying a clustering technique that is widely used in molecular biology to construct an evolutionary tree from which three branches emerge. These are interpreted as stellar populations that separate in age and kinematics and can be thus attributed to the thin disc, the thick disc and an intermediate population of probable distinct origin. We further find six lone stars of intermediate age that could not be assigned to any population with enough statistical significance. Combining the ages of the stars with their position on the tree, we are able to quantify the mean rate of chemical enrichment of each of the populations, and thus show in a purely empirical way that the star formation rate in the thick disc is much higher than that in the thin disc. We are also able to estimate the relative contribution of dynamical processes such as radial migration and disc heating to the distribution of chemical elements in the solar neighbourhood. Our method offers an alternative approach to chemical tagging methods with the advantage of visualizing the behaviour of chemical elements in evolutionary trees. This offers a new way to search for 'common ancestors' that can reveal the origin of solar neighbourhood stars.

  1. Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees.

    Science.gov (United States)

    Sansom, Robert S; Wills, Matthew A

    2013-01-01

    Fossils are vital for calibrating rates of molecular and morphological change through geological time, and are the only direct source of data documenting macroevolutionary transitions. Many evolutionary studies therefore require the robust phylogenetic placement of extinct organisms. Here, we demonstrate that the inevitable bias of the fossil record to preserve just hard, skeletal morphology systemically distorts phylogeny. Removal of soft part characters from 78 modern vertebrate and invertebrate morphological datasets resulted in significant changes to phylogenetic signal; it caused individual taxa to drift from their original position, predominately downward toward the root of their respective trees. This last bias could systematically inflate evolutionary rates inferred from molecular data because first fossil occurrences will not be recognised as such. Stem-ward slippage, whereby fundamental taphonomic biases cause fossils to be interpreted as erroneously primitive, is therefore a ubiquitous problem for all biologists attempting to infer macroevolutionary rates or sequences.

  2. Using Ancient DNA to Understand Evolutionary and Ecological Processes

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Cooper, Alan

    2014-01-01

    Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of ...

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

    Science.gov (United States)

    Hernández Blasi, Carlos; Causey, Kayla

    2010-02-01

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

  4. An Evolutionary Modelling Approach To Understanding The Factors Behind Plant Invasiveness And Community Susceptibility To Invasion

    DEFF Research Database (Denmark)

    Warren, John; Topping, Christopher John; James, Penri

    2011-01-01

    Ecologists have had limited success in understanding which introduced species may become invasive. An evolutionary model is used to investigate which traits are associated with invasiveness. Translocation experiments were simulated in which species were moved into similar but evolutionary younger...... observed to be species and community combination specific. This evolutionary study represents a novel in silico attempt to tackle invasiveness in an experimental framework, and may provide a new methodology for tackling these issues....

  5. Large sample approximations of probabilities of correct evolutionary tree estimation and biases of maximum likelihood estimation.

    Science.gov (United States)

    Susko, Edward

    2011-01-01

    Simulation studies have been the main way in which properties of maximum likelihood estimation of evolutionary trees from aligned sequence data have been studied. Because trees are unusual parameters and because fitting is computationally intensive, such studies have a heavy computational cost. We develop an asymptotic framework that can be used to obtain probabilities of correct topological reconstruction and study other properties of likelihood methods when a single split is poorly resolved. Simulations suggest that while approximations to log likelihood differences are better for less well-resolved topologies, approximations to probabilities of correct reconstruction are generally good. We used the approximations to investigate biases in estimation and found that maximum likelihood estimation has a long-branch-repels bias. This differs from the long-branch-attracts bias often reported in the literature because it is a different form of bias. For maximum likelihood estimation, usually long-branch-attracts bias results arise in the presence of model misspecification and are a form of statistical inconsistency where the estimated tree converges upon an incorrect tree with long edges together. Here, by bias we mean a tendency to favour a particular topology when data are generated from a four-taxon star tree. While we find a tendency to favour the tree with long branches apart, with more extreme long edges, a strong small sequence-length long-branch-attracts bias overwhelms the long-branch-repels bias. The long-branch-repels bias generalizes to five and six taxa in the sense that subtrees containing taxa that are all distant from the poorly resolved split repel each other.

  6. Using decision trees to understand structure in missing data.

    Science.gov (United States)

    Tierney, Nicholas J; Harden, Fiona A; Harden, Maurice J; Mengersen, Kerrie L

    2015-06-29

    Demonstrate the application of decision trees--classification and regression trees (CARTs), and their cousins, boosted regression trees (BRTs)--to understand structure in missing data. Data taken from employees at 3 different industrial sites in Australia. 7915 observations were included. The approach was evaluated using an occupational health data set comprising results of questionnaires, medical tests and environmental monitoring. Statistical methods included standard statistical tests and the 'rpart' and 'gbm' packages for CART and BRT analyses, respectively, from the statistical software 'R'. A simulation study was conducted to explore the capability of decision tree models in describing data with missingness artificially introduced. CART and BRT models were effective in highlighting a missingness structure in the data, related to the type of data (medical or environmental), the site in which it was collected, the number of visits, and the presence of extreme values. The simulation study revealed that CART models were able to identify variables and values responsible for inducing missingness. There was greater variation in variable importance for unstructured as compared to structured missingness. Both CART and BRT models were effective in describing structural missingness in data. CART models may be preferred over BRT models for exploratory analysis of missing data, and selecting variables important for predicting missingness. BRT models can show how values of other variables influence missingness, which may prove useful for researchers. Researchers are encouraged to use CART and BRT models to explore and understand missing data. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  7. An evolutionary medicine approach to understanding factors that contribute to chronic obstructive pulmonary disease.

    Science.gov (United States)

    Aoshiba, Kazutetsu; Tsuji, Takao; Itoh, Masayuki; Yamaguchi, Kazuhiro; Nakamura, Hiroyuki

    2015-01-01

    Although many studies have been published on the causes and mechanisms of chronic obstructive pulmonary disease (COPD), the reason for the existence of COPD and the reasons why COPD develops in humans have hardly been studied. Evolutionary medical approaches are required to explain not only the proximate factors, such as the causes and mechanisms of a disease, but the ultimate (evolutionary) factors as well, such as why the disease is present and why the disease develops in humans. According to the concepts of evolutionary medicine, disease susceptibility is acquired as a result of natural selection during the evolutionary process of traits linked to the genes involved in disease susceptibility. In this paper, we discuss the following six reasons why COPD develops in humans based on current evolutionary medical theories: (1) evolutionary constraints; (2) mismatch between environmental changes and evolution; (3) co-evolution with pathogenic microorganisms; (4) life history trade-off; (5) defenses and their costs, and (6) reproductive success at the expense of health. Our perspective pursues evolutionary answers to the fundamental question, 'Why are humans susceptible to this common disease, COPD, despite their long evolutionary history?' We believe that the perspectives offered by evolutionary medicine are essential for researchers to better understand the significance of their work.

  8. Of trees, geese and cirripedes: man's quest for understanding.

    Science.gov (United States)

    Buckeridge, John

    2011-03-01

    At least zoologists know that barnacles are arthropods rather than mollusks. However, this knowledge is surprisingly new, for it was as recent as 1830 before J. Vaughan Thompson showed, through a careful study of barnacle larvae, that they were crustaceans. In the 1850s, Charles Darwin unraveled much of the taxonomy of barnacles, and, significantly, his observations and classification of them follow the structure that was to be published later as his evolutionary theory. Irrespective of these works, knowledge of the systematic placement of barnacles remains surprisingly poor in the wider population today, with most non-biologists viewing barnacles as shallow-water fouling organisms related to oysters and limpets. The present paper reviews the way humans have perceived barnacles for at least a millennium; it evaluates why they were thought to have grown from trees and to have been part of the life cycle of birds; it concludes by contemplating the manner in which we perceive our environment and by doing so try to make sense of our world. © 2011 ISZS, Blackwell Publishing and IOZ/CAS.

  9. Fostering 21st-Century Evolutionary Reasoning: Teaching Tree Thinking to Introductory Biology Students.

    Science.gov (United States)

    Novick, Laura R; Catley, Kefyn M

    2016-01-01

    The ability to interpret and reason from Tree of Life (ToL) diagrams has become a vital component of science literacy in the 21st century. This article reports on the effectiveness of a research-based curriculum, including an instructional booklet, laboratory, and lectures, to teach the fundamentals of such tree thinking in an introductory biology class for science majors. We present the results of a study involving 117 undergraduates who received either our new research-based tree-thinking curriculum or business-as-usual instruction. We found greater gains in tree-thinking abilities for the experimental instruction group than for the business-as-usual group, as measured by performance on our novel assessment instrument. This was a medium size effect. These gains were observed on an unannounced test that was administered ∼5-6 weeks after the primary instruction in tree thinking. The nature of students' postinstruction difficulties with tree thinking suggests that the critical underlying concept for acquiring expert-level competence in this area is understanding that any specific phylogenetic tree is a subset of the complete, unimaginably large ToL. © 2016 L. R. Novick and K. M. Catley. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  10. The Use of Auxin Quantification for Understanding Clonal Tree Propagation

    Directory of Open Access Journals (Sweden)

    Carlos A. Stuepp

    2017-01-01

    Full Text Available Qualitative and quantitative hormone analyses have been essential for understanding the metabolic, physiological, and morphological processes that are influenced by plant hormones. Auxins are key hormones in the control of many aspects of plant growth and development and their endogenous levels are considered critical in the process of adventitious root induction. Exogenous auxins are used extensively in the clonal propagation of tree species by cuttings or tissue culture. Understanding of auxin effects has advanced with the development of increasingly accurate methods for auxin quantification. However, auxin analysis has been challenging because auxins typically occur at low concentrations, while compounds that interfere with their detection often occur at high concentrations, in plant tissues. Interference from other compounds has been addressed by extensive purification of plant extracts prior to auxin analysis, although this means that quantification methods have been limited by their expense. This review explores the extraction, purification, and quantification of auxins and the application of these techniques in developing improved methods for the clonal propagation of forestry trees.

  11. Understanding Boswellia papyrifera tree secondary metabolites through bark spectral analysis

    NARCIS (Netherlands)

    Girma, A.; Skidmore, A.K.; Bie, de C.A.J.M.; Bongers, F.

    2015-01-01

    Decision makers are concerned whether to tap or rest Boswellia Papyrifera trees. Tapping for the production of frankincense is known to deplete carbon reserves from the tree leading to production of less viable seeds, tree carbon starvation and ultimately tree mortality. Decision makers use

  12. Multiple evolutionary processes drive the patterns of genetic differentiation in a forest tree species complex

    Science.gov (United States)

    Jones, Rebecca C; Steane, Dorothy A; Lavery, Martyn; Vaillancourt, René E; Potts, Brad M

    2013-01-01

    Forest trees frequently form species complexes, complicating taxonomic classification and gene pool management. This is certainly the case in Eucalyptus, and well exemplified by the Eucalyptus globulus complex. This ecologically and economically significant complex comprises four taxa (sspp. bicostata, globulus, maidenii, pseudoglobulus) that are geographically and morphologically distinct, but linked by extensive “intergrade” populations. To resolve their genetic affinities, nine microsatellites were used to genotype 1200 trees from throughout the natural range of the complex in Australia, representing 33 morphological core and intergrade populations. There was significant spatial genetic structure (FST = 0.10), but variation was continuous. High genetic diversity in southern ssp. maidenii indicates that this region is the center of origin. Genetic diversity decreases and population differentiation increases with distance from this area, suggesting that drift is a major evolutionary process. Many of the intergrade populations, along with other populations morphologically classified as ssp. pseudoglobulus or ssp. globulus, belong to a “cryptic genetic entity” that is genetically and geographically intermediate between core ssp. bicostata, ssp. maidenii, and ssp. globulus. Geography, rather than morphology, therefore, is the best predictor of overall genetic affinities within the complex and should be used to classify germplasm into management units for conservation and breeding purposes. PMID:23403692

  13. Written Extended-Response Questions as Classroom Assessment Tools for Meaningful Understanding of Evolutionary Theory

    Science.gov (United States)

    Nieswandt, Martina; Bellomo, Katherine

    2009-01-01

    This qualitative study analyzed grade 12 biology students' answers to written extended-response questions that describe hypothetical scenarios of animals' evolution. We investigated whether these type of questions are suitable for students (n = 24) to express a meaningful understanding of evolutionary theory. Meaningful understanding is comprised…

  14. Toward an integrated evolutionary understanding of the mammalian placenta

    Science.gov (United States)

    Wildman, Derek E.

    2012-01-01

    The placenta is fundamentally important for the success of pregnancy. Disruptions outside the normal range for placenta function can result in pregnancy failure and other complications. The anatomy of the placenta varies greatly across mammals, as do key parameters in pregnancy such as neonatal body mass, length of gestation and number of offspring per pregnancy. An accurate understanding of the evolution of the mammalian placenta will require at minimum the integration of anatomical, developmental, physiological, genetic, and epigenetic data. Currently available data suggest that the placenta is a dynamic organ that has evolved rapidly in a lineage specific manner. Examination of the placenta from the perspective of human evolution shows that many anatomical features of the human placenta are relatively conserved. Despite the anatomical conservation of the human placenta there are many recently evolved placenta specific genes (e.g. CGB, LGALS13, GH2) that are important in the development and function of the human placenta. Other mammalian genomes have also evolved specific suites of placenta-expressed genes. For example, rodents have undergone expansions of the cathepsin and prolactin families, and artiodactyls have expanded their suite of pregnancy-associated glycoproteins. In addition to lineage-specific birth-and-death of gene family members, the pattern of imprinted loci varies greatly among species. Taken together, these studies suggest that a strategy reliant upon the sampling of placenta expressed and imprinted genes from a phylogenetically diverse range of species is appropriate for unraveling the conserved and derived aspects of placenta biology. PMID:21306776

  15. The Mismatch among Students' Views about Nature of Science, Acceptance of Evolution, and Evolutionary Science Understandings

    Science.gov (United States)

    Cavallo, Ann M. L.; White, Kevin J.; McCall, David

    2011-01-01

    This study explored interrelationships among high school students' views about nature of science (NOS), acceptance of evolution, and conceptual understanding of evolution, and the extent to which these may have shifted from pre- to post-instruction on evolutionary theory. Eighty-one students enrolled in ninth-grade Biology responded to…

  16. Does biodiversity make a difference? Relationships between species richness, evolutionary diversity, and aboveground live tree biomass across US forests

    Science.gov (United States)

    Kevin M. Potter; Christopher W. Woodall

    2014-01-01

    Biodiversity conveys numerous functional benefits to forested ecosystems, including community stability and resilience. In the context of managing forests for climate change mitigation/adaptation, maximizing and/or maintaining aboveground biomass will require understanding the interactions between tree biodiversity, site productivity, and the stocking of live trees....

  17. Interspecies gene transfer as a method for understanding the genetic basis for evolutionary change: Progress, Pitfalls and Prospects

    Directory of Open Access Journals (Sweden)

    Lachezar A. Nikolov

    2015-12-01

    Full Text Available The recent revolution in high throughput sequencing and associated applications provides excellent opportunities to catalogue variation in DNA sequences and gene expression between species. However, understanding the astonishing diversity of the Tree of Life requires understanding the phenotypic consequences of such variation and identification of those rare genetic changes that are causal to diversity. One way to study the genetic basis for trait diversity is to apply a transgenic approach and introduce genes of interest from a donor into a recipient species. Such interspecies gene transfer (IGT is based on the premise that if a gene is causal to the morphological divergence of the two species, the transfer will endow the recipient with properties of the donor. Extensions of this approach further allow identifying novel loci for the diversification of form and investigating cis- and trans-contributions to morphological evolution. Here we review recent examples from both plant and animal systems that have employed IGT to provide insight into the genetic basis of evolutionary change. We outline the practice of IGT, its methodological strengths and weaknesses, and consider guidelines for its application, emphasizing the importance of phylogenetic distance, character polarity, and life history. We also discuss future perspectives for exploiting IGT in the context of expanding genomic resources in emerging experimental systems and advances in genome editing.

  18. Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree-herbivore networks.

    Science.gov (United States)

    Robinson, Kathryn M; Hauzy, Céline; Loeuille, Nicolas; Albrectsen, Benedicte R

    2015-07-01

    Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant-herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen

  19. Snakes and Eels and Dogs! Oh, My! Evaluating High School Students' Tree-Thinking Skills: An Entry Point to Understanding Evolution

    Science.gov (United States)

    Catley, Kefyn M.; Phillips, Brenda C.; Novick, Laura R.

    2013-12-01

    The biological community is currently undertaking one its greatest scientific endeavours, that of constructing the Tree of Life, a phylogeny intended to be an evidenced-based, predictive road map of evolutionary relationships among Earth's biota. Unfortunately, we know very little about how such diagrams are understood, interpreted, or used as inferential tools by students—collectively referred to as tree thinking. The present study provides the first in-depth look at US high school students' competence at tree thinking and reports how they engage cognitively with tree representations as a precursor to developing curricula that will provide an entry point into macroevolution. Sixty tenth graders completed a 12-question instrument that assessed five basic tree-thinking skills. We present data that show patterns of misunderstandings are largely congruent between tenth graders and undergraduates and identify competences that are pivotal to address during instruction. Two general principles that emerge from this study are: (a) Students need to be taught that cladograms are an authoritative source of evidence that should be weighted more than other superficial or ecological similarities; (b) students need to understand the vital importance and critical difference between most recent common ancestry and common ancestry. Further, we show how the objectives of this study are closely aligned with US and International Standards and argue that scientifically-literate citizens need at least a basic understanding of the science behind the Tree of Life to understand and engage in twenty-first century societal issues such as human health, agriculture, and biotechnology.

  20. Application of network methods for understanding evolutionary dynamics in discrete habitats.

    Science.gov (United States)

    Greenbaum, Gili; Fefferman, Nina H

    2017-06-01

    In populations occupying discrete habitat patches, gene flow between habitat patches may form an intricate population structure. In such structures, the evolutionary dynamics resulting from interaction of gene-flow patterns with other evolutionary forces may be exceedingly complex. Several models describing gene flow between discrete habitat patches have been presented in the population-genetics literature; however, these models have usually addressed relatively simple settings of habitable patches and have stopped short of providing general methodologies for addressing nontrivial gene-flow patterns. In the last decades, network theory - a branch of discrete mathematics concerned with complex interactions between discrete elements - has been applied to address several problems in population genetics by modelling gene flow between habitat patches using networks. Here, we present the idea and concepts of modelling complex gene flows in discrete habitats using networks. Our goal is to raise awareness to existing network theory applications in molecular ecology studies, as well as to outline the current and potential contribution of network methods to the understanding of evolutionary dynamics in discrete habitats. We review the main branches of network theory that have been, or that we believe potentially could be, applied to population genetics and molecular ecology research. We address applications to theoretical modelling and to empirical population-genetic studies, and we highlight future directions for extending the integration of network science with molecular ecology. © 2017 John Wiley & Sons Ltd.

  1. Understanding herding based on a co-evolutionary model for strategy and game structure

    International Nuclear Information System (INIS)

    Wang, Tao; Huang, Keke; Cheng, Yuan; Zheng, Xiaoping

    2015-01-01

    Highlights: •We model herding effect in emergency from perspective of evolutionary game theory. •Rational subpopulation survives only when the game parameter is significantly large. •Herding effect may arise if the relative rewarding for rational agents is small. •Increasing the relative rewarding for rational agents will prevent herding effect. •The evolution result is unstable if the game parameter approaches critical points. -- Abstract: So far, there has been no conclusion on the mechanism for herding, which is often discussed in the academia. Assuming escaping behavior of individuals in emergency is rational rather than out of panic according to recent findings in social psychology, we investigate the behavioral evolution of large crowds from the perspective of evolutionary game theory. Specifically, evolution of the whole population divided into two subpopulations, namely the co-evolution of strategy and game structure, is numerically simulated based on the game theoretical models built and the evolutionary rule designed, and a series of phenomena including extinction of one subpopulation and herding effect are predicted in the proposed framework. Furthermore, if the rewarding for rational agents becomes significantly larger than that for emotional ones, herding effect will disappear. It is exciting that some phase transition points with interesting properties for the system can be found. In addition, our model framework is able to explain the fact that it is difficult for mavericks to prevail in society. The current results of this work will be helpful in understanding and restraining herding effect in real life

  2. Leveraging the Novel Climates of Arboreta to Understand Tree Responses to Climate Change

    Science.gov (United States)

    Ettinger, A.; Wolkovich, E. M.; Joly, S.

    2016-12-01

    Rising global temperatures are expected to cause large-scale changes to forests, including altered mortality and recruitment rates, and dramatic changes in species composition, but exactly how tree growth will be affected by climate change is uncertain. Studies to date suggest that temperate and boreal tree responses to warming range from growing faster, slower, or at unchanged rates. Here we present an approach and preliminary findings that will improve predictions of tree responses to climate change by studying how tree traits, including phenology (e.g. the timing of leaf-out), wood density, leaf mass area, and height, relate to climate sensitivity (i.e. growth responses to annual changes in climate, Figure 1). We demonstrate how arboreta can be used to understand tree responses to climate change using 500 individuals across 65 tree species growing at the Arnold Arboretum, Boston, Massachusetts. Arboretum provide a unique opportunities for understanding temperate tree responses to climate change: they provide large collections of woody species growing together that enable traits to be studied across diverse species in a phylogenetic context. Furthermore, many species in arboreta are nonnative and have been exposed to "novel" climates that may resemble future conditions in their native distributions. We use a phylogenetic approach to understand how annual growth and climate sensitivity relate to focal traits, and asses what these findings may tell us about tree responses to climate change.

  3. Fostering 21st-Century Evolutionary Reasoning: Teaching Tree Thinking to Introductory Biology Students

    OpenAIRE

    Novick, Laura R.; Catley, Kefyn M.

    2016-01-01

    The ability to interpret and reason from Tree of Life (ToL) diagrams has become a vital component of science literacy in the 21st century. This article reports on the effectiveness of a research-based curriculum, including an instructional booklet, laboratory, and lectures, to teach the fundamentals of such tree thinking in an introductory biology class for science majors. We present the results of a study involving 117 undergraduates who received either our new research-based tree-thinking c...

  4. Towards a general, population-level understanding of eco-evolutionary change

    NARCIS (Netherlands)

    Smallegange, I.M.; Coulson, T.

    2013-01-01

    Most population-level studies of eco-evolutionary dynamics assume that evolutionary change occurs in response to ecological change and vice versa. However, a growing number of papers report simultaneous ecological and evolutionary change, suggesting that the eco-evolutionary consequences of

  5. Research frontiers for improving our understanding of drought‐induced tree and forest mortality

    Science.gov (United States)

    Hartmann, Henrik; Moura, Catarina; Anderegg, William R. L.; Ruehr, Nadine; Salmon, Yann; Allen, Craig D.; Arndt, Stefan K.; Breshears, David D.; Davi, Hendrik; Galbraith, David; Ruthrof, Katinka X.; Wunder, Jan; Adams, Henry D.; Bloemen, Jasper; Cailleret, Maxime; Cobb, Richard; Gessler, Arthur; Grams, Thorsten E. E.; Jansen, Steven; Kautz, Markus; Lloret, Francisco; O’Brien, Michael

    2018-01-01

    Accumulating evidence highlights increased mortality risks for trees during severe drought, particularly under warmer temperatures and increasing vapour pressure deficit (VPD). Resulting forest die‐off events have severe consequences for ecosystem services, biophysical and biogeochemical land–atmosphere processes. Despite advances in monitoring, modelling and experimental studies of the causes and consequences of tree death from individual tree to ecosystem and global scale, a general mechanistic understanding and realistic predictions of drought mortality under future climate conditions are still lacking. We update a global tree mortality map and present a roadmap to a more holistic understanding of forest mortality across scales. We highlight priority research frontiers that promote: (1) new avenues for research on key tree ecophysiological responses to drought; (2) scaling from the tree/plot level to the ecosystem and region; (3) improvements of mortality risk predictions based on both empirical and mechanistic insights; and (4) a global monitoring network of forest mortality. In light of recent and anticipated large forest die‐off events such a research agenda is timely and needed to achieve scientific understanding for realistic predictions of drought‐induced tree mortality. The implementation of a sustainable network will require support by stakeholders and political authorities at the international level.

  6. Remembering the Forest While Viewing the Trees: Evolutionary Thinking in the Teaching of Molecular Biology

    Science.gov (United States)

    Saraswati, Sitaraman; Sitaraman, Ramakrishnan

    2014-01-01

    Given the centrality of evolutionary theory to the study of biology, we present a strategy for reinforcing its importance by appropriately recontextualizing classic and well-known experiments that are not explicitly linked with evolution in conventional texts. This exercise gives students an appreciation of the applicability of the theory of…

  7. Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees

    Directory of Open Access Journals (Sweden)

    Kyle Dexter

    2016-09-01

    Full Text Available Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. The drivers of this variation are not well understood. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to contribute to explaining the variation. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics; closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species. Our results suggest that phylogenetically correlated intrinsic factors, namely traits of the genera themselves, shape among lineage variation in range size, abundance and species richness. We postulate that tree stature may be one particularly relevant trait. However, other traits may also be relevant, and our study reinforces the need for ambitious compilations of trait data for Amazonian trees. In the meantime, our study shows how large-scale phylogenies can help to elucidate, and contribute to explaining, macroecological and macroevolutionary patterns in hyperdiverse, yet poorly understood regions like the Amazon Basin.

  8. Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing.

    Science.gov (United States)

    Nguyen, Nga Thi Thuy; Vincens, Pierre; Roest Crollius, Hugues; Louis, Alexandra

    2018-01-04

    Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as well as ancestral gene content and gene order for vertebrates and flowering plants, in an integrated evolutionary context. New analyses and visualization tools have recently been implemented in Genomicus Vertebrate. Karyotype structures from several genomes can now be compared along an evolutionary pathway (Multi-KaryotypeView), and synteny blocks can be computed and visualized between any two genomes (PhylDiagView). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Remembering the forest while viewing the trees: evolutionary thinking in the teaching of molecular biology.

    Science.gov (United States)

    Saraswati, Sitaraman; Sitaraman, Ramakrishnan

    2014-01-01

    Given the centrality of evolutionary theory to the study of biology, we present a strategy for reinforcing its importance by appropriately recontextualizing classic and well-known experiments that are not explicitly linked with evolution in conventional texts. This exercise gives students an appreciation of the applicability of the theory of evolution in diverse contexts, including those where it is not explicitly mentioned. © 2013 by The International Union of Biochemistry and Molecular Biology.

  10. Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees.

    OpenAIRE

    Sansom, Robert S.; Wills, Matthew A.

    2013-01-01

    Fossils are vital for calibrating rates of molecular and morphological change through geological time, and are the only direct source of data documenting macroevolutionary transitions. Many evolutionary studies therefore require the robust phylogenetic placement of extinct organisms. Here, we demonstrate that the inevitable bias of the fossil record to preserve just hard, skeletal morphology systemically distorts phylogeny. Removal of soft part characters from 78 modern vertebrate and inverte...

  11. Understanding the Scalability of Bayesian Network Inference Using Clique Tree Growth Curves

    Science.gov (United States)

    Mengshoel, Ole J.

    2010-01-01

    One of the main approaches to performing computation in Bayesian networks (BNs) is clique tree clustering and propagation. The clique tree approach consists of propagation in a clique tree compiled from a Bayesian network, and while it was introduced in the 1980s, there is still a lack of understanding of how clique tree computation time depends on variations in BN size and structure. In this article, we improve this understanding by developing an approach to characterizing clique tree growth as a function of parameters that can be computed in polynomial time from BNs, specifically: (i) the ratio of the number of a BN s non-root nodes to the number of root nodes, and (ii) the expected number of moral edges in their moral graphs. Analytically, we partition the set of cliques in a clique tree into different sets, and introduce a growth curve for the total size of each set. For the special case of bipartite BNs, there are two sets and two growth curves, a mixed clique growth curve and a root clique growth curve. In experiments, where random bipartite BNs generated using the BPART algorithm are studied, we systematically increase the out-degree of the root nodes in bipartite Bayesian networks, by increasing the number of leaf nodes. Surprisingly, root clique growth is well-approximated by Gompertz growth curves, an S-shaped family of curves that has previously been used to describe growth processes in biology, medicine, and neuroscience. We believe that this research improves the understanding of the scaling behavior of clique tree clustering for a certain class of Bayesian networks; presents an aid for trade-off studies of clique tree clustering using growth curves; and ultimately provides a foundation for benchmarking and developing improved BN inference and machine learning algorithms.

  12. The Natural Evolutionary Potential of Tree Populations to Cope with Newly Introduced Pests and Pathogens

    DEFF Research Database (Denmark)

    Budde, Katharina Birgit; Nielsen, Lene Rostgaard; Ravn, Hans Peter

    2016-01-01

    . Maintenance of broad genetic diversity is an important issue in conservation and forestry management. We expect that future research targeting the genetic background of biotic resistance towards emerging diseases and the role of endophytic communities in protecting trees will facilitate the informed...... and science-based guidance required to manage and maintain forests with high resilience. International cooperation on limiting disease spread and the provision of early invasive pest or pathogen detection systems are essential....

  13. Utilizing worldview theory to determine the factors influencing the understanding of evolutionary concepts

    Science.gov (United States)

    Hermann, Ronald S.

    2007-12-01

    The purpose of this study was to identify factors impacting students' ability to develop understanding of evolutionary theory. A novel approach to worldview theory was employed according to which individuals are seen as having one worldview that is comprised of many perspectives. One's worldview is comprised of numerous worldview assumptions, some of which coalesce to form worldview perspectives. Some assumptions are consistent with a scientific perspective while others are more consistent with a religious perspective. Scientific and religious perspectives were quantified based on participants' agreement with assumptions associated with each perspective. Participants completed a 103-item questionnaire addressing several variables: understanding of evolution, understanding of photosynthesis (non-confounding variable), strength of worldview perspectives and exposure to factors influencing the development of worldview perspectives. Increased exposure to factors influencing the development of a strong scientific worldview perspective was hypothesized to cause an increased understanding of evolution. The dependent variable understanding was measured by scores on two Likert-type measures. A causal-comparative study was conducted with 13 high school biology teachers and 67 high school biology students. To determine causation t-tests compared the mean scores on the variables measured. Extreme-group methods were used and data was analyzed for statistical differences between mean scores. Strong scientific worldview perspectives (t=1.003, p=3.19) and exposure to scientific factors (t=2.373, p=.02) were associated with a higher understanding of evolution. Strong religious worldview perspectives (t=-1.991, p=.05) and exposure to religious factors (t=-1.059, p=.31) were associated with a lower understanding of evolution. The results suggest that scientific worldview perspectives play an important role in increasing understanding of evolution; however, religious worldview

  14. Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family.

    Science.gov (United States)

    Song, Jia; Zheng, Sisi; Nguyen, Nhung; Wang, Youjun; Zhou, Yubin; Lin, Kui

    2017-10-03

    Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes. To the best of our knowledge, however, there still is no single unifying model or algorithm that can take all evolutionary processes into account through a stepwise or simultaneous method. On the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer and multispecies coalescent processes. As a case study, we applied this pipeline to the STIMATE (TMEM110) gene family, which has recently been reported to play an important role in store-operated Ca 2+ entry (SOCE) mediated by ORAI and STIM proteins. We inferred their phylogenetic trees in 69 sequenced chordate genomes. By integrating three tree reconstruction algorithms with diverse evolutionary models, a pipeline for inferring the evolutionary history of a gene family was developed, and its application was demonstrated.

  15. Compartmentalization: a conceptual framework for understanding how trees grow and defend themselves

    Science.gov (United States)

    Alex L. Shigo

    1984-01-01

    The purpose of this chapter is to describe a conceptual framework for understanding how trees grow and how they and other perennial plants defend themselves. The concept of compartmentalization has developed over many years, a synthesis of ideas from a number of investigators. It is derived from detailed studies of the gross morphology and cellular anatomy of the wood...

  16. The Emergence of New Industries in Space: An evolutionary understanding of industry emergence from a geographical perspective

    DEFF Research Database (Denmark)

    Tanner, Anne Nygaard

    of this paper to contribute to the recently emerged evolutionary thinking in economic geography (Boschma, Martin 2007, Boschma, Frenken 2006, Grabher 2009) with a conceptual clarification of industry emergence. The paper first reviews the definition of emerging industries as it appears in the field...... of industrial organisational economics (Porter 1980) and in evolutionary economics (Dosi 1984, Nelson, Winter 1982). Second, the paper discusses the particularity that characterizes the temporal scope of industry emergence and it is claimed that the literature often lack attention to periods that precede......, the paper draws on the recent conceptual framework of ‘regional branching’ that is able to capture the emergence of new industries in their geographical context. Regional branching builds on the evolutionary understanding of industry development and modifies previous understanding of industry emergence...

  17. Future directions in the ontogeny of plant defence: understanding the evolutionary causes and consequences.

    Science.gov (United States)

    Barton, Kasey E; Boege, Karina

    2017-04-01

    Plant defence often varies by orders of magnitude as plants develop from the seedling to juvenile to mature and senescent stages. Ontogenetic trajectories can involve switches among defence traits, leading to complex shifting phenotypes across plant lifetimes. While considerable research has characterised ontogenetic trajectories for now hundreds of plant species, we still lack a clear understanding of the molecular, ecological and evolutionary factors driving these patterns. In this study, we identify several non-mutually exclusive factors that may have led to the evolution of ontogenetic trajectories in plant defence, including developmental constraints, resource allocation costs, multi-functionality of defence traits, and herbivore selection pressure. Evidence from recent physiological studies is highlighted to shed light on the underlying molecular mechanisms involved in the regulation and activation of these developmental changes. Overall, our goal is to promote new research avenues that would provide evidence for the factors that have promoted the evolution of this complex lifetime phenotype. Future research focusing on the questions and approaches identified here will advance the field and shed light on why defence traits shift so dramatically across plant ontogeny, a widespread but poorly understood ecological pattern. © 2017 John Wiley & Sons Ltd/CNRS.

  18. A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree.

    Science.gov (United States)

    Särkinen, Tiina; Bohs, Lynn; Olmstead, Richard G; Knapp, Sandra

    2013-09-30

    The Solanaceae is a plant family of great economic importance. Despite a wealth of phylogenetic work on individual clades and a deep knowledge of particular cultivated species such as tomato and potato, a robust evolutionary framework with a dated molecular phylogeny for the family is still lacking. Here we investigate molecular divergence times for Solanaceae using a densely-sampled species-level phylogeny. We also review the fossil record of the family to derive robust calibration points, and estimate a chronogram using an uncorrelated relaxed molecular clock. Our densely-sampled phylogeny shows strong support for all previously identified clades of Solanaceae and strongly supported relationships between the major clades, particularly within Solanum. The Tomato clade is shown to be sister to section Petota, and the Regmandra clade is the first branching member of the Potato clade. The minimum age estimates for major splits within the family provided here correspond well with results from previous studies, indicating splits between tomato and potato around 8 Million years ago (Ma) with a 95% highest posterior density (HPD) 7-10 Ma, Solanum and Capsicum c. 19 Ma (95% HPD 17-21), and Solanum and Nicotiana c. 24 Ma (95% HPD 23-26). Our large time-calibrated phylogeny provides a significant step towards completing a fully sampled species-level phylogeny for Solanaceae, and provides age estimates for the whole family. The chronogram now includes 40% of known species and all but two monotypic genera, and is one of the best sampled angiosperm family phylogenies both in terms of taxon sampling and resolution published thus far. The increased resolution in the chronogram combined with the large increase in species sampling will provide much needed data for the examination of many biological questions using Solanaceae as a model system.

  19. Understanding of amount and dynamics of radioactive cesium deposited on trees in Fukushima

    Energy Technology Data Exchange (ETDEWEB)

    Endo, Izuki; Ohte, Nobuhito; Iseda, Kohei; Tanoi, Keitaro; Hirose, Atsushi; Kobayashi, Natsuko I. [The University of Tokyo, 113-8657, 1-1-1 Yayoi Bunkyo-ku, Tokyo (Japan); Ishii, Nobuyoshi [National Institute of Radiological Sciences, 263-8555, 4-9-1 Anagawa, Inage-ku, Chiba-shi, Chiba (Japan); Ohashi, Mizue [University of Hyogo, 670-0092, 1-1-12 Shinzaike-Honcho, Himeji, Hyogo (Japan)

    2014-07-01

    The accident of Fukushima Daiichi nuclear power plant after the earthquake and Tsunami in March 11, 2011 caused large amount of radioactive cesium ({sup 134}Cs, {sup 137}Cs) deposition onto the forest in the surrounding areas. River water from the forest area is used for food production and also for drinking water in these regions. In order to predict how radioactive Cs diffuse and discharge from the forest catchments, it is important to understand the amount and dynamics of radioactive Cs deposited on the trees. In this report, we show our preliminary results of {sup 137}Cs deposition in forest. Study was conducted in the forest at the upstream of Kami-Oguni River catchment, northern part of Fukushima Prefecture. Three plots (2 deciduous stands and 1 Japanese cedar (Cryptomeria japonica) plantation) were set in the forest. Quercus serrata and C. japonica, a representative of deciduous and evergreen tree species in this region, were chosen from each plot. Sample trees were logged in October 2012. Stem samples were collected every 2 m from above the ground to tree top and separated into bark, sapwood and heartwood. Litter traps were set in each plot and collected every month. Leaf litter was classified among species. Also, soil samples were collected in the cylinder of 5 cm in diameter and maximum 30 cm in depth from the forest floor every month. {sup 137}Cs concentration of all samples were measured by germanium semiconductor detector or NaI(Tl) scintillation counter. Deposited {sup 137}Cs was attached strongly on the bark of Q. serrata at high concentration (9-18 kBq/kg) but there were no clear relationship with tree height. In C. japonica, {sup 137}Cs concentration was about half times lower than that of Q. serrata at 0-10 m part of the tree. {sup 137}Cs concentration in wood of C. japonica was higher than Q. serrata. {sup 137}Cs concentration of sapwood was as high as that of heartwood in C. japonica, but in Q. serrata, {sup 137}Cs concentration in sapwood was

  20. Inherit the policy: A sociocultural approach to understanding evolutionary biology policy in South Carolina

    Science.gov (United States)

    Moore, Gregory D.

    South Carolina biology Indicator 5.6 calls for students to "Summarize ways that scientists use data from a variety of sources to investigate and critically analyze aspects of evolutionary theory" (South Carolina Department of Education, 2006). Levinson and Sutton (2001) offered a sociocultural approach to policy that considers cultural and historical influences at all levels of the policy process. Lipsky (1980/2010) and others have identified teachers as de facto policy makers, exercising broad discretion in the execution of their work. This study looks to Ajzen's Theory of Planned Behavior as an initial framework to inform how evolutionary biology policy in South Carolina is conceptualized and understood at different levels of the policy process. The results of this study indicate that actors in the state's evolutionary biology policy process draw upon a myriad of Discourses (Gee, 1999/2005). These Discourses shape cultural dynamics and the agency of the policy actors as they navigate conflicting messages between testing mandates and evolutionary biology policy. There indeed exist gaps between how evolutionary biology policy in South Carolina is conceptualized and understood at the different levels of the policy process. Evidence from this study suggests that appropriation-level policy actors must be brought into the Discourse related to the critical analysis of evolutionary biology and academic freedom legislation must be enacted if South Carolina biology Indicator 5.6 is to realize practical significance in educational policy.

  1. Evolutionary theories of aging. 1. The need to understand the process of natural selection.

    Science.gov (United States)

    Keller, L; Genoud, M

    1999-01-01

    In a Forum article Le Bourg (1998) criticized recent tests of evolutionary theories of aging and suggested alternative explanations for the long lifespan of ant queens and the positive relationship between body size and lifespan in mammals. Moreover, he attempts to criticize evolutionary theories of aging by showing that explanations other than evolutionary theories of aging probably account for the variation in human lifespan across countries. Here we show that the arguments of Le Bourg suffer several problems. First, many of the arguments reveal a misunderstanding of the process of natural selection. Second, some of the arguments reflect a lack of knowledge of evolutionary theories of aging (e.g. pre-reproductive mortality is not predicted to influence lifespan of organisms contrary to what is claimed). Finally, his final example on lifespan in humans simply is a straw-man because serious evolutionary biologists are well aware of the importance of confounding variables and would certainly not make the type of conclusion suggested by Le Bourg. Although a critical discussion of evolutionary theories of aging is welcome, we believe that the alternative explanations proposed by Le Bourg are implausible and reflect a misunderstanding of the process of natural selection. Copyright 1999 S. Karger AG, Basel

  2. Tree growth variation in the tropical forest: understanding effects of temperature, rainfall and CO2.

    Science.gov (United States)

    Schippers, Peter; Sterck, Frank; Vlam, Mart; Zuidema, Pieter A

    2015-01-28

    Tropical forest responses to climatic variability have important consequences for global carbon cycling, but are poorly understood. As empirical, correlative studies cannot disentangle the interactive effects of climatic variables on tree growth, we used a tree growth model (IBTREE) to unravel the climate effects on different physiological pathways and in turn on stem growth variation. We parameterized the model for canopy trees of Toona ciliata (Meliaceae) from a Thai monsoon forest and compared predicted and measured variation from a tree-ring study over a 30-year period. We used historical climatic variation of minimum and maximum day temperature, precipitation and carbon dioxide (CO 2 ) in different combinations to estimate the contribution of each climate factor in explaining the inter-annual variation in stem growth. Running the model with only variation in maximum temperature and rainfall yielded stem growth patterns that explained almost 70% of the observed inter-annual variation in stem growth. Our results show that maximum temperature had a strong negative effect on the stem growth by increasing respiration, reducing stomatal conductance and thus mitigating a higher transpiration demand, and - to a lesser extent - by directly reducing photosynthesis. Although stem growth was rather weakly sensitive to rain, stem growth variation responded strongly and positively to rainfall variation owing to the strong inter-annual fluctuations in rainfall. Minimum temperature and atmospheric CO 2 concentration did not significantly contribute to explaining the inter-annual variation in stem growth. Our innovative approach - combining a simulation model with historical data on tree-ring growth and climate - allowed disentangling the effects of strongly correlated climate variables on growth through different physiological pathways. Similar studies on different species and in different forest types are needed to further improve our understanding of the sensitivity of

  3. Parent-Offspring Conflict Theory: An Evolutionary Framework for Understanding Conflict within Human Families

    Science.gov (United States)

    Schlomer, Gabriel L.; Del Giudice, Marco; Ellis, Bruce J.

    2011-01-01

    Decades of research demonstrate that conflict shapes and permeates a broad range of family processes. In the current article, we argue that greater insight, integration of knowledge, and empirical achievement in the study of family conflict can be realized by utilizing a powerful theory from evolutionary biology that is barely known within…

  4. Inherit the Policy: A Sociocultural Approach to Understanding Evolutionary Biology Policy in South Carolina

    Science.gov (United States)

    Moore, Gregory D.

    2012-01-01

    South Carolina biology Indicator 5.6 calls for students to "Summarize ways that scientists use data from a variety of sources to investigate and critically analyze aspects of evolutionary theory" (South Carolina Department of Education, 2006). Levinson and Sutton (2001) offered a sociocultural approach to policy that considers cultural…

  5. Genes, communities & invasive species: understanding the ecological and evolutionary dynamics of host-pathogen interactions.

    Science.gov (United States)

    Burdon, J J; Thrall, P H; Ericson, L

    2013-08-01

    Reciprocal interactions between hosts and pathogens drive ecological, epidemiological and co-evolutionary trajectories, resulting in complex patterns of diversity at population, species and community levels. Recent results confirm the importance of negative frequency-dependent rather than 'arms-race' processes in the evolution of individual host-pathogen associations. At the community level, complex relationships between species abundance and diversity dampen or alter pathogen impacts. Invasive pathogens challenge these controls reflecting the earliest stages of evolutionary associations (akin to arms-race) where disease effects may be so great that they overwhelm the host's and community's ability to respond. Viewing these different stabilization/destabilization phases as a continuum provides a valuable perspective to assessment of the role of genetics and ecology in the dynamics of both natural and invasive host-pathogen associations. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Landscape community genomics: understanding eco-evolutionary processes in complex environments

    Science.gov (United States)

    Hand, Brian K.; Lowe, Winsor H.; Kovach, Ryan P.; Muhlfeld, Clint C.; Luikart, Gordon

    2015-01-01

    Extrinsic factors influencing evolutionary processes are often categorically lumped into interactions that are environmentally (e.g., climate, landscape) or community-driven, with little consideration of the overlap or influence of one on the other. However, genomic variation is strongly influenced by complex and dynamic interactions between environmental and community effects. Failure to consider both effects on evolutionary dynamics simultaneously can lead to incomplete, spurious, or erroneous conclusions about the mechanisms driving genomic variation. We highlight the need for a landscape community genomics (LCG) framework to help to motivate and challenge scientists in diverse fields to consider a more holistic, interdisciplinary perspective on the genomic evolution of multi-species communities in complex environments.

  7. A statistical approach to understanding reproductive isolation in two sympatric species of tree crickets.

    Science.gov (United States)

    Bhattacharya, Monisha; Isvaran, Kavita; Balakrishnan, Rohini

    2017-04-01

    In acoustically communicating animals, reproductive isolation between sympatric species is usually maintained through species-specific calls. This requires that the receiver be tuned to the conspecific signal. Mapping the response space of the receiver onto the signal space of the conspecific investigates this tuning. A combinatorial approach to investigating the response space is more informative as the influence on the receiver of the interactions between the features is also elucidated. However, most studies have examined individual preference functions rather than the multivariate response space. We studied the maintenance of reproductive isolation between two sympatric tree cricket species ( Oecanthus henryi and Oecanthus indicus ) through the temporal features of the calls. Individual response functions were determined experimentally for O. henryi , the results from which were combined in a statistical framework to generate a multivariate quantitative receiver response space. The predicted response was higher for the signals of the conspecific than for signals of the sympatric heterospecific, indicating maintenance of reproductive isolation through songs. The model allows prediction of response to untested combinations of temporal features as well as delineation of the evolutionary constraints on the signal space. The model can also be used to predict the response of O. henryi to other heterospecific signals, making it a useful tool for the study of the evolution and maintenance of reproductive isolation via long-range acoustic signals. © 2017. Published by The Company of Biologists Ltd.

  8. Evolutionary context for understanding and manipulating plant responses to past, present and future atmospheric [CO2

    Science.gov (United States)

    Leakey, Andrew D. B.; Lau, Jennifer A.

    2012-01-01

    Variation in atmospheric [CO2] is a prominent feature of the environmental history over which vascular plants have evolved. Periods of falling and low [CO2] in the palaeo-record appear to have created selective pressure for important adaptations in modern plants. Today, rising [CO2] is a key component of anthropogenic global environmental change that will impact plants and the ecosystem goods and services they deliver. Currently, there is limited evidence that natural plant populations have evolved in response to contemporary increases in [CO2] in ways that increase plant productivity or fitness, and no evidence for incidental breeding of crop varieties to achieve greater yield enhancement from rising [CO2]. Evolutionary responses to elevated [CO2] have been studied by applying selection in controlled environments, quantitative genetics and trait-based approaches. Findings to date suggest that adaptive changes in plant traits in response to future [CO2] will not be consistently observed across species or environments and will not be large in magnitude compared with physiological and ecological responses to future [CO2]. This lack of evidence for strong evolutionary effects of elevated [CO2] is surprising, given the large effects of elevated [CO2] on plant phenotypes. New studies under more stressful, complex environmental conditions associated with climate change may revise this view. Efforts are underway to engineer plants to: (i) overcome the limitations to photosynthesis from today's [CO2] and (ii) benefit maximally from future, greater [CO2]. Targets range in scale from manipulating the function of a single enzyme (e.g. Rubisco) to adding metabolic pathways from bacteria as well as engineering the structural and functional components necessary for C4 photosynthesis into C3 leaves. Successfully improving plant performance will depend on combining the knowledge of the evolutionary context, cellular basis and physiological integration of plant responses to varying

  9. Functional traits of trees on and off termite mounds: Understanding the origin of biotically-driven heterogeneity in savannas

    OpenAIRE

    van der Plas, F.; Howison, R.; Reinders, J.; Fokkema, W.; Olff, H.

    2013-01-01

    Questions In African savannas, Macrotermes termites contribute to small-scale heterogeneity by constructing large mounds. Operating as islands of high nutrient and water availability and low fire frequency, these mounds support distinct, diverse communities of trees that have been shown to be highly attractive to browsers. However, the distinct traits of tree species on termite mounds have hardly been studied, even though this may help to understand processes determining (1) their characteris...

  10. Growth habit of the late Paleozoic rhizomorphic tree-lycopsid family Diaphorodendraceae: phylogenetic, evolutionary, and paleoecological significance.

    Science.gov (United States)

    Dimichele, William A; Elrick, Scott D; Bateman, Richard M

    2013-08-01

    Rhizomorphic lycopsids evolved the tree habit independently of all other land plants. Newly discovered specimens allow radical revision of our understanding of the growth architectures of the extinct Paleozoic sister-genera Synchysidendron and Diaphorodendron. Detailed descriptions of six remarkable adpression specimens from the Pennsylvanian of the USA and three casts from the late Mississippian of Scotland are used to revise and reanalyze a previously published morphological cladistic matrix and to reinterpret their remarkable growth forms. Contrary to previous assertions, Synchysidendron resembled Diaphorodendron in having a distinct and relatively complex growth habit that emphasized serially homologous, closely spaced, deciduous lateral branches at the expense of reduced monocarpic crown branches. Lateral branches originated through several strongly anisotomous dichotomies before producing during extended periods large numbers of Achlamydocarpon strobili. The comparatively large diameter of abscission scars remaining on the main trunk and the emergence of branches above the horizontal plane suggest that the lateral branch systems were robust. Lateral branches were borne in two opposite rows on the main trunk and continued upward into an isotomously branched, determinate crown; their striking distichous arrangement caused preferred orientation of fallen trunks on bedding planes. This discovery identifies the plagiotropic growth habit, dominated by serial lateral branches, as ubiquitous in the Diaphorodendraceae and also as unequivocally primitive within Isoetales s.l., a conclusion supported by both the revised morphological cladistic analysis and relative first appearances of taxa in the fossil record. Previously assumed complete homology between crown branching in Lepidodendraceae and that of all earlier-divergent genera requires reassessment. Saltational phenotypic transitions via modification of key developmental switches remains the most credible

  11. The EvoDevoCI: A Concept Inventory for Gauging Students' Understanding of Evolutionary Developmental Biology

    Science.gov (United States)

    Perez, Kathryn E.; Hiatt, Anna; Davis, Gregory K.; Trujillo, Caleb; French, Donald P.; Terry, Mark; Price, Rebecca M.

    2013-01-01

    The American Association for the Advancement of Science 2011 report "Vision and Change in Undergraduate Biology Education" encourages the teaching of developmental biology as an important part of teaching evolution. Recently, however, we found that biology majors often lack the developmental knowledge needed to understand evolutionary…

  12. "Evo in the News:" Understanding Evolution and Students' Attitudes toward the Relevance of Evolutionary Biology

    Science.gov (United States)

    Infanti, Lynn M.; Wiles, Jason R.

    2014-01-01

    This investigation evaluated the effects of exposure to the "Evo in the News" section of the "Understanding Evolution" website on students' attitudes toward biological evolution in undergraduates in a mixed-majors introductory biology course at Syracuse University. Students' attitudes toward evolution and changes therein were…

  13. Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples.

    Science.gov (United States)

    U'ren, Jana M; Dalling, James W; Gallery, Rachel E; Maddison, David R; Davis, E Christine; Gibson, Cara M; Arnold, A Elizabeth

    2009-04-01

    Fungi associated with seeds of tropical trees pervasively affect seed survival and germination, and thus are an important, but understudied, component of forest ecology. Here, we examine the diversity and evolutionary origins of fungi isolated from seeds of an important pioneer tree (Cecropia insignis, Cecropiaceae) following burial in soil for five months in a tropical moist forest in Panama. Our approach, which relied on molecular sequence data because most isolates did not sporulate in culture, provides an opportunity to evaluate several methods currently used to analyse environmental samples of fungi. First, intra- and interspecific divergence were estimated for the nu-rITS and 5.8S gene for four genera of Ascomycota that are commonly recovered from seeds. Using these values we estimated species boundaries for 527 isolates, showing that seed-associated fungi are highly diverse, horizontally transmitted, and genotypically congruent with some foliar endophytes from the same site. We then examined methods for inferring the taxonomic placement and phylogenetic relationships of these fungi, evaluating the effects of manual versus automated alignment, model selection, and inference methods, as well as the quality of BLAST-based identification using GenBank. We found that common methods such as neighbor-joining and Bayesian inference differ in their sensitivity to alignment methods; analyses of particular fungal genera differ in their sensitivity to alignments; and numerous and sometimes intricate disparities exist between BLAST-based versus phylogeny-based identification methods. Lastly, we used our most robust methods to infer phylogenetic relationships of seed-associated fungi in four focal genera, and reconstructed ancestral states to generate preliminary hypotheses regarding the evolutionary origins of this guild. Our results illustrate the dynamic evolutionary relationships among endophytic fungi, pathogens, and seed-associated fungi, and the apparent

  14. Evolutionary perspectives on ageing.

    Science.gov (United States)

    Reichard, Martin

    2017-10-01

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

  15. Explaining forest productivity using tree functional traits and phylogenetic information: two sides of the same coin over evolutionary scale?

    OpenAIRE

    Paquette, Alain; Joly, Simon; Messier, Christian

    2015-01-01

    Given evidences that diverse ecosystems provide more services than depauperate ones, much attention has now turned toward finding meaningful and operational diversity indices. We ask two questions: (1) Does phylogenetic diversity contain additional information not explained by functional traits? And (2) What are the strength and nature of the correlation between phylogeny and functional traits according to the evolutionary scale considered? We used data from permanent forest plots of northeas...

  16. Explaining forest productivity using tree functional traits and phylogenetic information: two sides of the same coin over evolutionary scale?

    Science.gov (United States)

    Paquette, Alain; Joly, Simon; Messier, Christian

    2015-05-01

    Given evidences that diverse ecosystems provide more services than depauperate ones, much attention has now turned toward finding meaningful and operational diversity indices. We ask two questions: (1) Does phylogenetic diversity contain additional information not explained by functional traits? And (2) What are the strength and nature of the correlation between phylogeny and functional traits according to the evolutionary scale considered? We used data from permanent forest plots of northeastern Canada for which these links have been demonstrated and important functional traits identified. We show that the nature of the relationship between traits and phylogeny varies dramatically among traits, but also according to the evolutionary distance considered. The demonstration that different characters show phylogenetic autocorrelation at different evolutionary depths suggests that phylogenetic content of traits may be too crude to determine whether phylogenies contain relevant information. However, our study provides support for the use of phylogenies to assess ecosystem functioning when key functional traits are unavailable. We also highlight a potentially important contribution of phylogenetics for conservation and the study of the impact of biodiversity loss on ecosystem functioning and the provision of services, given the accumulating evidence that mechanisms promoting diversity effects shift over time to involve different traits.

  17. NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria.

    Science.gov (United States)

    Dedysh, Svetlana N; Ricke, Peter; Liesack, Werner

    2004-05-01

    The ability to utilize dinitrogen as a nitrogen source is an important phenotypic trait in most currently known methanotrophic bacteria (MB). This trait is especially important for acidophilic MB, which inhabit acidic oligotrophic environments, highly depleted in available nitrogen compounds. Phylogenetically, acidophilic MB are most closely related to heterotrophic dinitrogen-fixing bacteria of the genus BEIJERINCKIA: To further explore the phylogenetic linkage between these metabolically different organisms, the sequences of nifH and nifD gene fragments from acidophilic MB of the genera Methylocella and Methylocapsa, and from representatives of Beijerinckia, were determined. For reference, nifH and nifD sequences were also obtained from some type II MB of the alphaproteobacterial Methylosinus/Methylocystis group and from gammaproteobacterial type I MB. The trees constructed for the inferred amino acid sequences of nifH and nifD were highly congruent. The phylogenetic relationships among MB in the NifH and NifD trees also agreed well with the corresponding 16S rRNA-based phylogeny, except for two distinctive features. First, different methods used for phylogenetic analysis grouped the NifH and NifD sequences of strains of the gammaproteobacterial MB Methylococcus capsulatus within a clade mainly characterized by Alphaproteobacteria, including acidophilic MB and type II MB of the Methylosinus/Methylocystis group. From this and other genomic data from Methylococcus capsulatus Bath, it is proposed that an ancient event of lateral gene transfer was responsible for this aberrant branching. Second, the identity values of NifH and NifD sequences between Methylocapsa acidiphila B2 and representatives of Beijerinckia were clearly higher (98.5 and 96.6 %, respectively) than would be expected from their 16S rRNA-based relationships. Possibly, these two bacteria originated from a common acidophilic dinitrogen-fixing ancestor, and were subject to similar evolutionary pressure

  18. Undergraduate Students’ Difficulties in Reading and Constructing Phylogenetic Tree

    Science.gov (United States)

    Sa'adah, S.; Tapilouw, F. S.; Hidayat, T.

    2017-02-01

    Representation is a very important communication tool to communicate scientific concepts. Biologists produce phylogenetic representation to express their understanding of evolutionary relationships. The phylogenetic tree is visual representation depict a hypothesis about the evolutionary relationship and widely used in the biological sciences. Phylogenetic tree currently growing for many disciplines in biology. Consequently, learning about phylogenetic tree become an important part of biological education and an interesting area for biology education research. However, research showed many students often struggle with interpreting the information that phylogenetic trees depict. The purpose of this study was to investigate undergraduate students’ difficulties in reading and constructing a phylogenetic tree. The method of this study is a descriptive method. In this study, we used questionnaires, interviews, multiple choice and open-ended questions, reflective journals and observations. The findings showed students experiencing difficulties, especially in constructing a phylogenetic tree. The students’ responds indicated that main reasons for difficulties in constructing a phylogenetic tree are difficult to placing taxa in a phylogenetic tree based on the data provided so that the phylogenetic tree constructed does not describe the actual evolutionary relationship (incorrect relatedness). Students also have difficulties in determining the sister group, character synapomorphy, autapomorphy from data provided (character table) and comparing among phylogenetic tree. According to them building the phylogenetic tree is more difficult than reading the phylogenetic tree. Finding this studies provide information to undergraduate instructor and students to overcome learning difficulties of reading and constructing phylogenetic tree.

  19. Tree growth variation in the tropical forest: understanding effects of temperature, rainfall and CO2

    NARCIS (Netherlands)

    Schippers, P.; Sterck, F.J.; Vlam, M.; Zuidema, P.A.

    2015-01-01

    Tropical forest responses to climatic variability have important consequences for global carbon cycling, but are poorly understood. As empirical, correlative studies cannot disentangle the interactive effects of climatic variables on tree growth, we used a tree growth model (IBTREE) to unravel the

  20. Understanding the Roles of Forests and Tree-based Systems in Food Provision

    NARCIS (Netherlands)

    Jamnadass, R.; McMullin, S.; Dawson, M.I.I.K.; Powell, B.; Termote, C.; Lckowitz, A.; Kehlenbeck, K.; Vinceti, B.; Vliet, van N.; Keding, G.; Stadlmayr, B.; Damme, van P.; Carsan, S.; Sunderland, T.; Njenga, M.; Gyau, A.; Cerutti, P.; Schure, J.M.; Kouame, C.; Obiri, B.D.; Ofori, D.; Agarwal, B.; Neufeldt, H.; Degrande, A.; Serban, A.

    2015-01-01

    Forests and other tree-based systems such as agroforestry contribute to food and nutritional security in myriad ways. Directly, trees provide a variety of healthy foods including fruits, leafy vegetables, nuts, seeds and edible oils that can diversify diets and address seasonal food and nutritional

  1. Snakes and Eels and Dogs! Oh, My! Evaluating High School Students' Tree-Thinking Skills: An Entry Point to Understanding Evolution

    Science.gov (United States)

    Catley, Kefyn M.; Phillips, Brenda C.; Novick, Laura R.

    2013-01-01

    The biological community is currently undertaking one its greatest scientific endeavours, that of constructing the Tree of Life, a phylogeny intended to be an evidenced-based, predictive road map of evolutionary relationships among Earth's biota. Unfortunately, we know very little about how such diagrams are understood, interpreted, or used…

  2. Phylogenetic incongruence in E. coli O104: understanding the evolutionary relationships of emerging pathogens in the face of homologous recombination.

    Directory of Open Access Journals (Sweden)

    Weilong Hao

    Full Text Available Escherichia coli O104:H4 was identified as an emerging pathogen during the spring and summer of 2011 and was responsible for a widespread outbreak that resulted in the deaths of 50 people and sickened over 4075. Traditional phenotypic and genotypic assays, such as serotyping, pulsed field gel electrophoresis (PFGE, and multilocus sequence typing (MLST, permit identification and classification of bacterial pathogens, but cannot accurately resolve relationships among genotypically similar but pathotypically different isolates. To understand the evolutionary origins of E. coli O104:H4, we sequenced two strains isolated in Ontario, Canada. One was epidemiologically linked to the 2011 outbreak, and the second, unrelated isolate, was obtained in 2010. MLST analysis indicated that both isolates are of the same sequence type (ST678, but whole-genome sequencing revealed differences in chromosomal and plasmid content. Through comprehensive phylogenetic analysis of five O104:H4 ST678 genomes, we identified 167 genes in three gene clusters that have undergone homologous recombination with distantly related E. coli strains. These recombination events have resulted in unexpectedly high sequence diversity within the same sequence type. Failure to recognize or adjust for homologous recombination can result in phylogenetic incongruence. Understanding the extent of homologous recombination among different strains of the same sequence type may explain the pathotypic differences between the ON2010 and ON2011 strains and help shed new light on the emergence of this new pathogen.

  3. Evolutionary history of a vanishing radiation: isolation-dependent persistence and diversification in Pacific Island partulid tree snails.

    Science.gov (United States)

    Lee, Taehwan; Li, Jingchun; Churchill, Celia K C; Foighil, Diarmaid Ó

    2014-09-24

    Partulid tree snails are endemic to Pacific high islands and have experienced extraordinary rates of extinction in recent decades. Although they collectively range across a 10,000 km swath of Oceania, half of the family's total species diversity is endemic to a single Eastern Pacific hot spot archipelago (the Society Islands) and all three partulid genera display highly distinctive distributions. Our goal was to investigate broad scale (range wide) and fine scale (within-Society Islands) molecular phylogenetic relationships of the two widespread genera, Partula and Samoana. What can such data tell us regarding the genesis of such divergent generic distribution patterns, and nominal species diversity levels across Oceania? Museum, captive (zoo) and contemporary field specimens enabled us to genotype 54 of the ~120 recognized species, including many extinct or extirpated taxa, from 14 archipelagoes. The genera Partula and Samoana are products of very distinct diversification processes. Originating at the western edge of the familial range, the derived genus Samoana is a relatively recent arrival in the far eastern archipelagoes (Society, Austral, Marquesas) where it exhibits a stepping-stone phylogenetic pattern and has proven adept at both intra-and inter- archipelago colonization. The pronounced east-west geographic disjunction exhibited by the genus Partula stems from a much older long-distance dispersal event and its high taxonomic diversity in the Society Islands is a product of a long history of within-archipelago diversification. The central importance of isolation for partulid lineage persistence and diversification is evident in time-calibrated phylogenetic trees that show that remote archipelagoes least impacted by continental biotas bear the oldest clades and/or the most speciose radiations. In contemporary Oceania, that isolation is being progressively undermined and these tree snails are now directly exposed to introduced continental predators

  4. Climate change impacts on tree ranges: model intercomparison facilitates understanding and quantification of uncertainty.

    Science.gov (United States)

    Cheaib, Alissar; Badeau, Vincent; Boe, Julien; Chuine, Isabelle; Delire, Christine; Dufrêne, Eric; François, Christophe; Gritti, Emmanuel S; Legay, Myriam; Pagé, Christian; Thuiller, Wilfried; Viovy, Nicolas; Leadley, Paul

    2012-06-01

    Model-based projections of shifts in tree species range due to climate change are becoming an important decision support tool for forest management. However, poorly evaluated sources of uncertainty require more scrutiny before relying heavily on models for decision-making. We evaluated uncertainty arising from differences in model formulations of tree response to climate change based on a rigorous intercomparison of projections of tree distributions in France. We compared eight models ranging from niche-based to process-based models. On average, models project large range contractions of temperate tree species in lowlands due to climate change. There was substantial disagreement between models for temperate broadleaf deciduous tree species, but differences in the capacity of models to account for rising CO(2) impacts explained much of the disagreement. There was good quantitative agreement among models concerning the range contractions for Scots pine. For the dominant Mediterranean tree species, Holm oak, all models foresee substantial range expansion. © 2012 Blackwell Publishing Ltd/CNRS.

  5. Integrating geochemical investigations and geospatial assessment to understand the evolutionary process of hydrochemistry and groundwater quality in arid areas.

    Science.gov (United States)

    El Alfy, Mohamed; Alharbi, Talal; Mansour, Basma

    2018-04-12

    Groundwater is the key for life in arid areas. Aquifer overexploitation and climatic conditions can significantly deteriorate groundwater quality. The Al-Qassim area in central Saudi Arabia is characterized by dense agricultural use and is irrigated mainly by fossil groundwater from the Saq Aquifer. Understanding the area's hydrochemistry, major factors governing groundwater quality, and alternative uses of the groundwater are the main goals of this study. Groundwater samples were collected and examined for major, minor, and trace elements. Ionic relationships, hydrochemical facies, geospatial distributions, and multivariate analyses were conducted to assess the hydrochemical processes at play. The salinity and nitrate concentrations of the Saq Aquifer's groundwater were found to increase in the outcrop areas more than the confined areas. The spatial distributions were fragmented by three main factors: (i) modern recharge by relatively brackish water, (ii) irrigation return flow in intensive farming areas, and (iii) overexploitation and draining of deep and relatively saline zones of the aquifer. Seven water types were found representing the alkaline water with a predominance of sulfate-chloride ions and earth alkaline water with a predominance of sulfate and chloride. Mixing between fresh and brackish water, dissolution of mineral phases, silicate weathering, and reverse ion exchange were recognized as the evolutionary processes, while evaporation played a minor role. Cluster analyses characterized the fresh groundwater zone, modern groundwater recharge zone, and anthropogenic influence zone. In the confined areas, nearly all the groundwater was appropriate for domestic use and irrigation. In the outcrop areas, some limitations were found due to unsuitable conditions.

  6. Limited resources and evolutionary learning may help to understand the mistimed reproduction in birds caused by climate change.

    Science.gov (United States)

    Campos, Daniel; Llebot, Josep E; Méndez, Vicenç

    2008-08-01

    We present an agent-based model inspired by the Evolutionary Minority Game (EMG), albeit strongly adapted, to the case of competition for limited resources in ecology. The agents in this game become able, after some time, to predict the a priori best option as a result of an evolution-driven learning process. We show that a self-segregated social structure can emerge from this process, i.e., extreme learning strategies are always favoured while intermediate learning strategies tend to die out. This result may contribute to understanding some levels of organization and cooperative behaviour in ecological and social systems. We use the ideas and results reported here to discuss an issue of current interest in ecology: the mistimings in egg laying observed for some species of bird as a consequence of their slower rate of adaptation to climate change in comparison with that shown by their prey. Our model supports the hypothesis that habitat-specific constraints could explain why different populations are adapting differently to this situation, in agreement with recent experiments.

  7. Molecular insights into the historic demography of bowhead whales: understanding the evolutionary basis of contemporary management practices.

    Science.gov (United States)

    Phillips, C D; Hoffman, J I; George, J C; Suydam, R S; Huebinger, R M; Patton, J C; Bickham, J W

    2012-01-01

    Patterns of genetic variation observed within species reflect evolutionary histories that include signatures of past demography. Understanding the demographic component of species' history is fundamental to informed management because changes in effective population size affect response to environmental change and evolvability, the strength of genetic drift, and maintenance of genetic variability. Species experiencing anthropogenic population reductions provide valuable case studies for understanding the genetic response to demographic change because historic changes in the census size are often well documented. A classic example is the bowhead whale, Balaena mysticetus, which experienced dramatic population depletion due to commercial whaling in the late 19th and early 20th centuries. Consequently, we analyzed a large multi-marker dataset of bowhead whales using a variety of analytical methods, including extended Bayesian skyline analysis and approximate Bayesian computation, to characterize genetic signatures of both ancient and contemporary demographic histories. No genetic signature of recent population depletion was recovered through any analysis incorporating realistic mutation assumptions, probably due to the combined influences of long generation time, short bottleneck duration, and the magnitude of population depletion. In contrast, a robust signal of population expansion was detected around 70,000 years ago, followed by a population decline around 15,000 years ago. The timing of these events coincides to a historic glacial period and the onset of warming at the end of the last glacial maximum, respectively. By implication, climate driven long-term variation in Arctic Ocean productivity, rather than recent anthropogenic disturbance, appears to have been the primary driver of historic bowhead whale demography.

  8. Molecular insights into the historic demography of bowhead whales: understanding the evolutionary basis of contemporary management practices

    Science.gov (United States)

    Phillips, C D; Hoffman, J I; George, J C; Suydam, R S; Huebinger, R M; Patton, J C; Bickham, J W

    2013-01-01

    Patterns of genetic variation observed within species reflect evolutionary histories that include signatures of past demography. Understanding the demographic component of species' history is fundamental to informed management because changes in effective population size affect response to environmental change and evolvability, the strength of genetic drift, and maintenance of genetic variability. Species experiencing anthropogenic population reductions provide valuable case studies for understanding the genetic response to demographic change because historic changes in the census size are often well documented. A classic example is the bowhead whale, Balaena mysticetus, which experienced dramatic population depletion due to commercial whaling in the late 19th and early 20th centuries. Consequently, we analyzed a large multi-marker dataset of bowhead whales using a variety of analytical methods, including extended Bayesian skyline analysis and approximate Bayesian computation, to characterize genetic signatures of both ancient and contemporary demographic histories. No genetic signature of recent population depletion was recovered through any analysis incorporating realistic mutation assumptions, probably due to the combined influences of long generation time, short bottleneck duration, and the magnitude of population depletion. In contrast, a robust signal of population expansion was detected around 70,000 years ago, followed by a population decline around 15,000 years ago. The timing of these events coincides to a historic glacial period and the onset of warming at the end of the last glacial maximum, respectively. By implication, climate driven long-term variation in Arctic Ocean productivity, rather than recent anthropogenic disturbance, appears to have been the primary driver of historic bowhead whale demography. PMID:23403722

  9. Understanding and Acceptance of Evolutionary Theory Among Turkish University Students = Türk Üniversite Öğrencileri Arasında Evrim Teorisini Anlama ve Kabul Etme

    Directory of Open Access Journals (Sweden)

    Hasan BAHÇEKAPILI

    2012-03-01

    Full Text Available Acceptance level of evolutionary theory and factors predicting it were examined among Psychology majors from Doğuş University and Bahçeşehir University (N=99. About half of the students accepted evolutionary theory, which is a higher percentage than in previous reports. Positive attitudes towards science and parents’ education were positively correlated with acceptance whereas religiosity was negatively correlated. Understanding of evolutionary theory was surprisingly low. Understanding the theory and understanding the nature of science were unrelated to acceptance. Recommendations are made to improve the teaching of evolutionary theory.

  10. Approaches to understanding the impact of life-history features on plant-pathogen co-evolutionary dynamics

    Science.gov (United States)

    Jeremy J. Burdon; Peter H. Thrall; Adnane Nemri

    2012-01-01

    Natural plant-pathogen associations are complex interactions in which the interplay of environment, host, and pathogen factors results in spatially heterogeneous ecological and epidemiological dynamics. The evolutionary patterns that result from the interaction of these factors are still relatively poorly understood. Recently, integration of the appropriate spatial and...

  11. Evolutionary history and population genetic structure of the endemic tree frog Hyla tsinlingensis (Amphibia: Anura: Hylidae) inferred from mitochondrial gene analysis.

    Science.gov (United States)

    Zhang, Yan-Hua; Zhao, Yan-Yu; Li, Xue-Ying; Li, Xiao-Chen

    2016-01-01

    The influence of topography and Pleistocenic climatic fluctuations on the population genetic structure of amphibians in the Tsinling-Dabieshan Mountains of China is poorly investigated. Hyla tsinlingensis is a tree frog endemic to the Tsinling-Dabieshan Mountains, with a restricted and patchy distribution that is currently shrinking. We speculated on the evolutionary history of amphibians in this region by studying the population genetic structure of H. tsinlingensis. Using a total of 212 samples, 32 haplotypes and four haplogroups were found in the present study. Population genetic structure showed significant differentiation (F(ST)) between most populations of H. tsinlingensis in the Tsinling-Dabieshan Mountains. An analysis of molecular variance (AMOVA) suggested that most of the observed genetic variation occurs between the two regions (the Tsinling and Dabieshan Mountains). Mantel tests indicated that the genetic divergence was induced through isolation by distance. Using Monmonier's maximum difference algorithm to predict the genetic barrier, two putative barriers in gene flow that separate lineages of H. tsinlingensis were identified. Mismatch distribution and neutrality tests found a sudden population expansion in all haplogroups except the Tsinling population and total population. This population expansion was identified between 0.5 Myr to 0.1 Myr (Quaternary) by Bayesian skyline plot (BSP). Divergence dating indicated the divergence time between the Tsinling population and Dabieshan population to be 3.26 MYA (Pliocene). In conclusion, the topography of the Tsinling and Dabieshan Mountains exerts a significant impact on the population genetic structure of H. tsinlingensis, and climatic oscillations during glacial periods in the Quaternary affected the distribution of H. tsinlingensis.

  12. Tree-based approaches for understanding growth patterns in the European regions

    Directory of Open Access Journals (Sweden)

    Paola Annoni

    2016-09-01

    transport infrastructure, human capital, labour market and research and innovation - and incorporates the institutional quality and two variables which aim to reflect the macroeconomic conditions in which the regions operate. Given the scarcity of reliable and comparable regional data at the EU level, large part of the analysis has been devoted to build reliable and consistent panel data on potential factors of growth. Two non-parametric, decision-tree techniques, randomized Classication and Regression Tree and Multivariate Adaptive Regression Splines, are employed for their ability to address data complexities such as non-linearities and interaction eects, which are generally a challenge for more traditional statistical procedures such as linear regression. Results show that the dependence of growth rates on the factors included in the analysis is clearly non-linear with important factor interactions. This means that growth is determined by the simultaneous presence of multiple stimulus factors rather than the presence of a single area of excellence. Results also conrm the critical importance of the macroeconomic framework together with human capital as major drivers of economic growth of countries and regions. This is overall in line with most of the economic literature, which has persistently underlined the major role of these factors on economic growth but with the novelty that the macroeconomic conditions are here incorporated. Human capital also has an important role, with low-skilled workforce having a higher detrimental eect on growth than high-skilled. Not surprisingly, other important factors are the quality of governance and, in line with the neoclassical growth theory, the stage of development, with less developed economies growing at a faster pace than the others. The evidence given by the model about the impact of other factors on economic growth such as those on the quality of infrastructure or the level of innovation seems to be more limited and

  13. Using simple causal modeling to understand how water and temperature affect daily stem radial variation in trees.

    Science.gov (United States)

    Deslauriers, Annie; Anfodillo, Tommaso; Rossi, Sergio; Carraro, Vinicio

    2007-08-01

    Variation in tree stem diameter results from reversible shrinking and swelling and irreversible radial growth, all processes that are influenced by tree water status. To assess the causal effects of water and temperature on stem radial variation (DeltaR) and maximum daily shrinkage (MDS), the diurnal cycle was divided into three phases: contraction, expansion and stem radius increment. Diurnal cycles were measured during 1996-2004 in Picea abies (L.) Karst., Pinus cembra L. and Larix decidua Mill. in a timberline ecotone to understand the links between stem diameter variation (v; defined as MDS or DR), phase duration (h), and weather or sap flow descriptors (d). We demonstrated that a high proportion of MDS and DeltaR was explained by h because of the nonlinearity of the physiological responses to weather d. By causal modeling, we tested whether the relationship between d and v was due to h (lack of causal relationship between d and v) or to both d and h (double cause). The results of this modeling added new physiological insight into daily growth-climate relationships. Negative correlations were found between DeltaR and air temperature owing to the negative effect of temperature on h only, and did not correspond to a direct effect on tree growth mediated by an alteration in metabolic activities. Precipitation had two main effects: a direct effect on DeltaR and an indirect effect mediated through an effect on h. A reduction in sap flow at night led to an increase in DeltaR for P. abies and L. decidua, but not for P. cembra.

  14. Biochemist-Tree: Using Modular Origami to Understand the Integration of Intermediary Metabolism

    Science.gov (United States)

    Sharp, Duncan

    2013-01-01

    Intermediary metabolism can be a complex area to study due to the inherent modularity of the catabolic biochemical processes. This article outlines a novel, cost-effective, and universally applicable teaching activity to enhance students understanding of the inter-relationship between the key processes of intermediary metabolism. A simple origami…

  15. Understanding the roles of nonstructural carbohydrates in forest trees - from what we can measure to what we want to know.

    Science.gov (United States)

    Hartmann, Henrik; Trumbore, Susan

    2016-07-01

    Contents 386 I. 386 II. 388 III. 392 IV. 392 V. 396 VI. 399 399 References 399 SUMMARY: Carbohydrates provide the building blocks for plant structures as well as versatile resources for metabolic processes. The nonstructural carbohydrates (NSC), mainly sugars and starch, fulfil distinct functional roles, including transport, energy metabolism and osmoregulation, and provide substrates for the synthesis of defence compounds or exchange with symbionts involved in nutrient acquisition or defence. At the whole-plant level, NSC storage buffers the asynchrony of supply and demand on diel, seasonal or decadal temporal scales and across plant organs. Despite its central role in plant function and in stand-level carbon cycling, our understanding of storage dynamics, its controls and response to environmental stresses is very limited, even after a century of research. This reflects the fact that often storage is defined by what we can measure, that is, NSC concentrations, and the interpretation of these as a proxy for a single function, storage, rather than the outcome of a range of NSC source and sink functions. New isotopic tools allow direct quantification of timescales involved in NSC dynamics, and show that NSC-C fixed years to decades previously is used to support tree functions. Here we review recent advances, with emphasis on the context of the interactions between NSC, drought and tree mortality. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  16. Bijective Diameters of Gene Tree Parsimony Costs.

    Science.gov (United States)

    Gorecki, Pawel; Eulenstein, Oliver

    2017-08-04

    Synthesizing median trees from a collection of gene trees under the biologically motivated gene tree parsimony (GTP) costs has provided credible species tree estimates. GTP costs are defined for each of the classic evolutionary processes. These costs count the minimum number of events necessary to reconcile the gene tree with the species tree where the leaf-genes are mapped to the leaf-species through a function called labeling. To better understand the synthesis of median trees under these costs there is an increased interest in analyzing their diameters. The diameters of a GTP cost between a gene tree and a species tree are the maximum values of this cost of one or both topologies of the trees involved. We are concerned about the diameters of the GTP costs under bijective labelings. While these diameters are linear time computable for the gene duplication and deep coalescence costs, this has been unknown for the classic gene duplication and loss, and for the loss cost. For the first time, we show how to compute these diameters and proof that this can be achieved in linear time, and thus, completing the computational time analysis for all of the bijective diameters under the GTP costs.

  17. Evolutionary institutionalism.

    Science.gov (United States)

    Fürstenberg, Dr Kai

    Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.

  18. Trees are good, but…

    Science.gov (United States)

    E.G. McPherson; F. Ferrini

    2010-01-01

    We know that “trees are good,” and most people believe this to be true. But if this is so, why are so many trees neglected, and so many tree wells empty? An individual’s attitude toward trees may result from their firsthand encounters with specific trees. Understanding how attitudes about trees are shaped, particularly aversion to trees, is critical to the business of...

  19. Prevalence and Persistence of Misconceptions in Tree Thinking

    Directory of Open Access Journals (Sweden)

    Tyler A. Kummer

    2016-12-01

    Full Text Available Darwin described evolution as “descent with modification.” Descent, however, is not an explicit focus of most evolution instruction and often leaves deeply held misconceptions to dominate student understanding of common ancestry and species relatedness. Evolutionary trees are ways of visually depicting descent by illustrating the relationships between species and groups of species. The ability to properly interpret and use evolutionary trees has become known as “tree thinking.” We used a 20-question assessment to measure misconceptions in tree thinking and compare the proportion of students who hold these misconceptions in an introductory biology course with students in two higher-level courses including a senior level biology course. We found that misconceptions related to reading the graphic (reading the tips and node counting were variably influenced across time with reading the tips decreasing and node counting increasing in prevalence. On the other hand, misconceptions related to the fundamental underpinnings of evolutionary theory (ladder thinking and similarity equals relatedness proved resistant to change during a typical undergraduate study of biology. A possible new misconception relating to the length of the branches in an evolutionary tree is described. Understanding the prevalence and persistence of misconceptions informs educators as to which misconceptions should be targeted in their courses.

  20. Prevalence and Persistence of Misconceptions in Tree Thinking.

    Science.gov (United States)

    Kummer, Tyler A; Whipple, Clinton J; Jensen, Jamie L

    2016-12-01

    Darwin described evolution as "descent with modification." Descent, however, is not an explicit focus of most evolution instruction and often leaves deeply held misconceptions to dominate student understanding of common ancestry and species relatedness. Evolutionary trees are ways of visually depicting descent by illustrating the relationships between species and groups of species. The ability to properly interpret and use evolutionary trees has become known as "tree thinking." We used a 20-question assessment to measure misconceptions in tree thinking and compare the proportion of students who hold these misconceptions in an introductory biology course with students in two higher-level courses including a senior level biology course. We found that misconceptions related to reading the graphic ( reading the tips and node counting ) were variably influenced across time with reading the tips decreasing and node counting increasing in prevalence. On the other hand, misconceptions related to the fundamental underpinnings of evolutionary theory ( ladder thinking and similarity equals relatedness ) proved resistant to change during a typical undergraduate study of biology. A possible new misconception relating to the length of the branches in an evolutionary tree is described. Understanding the prevalence and persistence of misconceptions informs educators as to which misconceptions should be targeted in their courses.

  1. Prevalence and Persistence of Misconceptions in Tree Thinking†

    Science.gov (United States)

    Kummer, Tyler A.; Whipple, Clinton J.; Jensen, Jamie L.

    2016-01-01

    Darwin described evolution as “descent with modification.” Descent, however, is not an explicit focus of most evolution instruction and often leaves deeply held misconceptions to dominate student understanding of common ancestry and species relatedness. Evolutionary trees are ways of visually depicting descent by illustrating the relationships between species and groups of species. The ability to properly interpret and use evolutionary trees has become known as “tree thinking.” We used a 20-question assessment to measure misconceptions in tree thinking and compare the proportion of students who hold these misconceptions in an introductory biology course with students in two higher-level courses including a senior level biology course. We found that misconceptions related to reading the graphic (reading the tips and node counting) were variably influenced across time with reading the tips decreasing and node counting increasing in prevalence. On the other hand, misconceptions related to the fundamental underpinnings of evolutionary theory (ladder thinking and similarity equals relatedness) proved resistant to change during a typical undergraduate study of biology. A possible new misconception relating to the length of the branches in an evolutionary tree is described. Understanding the prevalence and persistence of misconceptions informs educators as to which misconceptions should be targeted in their courses. PMID:28101265

  2. Understanding causes of tree growth response to gap formation: D13C-values in tree rings reveal a predominant effect of light

    NARCIS (Netherlands)

    Sleen, van der J.P.; Soliz-Gamboa, C.C.; Helle, G.; Pons, T.L.; Anten, N.P.R.; Zuidema, P.A.

    2014-01-01

    Carbon isotope ratios in growth rings of a tropical tree species show that treefall gaps stimulate diameter growth mainly through changes in the availability of light and not water. The formation of treefall gaps in closed canopy forests usually entails considerable increases in light and nutrient

  3. Understanding causes of tree growth response to gap formation: D13C-values in tree rings reveal a predominant effect of light

    NARCIS (Netherlands)

    van der Sleen, Peter; Soliz Gamboa, Claudia; Helle, G.; Pons, Thijs; Anten, Niels; Zuidema, Pieter

    2014-01-01

    Key message Carbon isotope ratios in growth rings of a tropical tree species show that treefall gaps stimulate diameter growth mainly through changes in the availability of light and not water. The formation of treefall gaps in closed canopy forests usually entails considerable increases in light

  4. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 9. Evolutionary Stable Strategy: Application of Nash Equilibrium in Biology. General ... Using some examples of classical games, we show how evolutionary game theory can help understand behavioural decisions of animals.

  5. Exploring the Complexity of Tree Thinking Expertise in an Undergraduate Systematics Course

    Science.gov (United States)

    Halverson, Kristy L.; Pires, Chris J.; Abell, Sandra K.

    2011-01-01

    Student understanding of biological representations has not been well studied. Yet, we know that to be efficient problem solvers in evolutionary biology and systematics, college students must develop expertise in thinking with a particular type of representation, phylogenetic trees. The purpose of this study was to understand how undergraduates…

  6. Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation.

    Science.gov (United States)

    Koza, Anna; Kusmierska, Anna; McLaughlin, Kimberley; Moshynets, Olena; Spiers, Andrew J

    2017-07-03

    Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader (WS). In these microcosms, the ecosystem engineering of the early wild-type colonists establishes the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that deregulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface. These structures allow Wrinkly Spreaders to intercept O2 diffusing into the liquid column and limit the growth of competitors lower down. As the biofilm matures, competition increasingly occurs between WS lineages, and niche divergence within the biofilm may support further diversification before system failure when the structure finally sinks. A combination of pleiotropic and epistasis effects, as well as secondary mutations, may explain variations in WS phenotype and fitness. Understanding how mutations subvert regulatory networks to express intrinsic genome potential and key innovations providing a selective advantage in novel environments is key to understanding the versatility of bacteria, and how selection and ecological opportunity can rapidly lead to substantive changes in phenotype and in community structure and function. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing.

    Directory of Open Access Journals (Sweden)

    Noushin Niknafs

    2015-10-01

    Full Text Available Recent improvements in next-generation sequencing of tumor samples and the ability to identify somatic mutations at low allelic fractions have opened the way for new approaches to model the evolution of individual cancers. The power and utility of these models is increased when tumor samples from multiple sites are sequenced. Temporal ordering of the samples may provide insight into the etiology of both primary and metastatic lesions and rationalizations for tumor recurrence and therapeutic failures. Additional insights may be provided by temporal ordering of evolving subclones--cellular subpopulations with unique mutational profiles. Current methods for subclone hierarchy inference tightly couple the problem of temporal ordering with that of estimating the fraction of cancer cells harboring each mutation. We present a new framework that includes a rigorous statistical hypothesis test and a collection of tools that make it possible to decouple these problems, which we believe will enable substantial progress in the field of subclone hierarchy inference. The methods presented here can be flexibly combined with methods developed by others addressing either of these problems. We provide tools to interpret hypothesis test results, which inform phylogenetic tree construction, and we introduce the first genetic algorithm designed for this purpose. The utility of our framework is systematically demonstrated in simulations. For most tested combinations of tumor purity, sequencing coverage, and tree complexity, good power (≥ 0.8 can be achieved and Type 1 error is well controlled when at least three tumor samples are available from a patient. Using data from three published multi-region tumor sequencing studies of (murine small cell lung cancer, acute myeloid leukemia, and chronic lymphocytic leukemia, in which the authors reconstructed subclonal phylogenetic trees by manual expert curation, we show how different configurations of our tools can

  8. Phages of lactic acid bacteria: The role of genetics in understanding phage-host interactions and their co-evolutionary processes

    International Nuclear Information System (INIS)

    Mahony, Jennifer; Ainsworth, Stuart; Stockdale, Stephen; Sinderen, Douwe van

    2012-01-01

    Dairy fermentations are among the oldest food processing applications, aimed at preservation and shelf-life extension through the use of lactic acid bacteria (LAB) starter cultures, in particular strains of Lactococcus lactis, Streptococcus thermophilus, Lactobacillus spp. and Leuconostoc spp. Traditionally this was performed by continuous passaging of undefined cultures from a finished fermentation to initiate the next fermentation. More recently, consumer demands on consistent and desired flavours and textures of dairy products have led to a more defined approach to such processes. Dairy (starter) companies have responded to the need to define the nature and complexity of the starter culture mixes, and dairy fermentations are now frequently based on defined starter cultures of low complexity, where each starter component imparts specific technological properties that are desirable to the product. Both mixed and defined starter culture approaches create the perfect environment for the proliferation of (bacterio)phages capable of infecting these LAB. The repeated use of the same starter cultures in a single plant, coupled to the drive towards higher and consistent production levels, increases the risk and negative impact of phage infection. In this review we will discuss recent advances in tracking the adaptation of phages to the dairy industry, the advances in understanding LAB phage-host interactions, including evolutionary and genomic aspects.

  9. Phages of lactic acid bacteria: The role of genetics in understanding phage-host interactions and their co-evolutionary processes

    Energy Technology Data Exchange (ETDEWEB)

    Mahony, Jennifer, E-mail: j.mahony@ucc.ie [Department of Microbiology, University College Cork, Western Road, Cork (Ireland); Ainsworth, Stuart; Stockdale, Stephen [Department of Microbiology, University College Cork, Western Road, Cork (Ireland); Sinderen, Douwe van, E-mail: d.vansinderen@ucc.ie [Department of Microbiology, University College Cork, Western Road, Cork (Ireland); Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Western Road, Cork (Ireland)

    2012-12-20

    Dairy fermentations are among the oldest food processing applications, aimed at preservation and shelf-life extension through the use of lactic acid bacteria (LAB) starter cultures, in particular strains of Lactococcus lactis, Streptococcus thermophilus, Lactobacillus spp. and Leuconostoc spp. Traditionally this was performed by continuous passaging of undefined cultures from a finished fermentation to initiate the next fermentation. More recently, consumer demands on consistent and desired flavours and textures of dairy products have led to a more defined approach to such processes. Dairy (starter) companies have responded to the need to define the nature and complexity of the starter culture mixes, and dairy fermentations are now frequently based on defined starter cultures of low complexity, where each starter component imparts specific technological properties that are desirable to the product. Both mixed and defined starter culture approaches create the perfect environment for the proliferation of (bacterio)phages capable of infecting these LAB. The repeated use of the same starter cultures in a single plant, coupled to the drive towards higher and consistent production levels, increases the risk and negative impact of phage infection. In this review we will discuss recent advances in tracking the adaptation of phages to the dairy industry, the advances in understanding LAB phage-host interactions, including evolutionary and genomic aspects.

  10. Evolutionary Mechanisms for Loneliness

    Science.gov (United States)

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

    2013-01-01

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

  11. Using the House-Tree-Person (H-T-P) as a Method to Understanding Individual Cultural Differences among Children.

    Science.gov (United States)

    Lambeth, Pauline J.

    Finding innovative and effective methods to infer the ability of culturally diverse students continues to present a problem for educators. This paper proposes the House-Tree-Person (HTP) projective technique as a way for school educators to gather important data about student functioning without the use of culturally biased instruments. This…

  12. Functional traits of trees on and off termite mounds : Understanding the origin of biotically-driven heterogeneity in savannas

    NARCIS (Netherlands)

    van der Plas, F.; Howison, R.; Reinders, J.; Fokkema, W.; Olff, H.

    Questions In African savannas, Macrotermes termites contribute to small-scale heterogeneity by constructing large mounds. Operating as islands of high nutrient and water availability and low fire frequency, these mounds support distinct, diverse communities of trees that have been shown to be highly

  13. Evolutionary Nephrology.

    Science.gov (United States)

    Chevalier, Robert L

    2017-05-01

    Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

  14. Serine/Threonine protein kinases from bacteria, archaea and eukarya share a common evolutionary origin deeply rooted in the tree of life

    DEFF Research Database (Denmark)

    Stancik, Ivan Andreas; Šestak, Martin Sebastijan; Ji, Boyang

    2018-01-01

    The main family of serine/threonine/tyrosine protein kinases present in eukarya was defined and described by Hanks et al. in 1988. It was initially believed that these kinases do not exist in bacteria, but extensive genome sequencing revealed their existence in many bacteria. For historical reasons......, the term "eukaryotic-type kinases" propagated in the literature to describe bacterial members of this protein family. Here, we argue that this term should be abandoned as a misnomer, and we provide several lines of evidence to support this claim. Our comprehensive phylostratigraphic analysis suggests...... that Hanks-type kinases present in eukarya, bacteria and archaea all share a common evolutionary origin in the lineage leading to the last universal common ancestor (LUCA). We found no evidence to suggest substantial horizontal transfer of genes encoding Hanks-type kinases from eukarya to bacteria. Moreover...

  15. Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play

    Science.gov (United States)

    Post, David M.; Palkovacs, Eric P.

    2009-01-01

    Interactions between natural selection and environmental change are well recognized and sit at the core of ecology and evolutionary biology. Reciprocal interactions between ecology and evolution, eco-evolutionary feedbacks, are less well studied, even though they may be critical for understanding the evolution of biological diversity, the structure of communities and the function of ecosystems. Eco-evolutionary feedbacks require that populations alter their environment (niche construction) and that those changes in the environment feed back to influence the subsequent evolution of the population. There is strong evidence that organisms influence their environment through predation, nutrient excretion and habitat modification, and that populations evolve in response to changes in their environment at time-scales congruent with ecological change (contemporary evolution). Here, we outline how the niche construction and contemporary evolution interact to alter the direction of evolution and the structure and function of communities and ecosystems. We then present five empirical systems that highlight important characteristics of eco-evolutionary feedbacks: rotifer–algae chemostats; alewife–zooplankton interactions in lakes; guppy life-history evolution and nutrient cycling in streams; avian seed predators and plants; and tree leaf chemistry and soil processes. The alewife–zooplankton system provides the most complete evidence for eco-evolutionary feedbacks, but other systems highlight the potential for eco-evolutionary feedbacks in a wide variety of natural systems. PMID:19414476

  16. Evolutionary Demography

    DEFF Research Database (Denmark)

    Levitis, Daniel

    2015-01-01

    of biological and cultural evolution. Demographic variation within and among human populations is influenced by our biology, and therefore by natural selection and our evolutionary background. Demographic methods are necessary for studying populations of other species, and for quantifying evolutionary fitness...

  17. Marine Dispersal Scales Are Congruent over Evolutionary and Ecological Time

    KAUST Repository

    Pinsky, Malin L.

    2016-12-15

    The degree to which offspring remain near their parents or disperse widely is critical for understanding population dynamics, evolution, and biogeography, and for designing conservation actions. In the ocean, most estimates suggesting short-distance dispersal are based on direct ecological observations of dispersing individuals, while indirect evolutionary estimates often suggest substantially greater homogeneity among populations. Reconciling these two approaches and their seemingly competing perspectives on dispersal has been a major challenge. Here we show for the first time that evolutionary and ecological measures of larval dispersal can closely agree by using both to estimate the distribution of dispersal distances. In orange clownfish (Amphiprion percula) populations in Kimbe Bay, Papua New Guinea, we found that evolutionary dispersal kernels were 17 km (95% confidence interval: 12–24 km) wide, while an exhaustive set of direct larval dispersal observations suggested kernel widths of 27 km (19–36 km) or 19 km (15–27 km) across two years. The similarity between these two approaches suggests that ecological and evolutionary dispersal kernels can be equivalent, and that the apparent disagreement between direct and indirect measurements can be overcome. Our results suggest that carefully applied evolutionary methods, which are often less expensive, can be broadly relevant for understanding ecological dispersal across the tree of life.

  18. Anxiety: an evolutionary approach.

    OpenAIRE

    Bateson, M; Brilot, B; Nettle, D

    2011-01-01

    Anxiety disorders are among the most common mental illnesses, with huge attendant suffering. Current treatments are not universally effective, suggesting that a deeper understanding of the causes of anxiety is needed. To understand anxiety disorders better, it is first necessary to understand the normal anxiety response. This entails considering its evolutionary function as well as the mechanisms underlying it. We argue that the function of the human anxiety response, and homologues in other ...

  19. Creating creationists: The influence of 'issues framing' on our understanding of public perceptions of clash narratives between evolutionary science and belief.

    Science.gov (United States)

    Elsdon-Baker, Fern

    2015-05-01

    Clash narratives relating to evolutionary science and personal belief are a recurrent theme in media or public space discourse. However, a 2009 British Council poll undertaken in 10 countries worldwide shows that the perception of a necessary clash between evolutionary worldviews and belief in a God is a minority viewpoint. How then does the popular conception that there is an ongoing conflict between evolution and belief in God arise? One contributing factor is the framing and categorization of creationism and evolutionism within large-scale surveys for use within media campaigns. This article examines the issue framing within four polls conducted in the United Kingdom and internationally between 2008 and 2013. It argues that by ignoring the complexity and range of perspectives individuals hold, or by framing evolutionary science as atheistic, we are potentially creating 'creationists' - including 'Islamic creationists' - both figuratively and literally. © The Author(s) 2015.

  20. Evolutionary thinking

    Science.gov (United States)

    Hunt, Tam

    2014-01-01

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

  1. Evolutionary Demography

    DEFF Research Database (Denmark)

    Levitis, Daniel

    2015-01-01

    Demography is the quantitative study of population processes, while evolution is a population process that influences all aspects of biological organisms, including their demography. Demographic traits common to all human populations are the products of biological evolution or the interaction...... of biological and cultural evolution. Demographic variation within and among human populations is influenced by our biology, and therefore by natural selection and our evolutionary background. Demographic methods are necessary for studying populations of other species, and for quantifying evolutionary fitness...

  2. Effects of Phylogenetic Tree Style on Student Comprehension

    Science.gov (United States)

    Dees, Jonathan Andrew

    Phylogenetic trees are powerful tools of evolutionary biology that have become prominent across the life sciences. Consequently, learning to interpret and reason from phylogenetic trees is now an essential component of biology education. However, students often struggle to understand these diagrams, even after explicit instruction. One factor that has been observed to affect student understanding of phylogenetic trees is style (i.e., diagonal or bracket). The goal of this dissertation research was to systematically explore effects of style on student interpretations and construction of phylogenetic trees in the context of an introductory biology course. Before instruction, students were significantly more accurate with bracket phylogenetic trees for a variety of interpretation and construction tasks. Explicit instruction that balanced the use of diagonal and bracket phylogenetic trees mitigated some, but not all, style effects. After instruction, students were significantly more accurate for interpretation tasks involving taxa relatedness and construction exercises when using the bracket style. Based on this dissertation research and prior studies on style effects, I advocate for introductory biology instructors to use only the bracket style. Future research should examine causes of style effects and variables other than style to inform the development of research-based instruction that best supports student understanding of phylogenetic trees.

  3. Origins of evolutionary transitions

    Indian Academy of Sciences (India)

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

  4. Fault-Tree Compiler

    Science.gov (United States)

    Butler, Ricky W.; Boerschlein, David P.

    1993-01-01

    Fault-Tree Compiler (FTC) program, is software tool used to calculate probability of top event in fault tree. Gates of five different types allowed in fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. High-level input language easy to understand and use. In addition, program supports hierarchical fault-tree definition feature, which simplifies tree-description process and reduces execution time. Set of programs created forming basis for reliability-analysis workstation: SURE, ASSIST, PAWS/STEM, and FTC fault-tree tool (LAR-14586). Written in PASCAL, ANSI-compliant C language, and FORTRAN 77. Other versions available upon request.

  5. Evolutionary Awareness

    Directory of Open Access Journals (Sweden)

    Gregory Gorelik

    2014-10-01

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

  6. Evolutionary macroecology

    Directory of Open Access Journals (Sweden)

    José Alexandre F. Diniz-Filho

    2013-10-01

    Full Text Available Macroecology focuses on ecological questions at broad spatial and temporal scales, providing a statistical description of patterns in species abundance, distribution and diversity. More recently, historical components of these patterns have begun to be investigated more deeply. We tentatively refer to the practice of explicitly taking species history into account, both analytically and conceptually, as ‘evolutionary macroecology’. We discuss how the evolutionary dimension can be incorporated into macroecology through two orthogonal and complementary data types: fossils and phylogenies. Research traditions dealing with these data have developed more‐or‐less independently over the last 20–30 years, but merging them will help elucidate the historical components of diversity gradients and the evolutionary dynamics of species’ traits. Here we highlight conceptual and methodological advances in merging these two research traditions and review the viewpoints and toolboxes that can, in combination, help address patterns and unveil processes at temporal and spatial macro‐scales.

  7. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    , they are correlated among people who share environments because these individuals satisfice within their cognitive bounds by using cues in order of validity, as opposed to using cues arbitrarily. Any difference in expectations thereby arise from differences in cognitive ability, because two individuals with identical......The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover...... cognitive bounds will perceive business opportunities identically. In addition, because cues provide information about latent causal structures of the environment, changes in causality must be accompanied by changes in cognitive representations if adaptation is to be maintained. The concept of evolutionary...

  8. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  9. Evolutionary robotics

    Indian Academy of Sciences (India)

    In evolutionary robotics, a suitable robot control system is developed automatically through evolution due to the interactions between the robot and its environment. It is a complicated task, as the robot and the environment constitute a highly dynamical system. Several methods have been tried by various investigators to ...

  10. Investigating how students communicate tree-thinking

    Science.gov (United States)

    Boyce, Carrie Jo

    Learning is often an active endeavor that requires students work at building conceptual understandings of complex topics. Personal experiences, ideas, and communication all play large roles in developing knowledge of and understanding complex topics. Sometimes these experiences can promote formation of scientifically inaccurate or incomplete ideas. Representations are tools used to help individuals understand complex topics. In biology, one way that educators help people understand evolutionary histories of organisms is by using representations called phylogenetic trees. In order to understand phylogenetics trees, individuals need to understand the conventions associated with phylogenies. My dissertation, supported by the Tree-Thinking Representational Competence and Word Association frameworks, is a mixed-methods study investigating the changes in students' tree-reading, representational competence and mental association of phylogenetic terminology after participation in varied instruction. Participants included 128 introductory biology majors from a mid-sized southern research university. Participants were enrolled in either Introductory Biology I, where they were not taught phylogenetics, or Introductory Biology II, where they were explicitly taught phylogenetics. I collected data using a pre- and post-assessment consisting of a word association task and tree-thinking diagnostic (n=128). Additionally, I recruited a subset of students from both courses (n=37) to complete a computer simulation designed to teach students about phylogenetic trees. I then conducted semi-structured interviews consisting of a word association exercise with card sort task, a retrospective pre-assessment discussion, a post-assessment discussion, and interview questions. I found that students who received explicit lecture instruction had a significantly higher increase in scores on a tree-thinking diagnostic than students who did not receive lecture instruction. Students who received both

  11. Applying Evolutionary Anthropology

    Science.gov (United States)

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

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

  12. Furcation and fusion: The phylogenetics of evolutionary novelty.

    Science.gov (United States)

    Oakley, Todd H

    2017-11-01

    Novelty and innovation are fundamental yet relatively understudied concepts in evolution. We may study the history and provenance of novelty using phylogenetics, where key questions include when evolution occurs by tree-like branching and when it occurs by movement of distantly related parts in processes akin to horizontal transfer. Perfectly vertical inheritance, often an assumption of evolutionary trees, requires simultaneous co-duplication of the parts of a duplicating or speciating (processes I collectively call 'furcating') biological feature. However, simultaneous co-duplication of many parts usually requires variational processes that are rare. Therefore, instead of always being perfectly tree-like, evolution often involves events that incorporate or fuse more distantly related parts into new units during evolution, which herein I call 'fusion'. Exon shuffling, horizontal gene transfer, introgression, and co-option are such fusion processes at different levels of organization. The ubiquity of processes that fuse distantly related parts has wide ranging implications for the study of macroevolution. For one, the central metaphor of a tree of life will often be incomplete, to the point where we may consider a different metaphor, such as economic public goods, or a 'web of life'. Secondly, we often may need to expand commonly used phylogenetic models and methods, highlighting a need for an expansive toolkit for studying evolutionary history. Even though furcation - the splitting and individuation of biological features - does happen, fusion of distant parts may often be just as critical for the evolution of novelties, and must formally be incorporated into the metaphors, models, and visualization of evolutionary history. This will allow us to understand the timing, order of appearance, and diversification rates of developmental systems, including cell types, organs, behavior, and language, which very commonly evolve through co-option. Copyright © 2017

  13. The adaptive value of shoot differentiation in deciduous trees and its evolutionary relevance Valor adaptativo de la diferenciación de brotes en árboles deciduos y su relevancia evolutiva

    Directory of Open Access Journals (Sweden)

    Veit M. Dörken

    2009-12-01

    Full Text Available Pronounced long shoot/short shoot differentiation is typical for deciduous angiosperm trees. It also occurs in a number of gymnosperms and very few evergreen angiosperm trees. The study of 719 angiosperm tree species (602 deciduous and 117 evergreen species demonstrated that the deciduous condition is nearly always associated with shoot differentiation. Detailed measurements in 38 angiosperms showed that the leaf area of an entire short shoot equals the leaf area of a single long shoot leaf of the same species and individual. In the few cases where the leaf area of the short shoot is slightly larger than that of a single long-shoot leaf, the short shoot leaves shade each other and the projection of the short shoot equals the area of a single long shoot leaf. Calculations of the stem biomass needed to expose a given assimilatory surface show two interesting aspects. First, the stem biomass (dry weight to expose leaf surface is about 10 times less in short shoots than in long shoots. Second, this biomass in long shoots and short shoots appears to be species independent. Regarding shoot structure efficiency, leaf size and shape do not matter. Some evergreen species resemble in all parameters more to deciduous species than to typical evergreen species. Phytogeographical data as well as morphological data suggest that these atypical evergreen species are derived from deciduous ancestors. As measured parameters differ markedly between all gymnosperms, except Ginkgo, and angiosperms, we suppose that the evolutionary pathway leading to shoot differentiation was different for gymnosperms and angiosperms.En Angiospermas arbóreas deciduas, es común encontrar un alto grado de diferenciación entre brotes largos y brotes cortos. También se presenta esta característica en un número de gimnospermas y en muy pocas angiospermas arbóreas siempreverdes. El estudio de 719 especies de angiospermas arbóreas (602 deciduas y 117 siempreverdes demostró que la

  14. Core principles of evolutionary medicine

    Science.gov (United States)

    Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

    2018-01-01

    Abstract Background and objectives Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. Methodology The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Results Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. Conclusions and implications This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further. PMID:29493660

  15. Proteomics in evolutionary ecology.

    Science.gov (United States)

    Baer, B; Millar, A H

    2016-03-01

    modifications and protein interactions of interest with high accuracy and assess protein diversity and function. Therefore, proteomic technologies can be viewed as providing evolutionary biologist with exciting novel opportunities to understand very early events in functional variation of cellular molecular machinery that are acting as part of evolutionary processes. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Phylogenetic inference with weighted codon evolutionary distances.

    Science.gov (United States)

    Criscuolo, Alexis; Michel, Christian J

    2009-04-01

    We develop a new approach to estimate a matrix of pairwise evolutionary distances from a codon-based alignment based on a codon evolutionary model. The method first computes a standard distance matrix for each of the three codon positions. Then these three distance matrices are weighted according to an estimate of the global evolutionary rate of each codon position and averaged into a unique distance matrix. Using a large set of both real and simulated codon-based alignments of nucleotide sequences, we show that this approach leads to distance matrices that have a significantly better treelikeness compared to those obtained by standard nucleotide evolutionary distances. We also propose an alternative weighting to eliminate the part of the noise often associated with some codon positions, particularly the third position, which is known to induce a fast evolutionary rate. Simulation results show that fast distance-based tree reconstruction algorithms on distance matrices based on this codon position weighting can lead to phylogenetic trees that are at least as accurate as, if not better, than those inferred by maximum likelihood. Finally, a well-known multigene dataset composed of eight yeast species and 106 codon-based alignments is reanalyzed and shows that our codon evolutionary distances allow building a phylogenetic tree which is similar to those obtained by non-distance-based methods (e.g., maximum parsimony and maximum likelihood) and also significantly improved compared to standard nucleotide evolutionary distance estimates.

  17. Evolutionary Finance

    OpenAIRE

    Igor V. Evstigneev; Thorsten Hens; Klaus Reiner Schenk-Hoppé

    2008-01-01

    Evolutionary finance studies the dynamic interaction of investment strategies in financial markets. This market interaction generates a stochastic wealth dynamics on a heterogenous population of traders through the fluctuation of asset prices and their random payoffs. Asset prices are endogenously determined through short-term market clearing. Investors' portfolio choices are characterized by investment strategies which provide a descriptive model of decision behavior. The mathematical framew...

  18. Mathematics and evolutionary biology make bioinformatics education comprehensible.

    Science.gov (United States)

    Jungck, John R; Weisstein, Anton E

    2013-09-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

  19. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

  20. phyloXML: XML for evolutionary biology and comparative genomics.

    Science.gov (United States)

    Han, Mira V; Zmasek, Christian M

    2009-10-27

    Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types. We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data. PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at http://www.phyloxml.org.

  1. Predicting virus emergence amid evolutionary noise.

    Science.gov (United States)

    Geoghegan, Jemma L; Holmes, Edward C

    2017-10-01

    The study of virus disease emergence, whether it can be predicted and how it might be prevented, has become a major research topic in biomedicine. Here we show that efforts to predict disease emergence commonly conflate fundamentally different evolutionary and epidemiological time scales, and are likely to fail because of the enormous number of unsampled viruses that could conceivably emerge in humans. Although we know much about the patterns and processes of virus evolution on evolutionary time scales as depicted in family-scale phylogenetic trees, these data have little predictive power to reveal the short-term microevolutionary processes that underpin cross-species transmission and emergence. Truly understanding disease emergence therefore requires a new mechanistic and integrated view of the factors that allow or prevent viruses spreading in novel hosts. We present such a view, suggesting that both ecological and genetic aspects of virus emergence can be placed within a simple population genetic framework, which in turn highlights the importance of host population size and density in determining whether emergence will be successful. Despite this framework, we conclude that a more practical solution to preventing and containing the successful emergence of new diseases entails ongoing virological surveillance at the human-animal interface and regions of ecological disturbance. © 2017 The Authors.

  2. Reconciliation of Gene and Species Trees

    Directory of Open Access Journals (Sweden)

    L. Y. Rusin

    2014-01-01

    Full Text Available The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.

  3. A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms

    Science.gov (United States)

    Werner, Gijsbert D. A.; Cornwell, William K.; Sprent, Janet I.; Kattge, Jens; Kiers, E. Toby

    2014-01-01

    Symbiotic associations occur in every habitat on earth, but we know very little about their evolutionary histories. Current models of trait evolution cannot adequately reconstruct the deep history of symbiotic innovation, because they assume homogenous evolutionary processes across millions of years. Here we use a recently developed, heterogeneous and quantitative phylogenetic framework to study the origin of the symbiosis between angiosperms and nitrogen-fixing (N2) bacterial symbionts housed in nodules. We compile the largest database of global nodulating plant species and reconstruct the symbiosis’ evolution. We identify a single, cryptic evolutionary innovation driving symbiotic N2-fixation evolution, followed by multiple gains and losses of the symbiosis, and the subsequent emergence of ‘stable fixers’ (clades extremely unlikely to lose the symbiosis). Originating over 100 MYA, this innovation suggests deep homology in symbiotic N2-fixation. Identifying cryptic innovations on the tree of life is key to understanding the evolution of complex traits, including symbiotic partnerships. PMID:24912610

  4. Understanding evolutionary paradigm of knockdown resistance in mosquitoes by analyzing DNA sequence polymorphisms in voltage-gated sodium channel in Culex quinquefasciatus

    Directory of Open Access Journals (Sweden)

    Manas Sarkar

    2011-09-01

    Full Text Available The Voltage Gated Sodium Channel (VGSC is critical for binding of different insecticides and plays a key role in insecticide resistance. The insect sodium channel consists of four homologous domains (I to IV, each containing six transmembrane segments (S1 to S6. An important mechanism of resistance to DDT and pyrethroids is termed knockdown resistance (kdr, caused by a single nucleotide polymorphism in IIS6 domain of sodium channels. We analyzed the polymorphisms, nucleotide diversity, and phylogenies in VGSC-IIS6 gene in Culex quinquefasciatus from India. We analyzed the neutral model / hypothesis to infer if natural selection is acting upon the analyzed vgsc gene. Tajima’s D, Fu and Li’s D* and F* and Fu’s Fs test were performed to determine whether the distribution of nucleotide variation within the samples was consistent with neutral model. We theorized that the evolutionary pattern of intra-population distribution of variability in vgsc gene is consistent with the neutral expectation.

  5. Computational evolutionary perception.

    Science.gov (United States)

    Hoffman, Donald D; Singh, Manish

    2012-01-01

    Marr proposed that human vision constructs "a true description of what is there". He argued that to understand human vision one must discover the features of the world it recovers and the constraints it uses in the process. Bayesian decision theory (BDT) is used in modem vision research as a probabilistic framework for understanding human vision along the lines laid out by Marr. Marr's contribution to vision research is substantial and justly influential. We propose, however, that evolution by natural selection does not, in general, favor perceptions that are true descriptions of the objective world. Instead, research with evolutionary games shows that perceptual systems tuned solely to fitness routinely outcompete those tuned to truth. Fitness functions depend not just on the true state of the world, but also on the organism, its state, and the type of action. Thus, fitness and truth are distinct. Natural selection depends only on expected fitness. It shapes perceptual systems to guide fitter behavior, not to estimate truth. To study perception in an evolutionary context, we introduce the framework of Computational Evolutionary Perception (CEP). We show that CEP subsumes BDT, and reinterprets BDT as evaluating expected fitness rather than estimating truth.

  6. Kinematics of a Young Low-mass Star-forming Core: Understanding the Evolutionary State of the First-core Candidate L1451-mm

    Energy Technology Data Exchange (ETDEWEB)

    Maureira, María José; Arce, Héctor G. [Astronomy Department, Yale University, New Haven, CT 06511 (United States); Dunham, Michael M. [Department of Physics, State University of New York at Fredonia, Fredonia, NY 14063 (United States); Pineda, Jaime E. [Max-Planck Institute for Extraterrestrial Physics, Giessenbachstrasse 1, D-85748 Garching (Germany); Fernández-López, Manuel [Instituto Argentino de Radioastronomía, CCT-La Plata (CONICET), C.C.5, 1894, Villa Elisa (Argentina); Chen, Xuepeng [Purple Mountain Observatory, Chinese Academy of Sciences, 2 West Beijing Road, Nanjing 210008 (China); Mardones, Diego, E-mail: mariajose.maureira@yale.edu, E-mail: hector.arce@yale.edu [Departamento de Astronomía, Universidad de Chile, Casilla 36-D, Santiago (Chile)

    2017-03-20

    We use 3 mm multiline and continuum CARMA observations toward the first hydrostatic core (FHSC) candidate L1451-mm to characterize the envelope kinematics at 1000 au scales and investigate its evolutionary state. We detect evidence of infall and rotation in the NH{sub 2}D(1{sub 1,1}–1{sub 0,1}), N{sub 2}H{sup +}(1–0), and HCN(1–0) molecular lines. We compare the position–velocity diagram of the NH{sub 2}D(1{sub 1,1}–1{sub 0,1}) line with a simple kinematic model and find that it is consistent with an envelope that is both infalling and rotating while conserving angular momentum around a central mass of about 0.06 M {sub ⊙}. The N{sub 2}H{sup +}(1–0) LTE mass of the envelope along with the inferred infall velocity leads to a mass infall rate of approximately 6 × 10{sup −6} M {sub ⊙} yr{sup −1}, implying a young age of 10{sup 4} years for this FHSC candidate. Assuming that the accretion onto the central object is the same as the infall rate, we obtain a minimum source size of 1.5–5 au, consistent with the size expected for a first core. We do not see any evidence of outflow motions or signs of outflow–envelope interaction at scales ≳2000 au. This is consistent with previous observations that revealed a very compact outflow (≲500 au). We conclude that L1451-mm is indeed at a very early stage of evolution, either a first core or an extremely young Class 0 protostar. Our results provide strong evidence that L1451-mm is the best candidate for being a bona fide first core.

  7. DensiTree: making sense of sets of phylogenetic trees.

    Science.gov (United States)

    Bouckaert, Remco R

    2010-05-15

    Bayesian analysis through programs like BEAST (Drummond and Rumbaut, 2007) and MrBayes (Huelsenbeck et al., 2001) provides a powerful method for reconstruction of evolutionary relationships. One of the benefits of Bayesian methods is that well-founded estimates of uncertainty in models can be made available. So, for example, not only the mean time of a most recent common ancestor (tMRCA) is estimated, but also the spread. This distribution over model space is represented by a set of trees, which can be rather large and difficult to interpret. DensiTree is a tool that helps navigating these sets of trees. The main idea behind DensiTree is to draw all trees in the set transparently. As a result, areas where a lot of the trees agree in topology and branch lengths show up as highly colored areas, while areas with little agreement show up as webs. This makes it possible to quickly get an impression of properties of the tree set such as well-supported clades, distribution of tMRCA and areas of topological uncertainty. Thus, DensiTree provides a quick method for qualitative analysis of tree sets. DensiTree is freely available from http://compevol.auckland.ac.nz/software/DensiTree/. The program is licensed under GPL and source code is available. remco@cs.auckland.ac.nz

  8. Tree biology and dendrochemistry

    Science.gov (United States)

    Kevin T. Smith; Walter C. Shortle

    1996-01-01

    Dendrochemistry, the interpretation of elemental analysis of dated tree rings, can provide a temporal record of environmental change. Using the dendrochemical record requires an understanding of tree biology. In this review, we pose four questions concerning assumptions that underlie recent dendrochemical research: 1) Does the chemical composition of the wood directly...

  9. Trees Are Terrific!

    Science.gov (United States)

    Braus, Judy, Ed.

    1992-01-01

    Ranger Rick's NatureScope is a creative education series dedicated to inspiring in children an understanding and appreciation of the natural world while developing the skills they will need to make responsible decisions about the environment. Contents are organized into the following sections: (1) "What Makes a Tree a Tree?," including…

  10. "Small size" in the Philippine human fossil record: is it meaningful for a better understanding of the evolutionary history of the negritos?

    Science.gov (United States)

    Détroit, Florent; Corny, Julien; Dizon, Eusebio Z; Mijares, Armand S

    2013-01-01

    "Pygmy populations" are recognized in several places over the world, especially in Western Africa and in Southeast Asia (Philippine "negritos," for instance). Broadly defined as "small-bodied Homo sapiens" (compared with neighboring populations), their origins and the nature of the processes involved in the maintenance of their phenotype over time are highly debated. Major results have been recently obtained from population genetics on present-day negrito populations, but their evolutionary history remains largely unresolved. We present and discuss the Upper Pleistocene human remains recovered from Tabon Cave and Callao Cave in the Philippines, which are potentially highly relevant to these research questions. Human fossils have been recovered in large numbers from Tabon Cave (Palawan Island) but mainly from reworked and mixed sediments from several archaeological layers. We review and synthesize the long and meticulous collaborative work done on the archives left from the 1960s excavations and on the field. The results demonstrate the long history of human occupations in the cave, since at least ~30,000 BP. The examination of the Tabon human remains shows a large variability: large and robust for one part of the sample, and small and gracile for the other part. The latter would fit quite comfortably within the range of variation of Philippine negritos. Farther north, on Luzon Island, the human third metatarsal recently recovered from Callao Cave and dated to ~66,000 BP is now the oldest direct evidence of human presence in the Philippines. Previous data show that, compared with H. sapiens (including Philippine negritos), this bone presents a very small size and several unusual morphological characteristics. We present a new analytical approach using three-dimensional geometric morphometrics for comparing the Callao fossil to a wide array of extant Asian mammals, including nonhuman primates and H. sapiens. The results demonstrate that the shape of the Callao

  11. Genome Trees from Conservation Profiles.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available The concept of the genome tree depends on the potential evolutionary significance in the clustering of species according to similarities in the gene content of their genomes. In this respect, genome trees have often been identified with species trees. With the rapid expansion of genome sequence data it becomes of increasing importance to develop accurate methods for grasping global trends for the phylogenetic signals that mutually link the various genomes. We therefore derive here the methodological concept of genome trees based on protein conservation profiles in multiple species. The basic idea in this derivation is that the multi-component "presence-absence" protein conservation profiles permit tracking of common evolutionary histories of genes across multiple genomes. We show that a significant reduction in informational redundancy is achieved by considering only the subset of distinct conservation profiles. Beyond these basic ideas, we point out various pitfalls and limitations associated with the data handling, paving the way for further improvements. As an illustration for the methods, we analyze a genome tree based on the above principles, along with a series of other trees derived from the same data and based on pair-wise comparisons (ancestral duplication-conservation and shared orthologs. In all trees we observe a sharp discrimination between the three primary domains of life: Bacteria, Archaea, and Eukarya. The new genome tree, based on conservation profiles, displays a significant correspondence with classically recognized taxonomical groupings, along with a series of departures from such conventional clusterings.

  12. Gender Inequality in Interaction--An Evolutionary Account

    Science.gov (United States)

    Hopcroft, Rosemary L.

    2009-01-01

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

  13. Evolutionary phenomena in galaxies

    International Nuclear Information System (INIS)

    Beckman, J.E.; Pagel, B.E.J.

    1989-01-01

    This book reviews the subject of evolutionary phenomena in galaxies, bringing together contributions by experts on all the relevant physics and astrophysics necessary to understand galaxies and how they work. The book is based on the proceedings of a conference held in July 1988 in Puerto de la Cruz, Tenerife which was timed to coincide with the first year of operation of the 4.2 m William Herschel Telescope. The broad topics covered include formation of galaxies and their ages, stellar dynamics, galactic scale gas and its role in star formation and the production and distribution of the chemical elements within galaxies. (author)

  14. Evolutionary genomics of Entamoeba

    Science.gov (United States)

    Weedall, Gareth D.; Hall, Neil

    2011-01-01

    Entamoeba histolytica is a human pathogen that causes amoebic dysentery and leads to significant morbidity and mortality worldwide. Understanding the genome and evolution of the parasite will help explain how, when and why it causes disease. Here we review current knowledge about the evolutionary genomics of Entamoeba: how differences between the genomes of different species may help explain different phenotypes, and how variation among E. histolytica parasites reveals patterns of population structure. The imminent expansion of the amount genome data will greatly improve our knowledge of the genus and of pathogenic species within it. PMID:21288488

  15. Pareto-optimal phylogenetic tree reconciliation.

    Science.gov (United States)

    Libeskind-Hadas, Ran; Wu, Yi-Chieh; Bansal, Mukul S; Kellis, Manolis

    2014-06-15

    Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies. Our Python tools are freely available at www.cs.hmc.edu/∼hadas/xscape. . © The Author 2014. Published by Oxford University Press.

  16. Two or three domains: a new view of tree of life in the genomics era.

    Science.gov (United States)

    Zhou, Zhichao; Liu, Yang; Li, Meng; Gu, Ji-Dong

    2018-04-01

    The deep phylogenetic topology of tree of life is in the center of a long-time dispute. The Woeseian three-domain tree theory, with the Eukarya evolving as a sister clade to Archaea, competes with the two-domain tree theory (the eocyte tree), with the Eukarya branched within Archaea. Revealed by the ongoing debate over the last three decades, sophisticated and proper phylogenetic methods should necessarily be paid with more emphasis, especially these are focusing on the compositional heterogeneity of sites and lineages, and the heterotachy issue. The newly emerging archaeal lineages with numerous eukaryotic-like features, such as membrane trafficking and cellular compartmentalization, are phylogenetically the closest to eukaryotes currently. These findings highlight the evolutionary history from an ancient archaeon to a more complex archaeon with protoeukaryotic-like features and complex cellular structures, thus providing clues to understand eukaryogenesis process. The increasing repertoire of precise genomic contents provides great advantages on understanding the deep phylogeny of tree of life and ancient evolutionary events on Eukarya branching process.

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

    Science.gov (United States)

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

    2011-01-01

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

  18. Efficient Computation of Popular Phylogenetic Tree Measures

    DEFF Research Database (Denmark)

    Tsirogiannis, Constantinos; Sandel, Brody Steven; Cheliotis, Dimitris

    2012-01-01

    Given a phylogenetic tree $\\mathcal{T}$ of n nodes, and a sample R of its tips (leaf nodes) a very common problem in ecological and evolutionary research is to evaluate a distance measure for the elements in R. Two of the most common measures of this kind are the Mean Pairwise Distance ($\\ensurem...... software package for processing phylogenetic trees....

  19. TreeFam: a curated database of phylogenetic trees of animal gene families

    DEFF Research Database (Denmark)

    Li, Heng; Coghlan, Avril; Ruan, Jue

    2006-01-01

    TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively......, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins...

  20. Deciphering the evolutionary history of open and closed mitosis.

    Science.gov (United States)

    Sazer, Shelley; Lynch, Michael; Needleman, Daniel

    2014-11-17

    The origin of the nucleus at the prokaryote-to-eukaryote transition represents one of the most important events in the evolution of cellular organization. The nuclear envelope encircles the chromosomes in interphase and is a selectively permeable barrier between the nucleoplasm and cytoplasm and an organizational scaffold for the nucleus. It remains intact in the 'closed' mitosis of some yeasts, but loses its integrity in the 'open' mitosis of mammals. Instances of both types of mitosis within two evolutionary clades indicate multiple evolutionary transitions between open and closed mitosis, although the underlying genetic changes that influenced these transitions remain unknown. A survey of the diversity of mitotic nuclei that fall between these extremes is the starting point from which to determine the physiologically relevant characteristics distinguishing open from closed mitosis and to understand how they evolved and why they are retained in present-day organisms. The field is now poised to begin addressing these issues by defining and documenting patterns of mitotic nuclear variation within and among species and mapping them onto a phylogenic tree. Deciphering the evolutionary history of open and closed mitosis will complement cell biological and genetic approaches aimed at deciphering the fundamental organizational principles of the nucleus. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Computing Refined Buneman Trees in Cubic Time

    DEFF Research Database (Denmark)

    Brodal, G.S.; Fagerberg, R.; Östlin, A.

    2003-01-01

    in the underlying distance data. Distance based methods based on the theory of Buneman trees and refined Buneman trees avoid this problem by only proposing evolutionary trees whose edges satisfy a number of constraints. These trees might not be fully resolved but there is strong combinatorial evidence for each...... proposed edge. The currently best algorithm for computing the refined Buneman tree from a given distance measure has a running time of O(n 5) and a space consumption of O(n 4). In this paper, we present an algorithm with running time O(n 3) and space consumption O(n 2). The improved complexity of our...

  2. Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?

    Science.gov (United States)

    Mendez, Martin; Jefferson, Thomas A; Kolokotronis, Sergios-Orestis; Krützen, Michael; Parra, Guido J; Collins, Tim; Minton, Giana; Baldwin, Robert; Berggren, Per; Särnblad, Anna; Amir, Omar A; Peddemors, Vic M; Karczmarski, Leszek; Guissamulo, Almeida; Smith, Brian; Sutaria, Dipani; Amato, George; Rosenbaum, Howard C

    2013-12-01

    The conservation of humpback dolphins, distributed in coastal waters of the Indo-West Pacific and eastern Atlantic Oceans, has been hindered by a lack of understanding about the number of species in the genus (Sousa) and their population structure. To address this issue, we present a combined analysis of genetic and morphologic data collected from beach-cast, remote-biopsied and museum specimens from throughout the known Sousa range. We extracted genetic sequence data from 235 samples from extant populations and explored the mitochondrial control region and four nuclear introns through phylogenetic, population-level and population aggregation frameworks. In addition, 180 cranial specimens from the same geographical regions allowed comparisons of 24 morphological characters through multivariate analyses. The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S. teuszii in the Atlantic off West Africa, S. plumbea in the central and western Indian Ocean, S. chinensis in the eastern Indian and West Pacific Oceans, and a new as-yet-unnamed species off northern Australia). © 2013 John Wiley & Sons Ltd.

  3. On the distribution of interspecies correlation for Markov models of character evolution on Yule trees.

    Science.gov (United States)

    Mulder, Willem H; Crawford, Forrest W

    2015-01-07

    Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule process, in which new species are "born" from existing lineages at a constant rate. Recent work has illuminated some of the structural properties of Yule trees, but it remains mostly unknown how these properties affect sequence and trait patterns observed at the tips of the phylogenetic tree. Understanding the interplay between speciation and mutation under simple models of evolution is essential for deriving valid phylogenetic inference methods and gives insight into the optimal design of phylogenetic studies. In this work, we derive the probability distribution of interspecies covariance under Brownian motion and Ornstein-Uhlenbeck models of phenotypic change on a Yule tree. We compute the probability distribution of the number of mutations shared between two randomly chosen taxa in a Yule tree under discrete Markov mutation models. Our results suggest summary measures of phylogenetic information content, illuminate the correlation between site patterns in sequences or traits of related organisms, and provide heuristics for experimental design and reconstruction of phylogenetic trees. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Evolutionary foundations for cancer biology.

    Science.gov (United States)

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

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

  5. Evolutionary genomics of environmental pollution.

    Science.gov (United States)

    Whitehead, Andrew

    2014-01-01

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

  6. Democratizing evolutionary biology, lessons from insects

    DEFF Research Database (Denmark)

    Dunn, Robert Roberdeau; Beasley, DeAnna E.

    2016-01-01

    The engagement of the public in the scientific process is an old practice. Yet with recent advances in technology, the role of the citizen scientist in studying evolutionary processes has increased. Insects provide ideal models for understanding these evolutionary processes at large scales...

  7. Evolutionary genetics: the Drosophila model

    Indian Academy of Sciences (India)

    Unknown

    ral selection is provided by studies—sometimes characterized as evolutionary ecology—that attempt to understand how and why particular fitness functions are defined on the distribution of phenotypes in a population by its ecology. Studying how the interaction between phenotype and environment results in a fitness ...

  8. ALCANCES E LIMITES DA PSICOLOGIA EVOLUTIVA PARA A COMPREENSÃO DA MENTE SCOPE AND LIMITS OF EVOLUTIONARY PSYCHOLOGY TO THE UNDERSTANDING OF MIND

    Directory of Open Access Journals (Sweden)

    Cleverson leite Bastos

    2011-03-01

    Full Text Available O que pretendemos, na extensão que um artigo permite, é convergir dois domínios de modelos contemporâneos para a compreensão da mente. Ambos são ferramentas heurísticas fundamentais que possibilitam, por um lado, a teoria da mente modular, entender aspectos importantes da cognição humana como linguagem, memória, aprendizagem (ciências cognitivas e, por outro, modelos advindos da psicologia evolutiva que explicam certos aparentes desperdícios comportamentais. Os pressupostos fundamentais de ambas as metáforas são distintos: o modelo modular é produto das ciências cognitivas e o modelo evolucionista é produto do princípio de seleção sexual. Basicamente, como ferramenta heurística a teoria modular demonstra ser a mente um cômputo, como produto da seleção (seleção natural, que processa informação; já a teoria da mente ornamental propõe uma ideia estranha que Amotz Zahavi chamou de princípio de handicap (seleção sexual.
    Our intent with this article, given its space limitations, is converging two contemporary models of mind domain. Both are fundamental heuristic tools, being the first, the modular theory of mind, which enables us to understand important aspects of human cognition such as language, memory, learning (cognitive sciences. The second, the ornamental mind theory, explains certain apparent wasteful behaviors. The fundamental presuppositions of both metaphors are distinct: whilst the modular model is a product of cognitive sciences, the ornamental model is the yield of the sexual selection principle. Basically, as heuristic tools, the modular theory demonstrates the mind as a computation, as a product of selection (natural selection which processes information; on its turn, the ornamental mind theory proposes an awkward idea, which Amotz Zahavi called the handicap principle (sexual selection.

  9. Evolutionary developmental biology its roots and characteristics.

    Science.gov (United States)

    Morange, Michel

    2011-09-01

    The rise of evolutionary developmental biology was not the progressive isolation and characterization of developmental genes and gene networks. Many obstacles had to be overcome: the idea that all genes were more or less involved in development; the evidence that developmental processes in insects had nothing in common with those of vertebrates. Different lines of research converged toward the creation of evolutionary developmental biology, giving this field of research its present heterogeneity. This does not prevent all those working in the field from sharing the conviction that a precise characterization of evolutionary variations is required to fully understand the evolutionary process. Some evolutionary developmental biologists directly challenge the Modern Synthesis. I propose some ways to reconcile these apparently opposed visions of evolution. The turbulence seen in evolutionary developmental biology reflects the present entry of history into biology. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. The Evolving Theory of Evolutionary Radiations.

    Science.gov (United States)

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

    2016-01-01

    Evolutionary radiations have intrigued biologists for more than 100 years, and our understanding of the patterns and processes associated with these radiations continues to grow and evolve. Recently it has been recognized that there are many different types of evolutionary radiation beyond the well-studied adaptive radiations. We focus here on multifarious types of evolutionary radiations, paying special attention to the abiotic factors that might trigger diversification in clades. We integrate concepts such as exaptation, species selection, coevolution, and the turnover-pulse hypothesis (TPH) into the theoretical framework of evolutionary radiations. We also discuss other phenomena that are related to, but distinct from, evolutionary radiations that have relevance for evolutionary biology. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Understanding Spatio-Temporal Variability in the Reproduction Ratio of the Bluetongue (BTV-1 Epidemic in Southern Spain (Andalusia in 2007 Using Epidemic Trees.

    Directory of Open Access Journals (Sweden)

    S Napp

    Full Text Available Andalusia (Southern Spain is considered one of the main routes of introduction of bluetongue virus (BTV into Europe, evidenced by a devastating epidemic caused by BTV-1 in 2007. Understanding the pattern and the drivers of BTV-1 spread in Andalusia is critical for effective detection and control of future epidemics. A long-standing metric for quantifying the behaviour of infectious diseases is the case-reproduction ratio (Rt, defined as the average number of secondary cases arising from a single infected case at time t (for t>0. Here we apply a method using epidemic trees to estimate the between-herd case reproduction ratio directly from epidemic data allowing the spatial and temporal variability in transmission to be described. We then relate this variability to predictors describing the hosts, vectors and the environment to better understand why the epidemic spread more quickly in some regions or periods. The Rt value for the BTV-1 epidemic in Andalusia peaked in July at 4.6, at the start of the epidemic, then decreased to 2.2 by August, dropped below 1 by September (0.8, and by October it had decreased to 0.02. BTV spread was the consequence of both local transmission within established disease foci and BTV expansion to distant new areas (i.e. new foci, which resulted in a high variability in BTV transmission, not only among different areas, but particularly through time, which suggests that general control measures applied at broad spatial scales are unlikely to be effective. This high variability through time was probably due to the impact of temperature on BTV transmission, as evidenced by a reduction in the value of Rt by 0.0041 for every unit increase (day in the extrinsic incubation period (EIP, which is itself directly dependent on temperature. Moreover, within the range of values at which BTV-1 transmission occurred in Andalusia (20.6°C to 29.5°C there was a positive correlation between temperature and Rt values, although the

  12. Using tree diversity to compare phylogenetic heuristics.

    Science.gov (United States)

    Sul, Seung-Jin; Matthews, Suzanne; Williams, Tiffani L

    2009-04-29

    Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best scores in the fastest time. We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms. Our results show that although Pauprat and Rec-I-DCM3 find the trees with the same best scores, topologically these trees are quite different. Furthermore, the Rec-I-DCM3 trees cluster distinctly from the Pauprat trees. In addition to our heatmap visualizations of using parsimony scores and the Robinson-Foulds distance to compare best-scoring trees found by the two heuristics, we also develop entropy-based methods to show the diversity of the trees found. Overall, Pauprat identifies more diverse trees than Rec-I-DCM3. Overall, our work shows that there is value to comparing heuristics beyond the parsimony scores that they find. Pauprat is a slower heuristic than Rec-I-DCM3. However, our work shows that there is tremendous value in using Pauprat to reconstruct trees-especially since it finds identical scoring but topologically distinct trees. Hence, instead of discounting Pauprat, effort should go in improving its implementation. Ultimately, improved performance measures lead to better phylogenetic heuristics and will result in better approximations of the true evolutionary history of the organisms of interest.

  13. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

    Directory of Open Access Journals (Sweden)

    Nakhleh Luay

    2008-07-01

    Full Text Available Abstract Background Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT, hybrid speciation, and interspecific recombination, collectively referred to as reticulate evolutionary events, result in networks, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX. Results In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or evolutionary networks, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1 evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2 evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks – trees, clusters, and tripartitions; (3 evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4 evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees. Conclusion The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in

  14. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships.

    Science.gov (United States)

    Than, Cuong; Ruths, Derek; Nakhleh, Luay

    2008-07-28

    Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as reticulate evolutionary events, result in networks, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX. In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or evolutionary networks, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1) evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2) evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks - trees, clusters, and tripartitions; (3) evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4) evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees. The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in analyzing large data sets, as well as in studying the

  15. Flowering Trees

    Indian Academy of Sciences (India)

    Dolichandrone atrovirens (Roth) K. Schum. (Spathe Trumpet Tree) of Bignoniaceae is a medium-sized handsome tree with a straight bole that branches at the top. Leaves are once pinnate, with two to three pairs of leaflets. Young parts of the tree are velvety. Inflorescence is a branched raceme borne at the branch ends.

  16. Litter feedbacks, evolutionary change and exotic plant

    NARCIS (Netherlands)

    Eppinga, M.B.; Kaproth, M.A.; Collins, A.R.; Molofsky, J.

    2011-01-01

    1. Understanding the mechanisms driving exotic plant invasions is important for designing successful invader control strategies. Previous studies have highlighted different invasion mechanisms, including alteration of nutrient cycles through plant–soil feedback and evolutionary change toward more

  17. Evolutionary understanding of the concept "Public relations"

    OpenAIRE

    Кам’янецька, О.В.

    2013-01-01

    The considered approaches to determination of notion of «public relations» different research and practical workers. The analyzed stages of development of communications with public and described their signs. Розглянуті підходи до визначення поняття «паблік рілейшнз» різних науковців та практиків. Проаналізовані етапи розвитку підходів до зв’язків з громадськістю та охарактеризовані їх ознаки....

  18. Tree compression with top trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

    2013-01-01

    We introduce a new compression scheme for labeled trees based on top trees [3]. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

  19. Tree compression with top trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

    2015-01-01

    We introduce a new compression scheme for labeled trees based on top trees. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

  20. An integrative approach to understanding bird origins.

    Science.gov (United States)

    Xu, Xing; Zhou, Zhonghe; Dudley, Robert; Mackem, Susan; Chuong, Cheng-Ming; Erickson, Gregory M; Varricchio, David J

    2014-12-12

    Recent discoveries of spectacular dinosaur fossils overwhelmingly support the hypothesis that birds are descended from maniraptoran theropod dinosaurs, and furthermore, demonstrate that distinctive bird characteristics such as feathers, flight, endothermic physiology, unique strategies for reproduction and growth, and a novel pulmonary system originated among Mesozoic terrestrial dinosaurs. The transition from ground-living to flight-capable theropod dinosaurs now probably represents one of the best-documented major evolutionary transitions in life history. Recent studies in developmental biology and other disciplines provide additional insights into how bird characteristics originated and evolved. The iconic features of extant birds for the most part evolved in a gradual and stepwise fashion throughout archosaur evolution. However, new data also highlight occasional bursts of morphological novelty at certain stages particularly close to the origin of birds and an unavoidable complex, mosaic evolutionary distribution of major bird characteristics on the theropod tree. Research into bird origins provides a premier example of how paleontological and neontological data can interact to reveal the complexity of major innovations, to answer key evolutionary questions, and to lead to new research directions. A better understanding of bird origins requires multifaceted and integrative approaches, yet fossils necessarily provide the final test of any evolutionary model. Copyright © 2014, American Association for the Advancement of Science.

  1. Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management

    Science.gov (United States)

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

    2017-01-01

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

  2. Fault-Tree Compiler Program

    Science.gov (United States)

    Butler, Ricky W.; Martensen, Anna L.

    1992-01-01

    FTC, Fault-Tree Compiler program, is reliability-analysis software tool used to calculate probability of top event of fault tree. Five different types of gates allowed in fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. High-level input language of FTC easy to understand and use. Program supports hierarchical fault-tree-definition feature simplifying process of description of tree and reduces execution time. Solution technique implemented in FORTRAN, and user interface in Pascal. Written to run on DEC VAX computer operating under VMS operating system.

  3. Attractive evolutionary equilibria

    NARCIS (Netherlands)

    Joosten, Reinoud A.M.G.; Roorda, Berend

    2011-01-01

    We present attractiveness, a refinement criterion for evolutionary equilibria. Equilibria surviving this criterion are robust to small perturbations of the underlying payoff system or the dynamics at hand. Furthermore, certain attractive equilibria are equivalent to others for certain evolutionary

  4. SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees

    OpenAIRE

    Beccati, Alan; Gerken, Jan; Quast, Christian; Yilmaz, Pelin; Glöckner, Frank Oliver

    2017-01-01

    Background Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. Results The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA T...

  5. Analyzing Evolutionary Optimization in Noisy Environments.

    Science.gov (United States)

    Qian, Chao; Yu, Yang; Zhou, Zhi-Hua

    2018-01-01

    Many optimization tasks must be handled in noisy environments, where the exact evaluation of a solution cannot be obtained, only a noisy one. For optimization of noisy tasks, evolutionary algorithms (EAs), a type of stochastic metaheuristic search algorithm, have been widely and successfully applied. Previous work mainly focuses on the empirical study and design of EAs for optimization under noisy conditions, while the theoretical understandings are largely insufficient. In this study, we first investigate how noisy fitness can affect the running time of EAs. Two kinds of noise-helpful problems are identified, on which the EAs will run faster with the presence of noise, and thus the noise should not be handled. Second, on a representative noise-harmful problem in which the noise has a strong negative effect, we examine two commonly employed mechanisms dealing with noise in EAs: reevaluation and threshold selection. The analysis discloses that using these two strategies simultaneously is effective for the one-bit noise but ineffective for the asymmetric one-bit noise. Smooth threshold selection is then proposed, which can be proved to be an effective strategy to further improve the noise tolerance ability in the problem. We then complement the theoretical analysis by experiments on both synthetic problems as well as two combinatorial problems, the minimum spanning tree and the maximum matching. The experimental results agree with the theoretical findings and also show that the proposed smooth threshold selection can deal with the noise better.

  6. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Evolutionary Biology Today - The Domain of Evolutionary Biology ... Keywords. Evolution; natural selection; biodiversity; fitness; adaptation. Author Affiliations. Amitabh Joshi1. Evolutionary and Organismal Biology Unit Jawaharlal Nehru Centre for Advanced Scientific Research P.Box 6436, Jakkur Bangalore 560 065, India.

  7. Spore: Spawning Evolutionary Misconceptions?

    Science.gov (United States)

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

    2010-10-01

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

  8. Environmental evolutionary graph theory.

    Science.gov (United States)

    Maciejewski, Wes; Puleo, Gregory J

    2014-11-07

    Understanding the influence of an environment on the evolution of its resident population is a major challenge in evolutionary biology. Great progress has been made in homogeneous population structures while heterogeneous structures have received relatively less attention. Here we present a structured population model where different individuals are best suited to different regions of their environment. The underlying structure is a graph: individuals occupy vertices, which are connected by edges. If an individual is suited for their vertex, they receive an increase in fecundity. This framework allows attention to be restricted to the spatial arrangement of suitable habitat. We prove some basic properties of this model and find some counter-intuitive results. Notably, (1) the arrangement of suitable sites is as important as their proportion, and (2) decreasing the proportion of suitable sites may result in a decrease in the fixation time of an allele. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. The evolutionary rate dynamically tracks changes in HIV-1 epidemics

    Energy Technology Data Exchange (ETDEWEB)

    Maljkovic-berry, Irina [Los Alamos National Laboratory; Athreya, Gayathri [Los Alamos National Laboratory; Daniels, Marcus [Los Alamos National Laboratory; Bruno, William [Los Alamos National Laboratory; Korber, Bette [Los Alamos National Laboratory; Kuiken, Carla [Los Alamos National Laboratory; Ribeiro, Ruy M [Los Alamos National Laboratory

    2009-01-01

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

  10. Using single cell sequencing data to model the evolutionary history of a tumor.

    Science.gov (United States)

    Kim, Kyung In; Simon, Richard

    2014-01-24

    The introduction of next-generation sequencing (NGS) technology has made it possible to detect genomic alterations within tumor cells on a large scale. However, most applications of NGS show the genetic content of mixtures of cells. Recently developed single cell sequencing technology can identify variation within a single cell. Characterization of multiple samples from a tumor using single cell sequencing can potentially provide information on the evolutionary history of that tumor. This may facilitate understanding how key mutations accumulate and evolve in lineages to form a heterogeneous tumor. We provide a computational method to infer an evolutionary mutation tree based on single cell sequencing data. Our approach differs from traditional phylogenetic tree approaches in that our mutation tree directly describes temporal order relationships among mutation sites. Our method also accommodates sequencing errors. Furthermore, we provide a method for estimating the proportion of time from the earliest mutation event of the sample to the most recent common ancestor of the sample of cells. Finally, we discuss current limitations on modeling with single cell sequencing data and possible improvements under those limitations. Inferring the temporal ordering of mutational sites using current single cell sequencing data is a challenge. Our proposed method may help elucidate relationships among key mutations and their role in tumor progression.

  11. Rate of tree carbon accumulation increases continuously with tree size

    Science.gov (United States)

    Stephenson, N.L.; Das, A.J.; Condit, R.; Russo, S.E.; Baker, P.J.; Beckman, N.G.; Coomes, D.A.; Lines, E.R.; Morris, W.K.; Rüger, N.; Álvarez, E.; Blundo, C.; Bunyavejchewin, S.; Chuyong, G.; Davies, S.J.; Duque, Á.; Ewango, C.N.; Flores, O.; Franklin, J.F.; Grau, H.R.; Hao, Z.; Harmon, M.E.; Hubbell, S.P.; Kenfack, D.; Lin, Y.; Makana, J.-R.; Malizia, A.; Malizia, L.R.; Pabst, R.J.; Pongpattananurak, N.; Su, S.-H.; Sun, I-F.; Tan, S.; Thomas, D.; van Mantgem, P.J.; Wang, X.; Wiser, S.K.; Zavala, M.A.

    2014-01-01

    Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle—particularly net primary productivity and carbon storage - increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree’s total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to understand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

  12. Maximum likelihood inference of small trees in the presence of long branches.

    Science.gov (United States)

    Parks, Sarah L; Goldman, Nick

    2014-09-01

    The statistical basis of maximum likelihood (ML), its robustness, and the fact that it appears to suffer less from biases lead to it being one of the most popular methods for tree reconstruction. Despite its popularity, very few analytical solutions for ML exist, so biases suffered by ML are not well understood. One possible bias is long branch attraction (LBA), a regularly cited term generally used to describe a propensity for long branches to be joined together in estimated trees. Although initially mentioned in connection with inconsistency of parsimony, LBA has been claimed to affect all major phylogenetic reconstruction methods, including ML. Despite the widespread use of this term in the literature, exactly what LBA is and what may be causing it is poorly understood, even for simple evolutionary models and small model trees. Studies looking at LBA have focused on the effect of two long branches on tree reconstruction. However, to understand the effect of two long branches it is also important to understand the effect of just one long branch. If ML struggles to reconstruct one long branch, then this may have an impact on LBA. In this study, we look at the effect of one long branch on three-taxon tree reconstruction. We show that, counterintuitively, long branches are preferentially placed at the tips of the tree. This can be understood through the use of analytical solutions to the ML equation and distance matrix methods. We go on to look at the placement of two long branches on four-taxon trees, showing that there is no attraction between long branches, but that for extreme branch lengths long branches are joined together disproportionally often. These results illustrate that even small model trees are still interesting to help understand how ML phylogenetic reconstruction works, and that LBA is a complicated phenomenon that deserves further study. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

  13. Genealogy and gene trees.

    Science.gov (United States)

    Rasmuson, Marianne

    2008-02-01

    Heredity can be followed in persons or in genes. Persons can be identified only a few generations back, but simplified models indicate that universal ancestors to all now living persons have occurred in the past. Genetic variability can be characterized as variants of DNA sequences. Data are available only from living persons, but from the pattern of variation gene trees can be inferred by means of coalescence models. The merging of lines backwards in time leads to a MRCA (most recent common ancestor). The time and place of living for this inferred person can give insights in human evolutionary history. Demographic processes are incorporated in the model, but since culture and customs are known to influence demography the models used ought to be tested against available genealogy. The Icelandic data base offers a possibility to do so and points to some discrepancies. Mitochondrial DNA and Y chromosome patterns give a rather consistent view of human evolutionary history during the latest 100 000 years but the earlier epochs of human evolution demand gene trees with longer branches. The results of such studies reveal as yet unsolved problems about the sources of our genome.

  14. Tree Rings in the Tropics: Insights into the Ecology and Climate Sensitivity of Tropical Trees

    NARCIS (Netherlands)

    Brienen, R.J.W.; Schöngart, J.; Zuidema, P.A.

    2016-01-01

    Tree-ring studies provide important contributions to understanding the climate sensitivity of tropical trees and the effects of global change on tropical forests. This chapter reviews recent advances in tropical tree-ring research. In tropical lowlands, tree ring formation is mainly driven by

  15. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Acrocarpus fraxinifolius Wight & Arn. (PINK CEDAR, AUSTRALIAN ASH) of. Caesalpiniaceae is a lofty unarmed deciduous native tree that attains a height of 30–60m with buttresses. Bark is thin and light grey. Leaves are compound and bright red when young. Flowers in dense, erect, axillary racemes.

  16. Flowering Trees

    Indian Academy of Sciences (India)

    Brachichiton acerifolius F. Muell., commonly called as the Illawara flame tree is a member of Malvaceae family and is native to sub-tropical parts of Australia. Due to its spectacular flowers and tolerance to wide range of climates, it's now cultivated all over the world for its beauty. The tree produces flowers during the.

  17. Flowering Trees

    Indian Academy of Sciences (India)

    Cassia siamia Lamk. (Siamese tree senna) of Caesalpiniaceae is a small or medium size handsome tree. Leaves are alternate, pinnately compound and glandular, upto 18 cm long with 8–12 pairs of leaflets. Inflorescence is axillary or terminal and branched. Flowering lasts for a long period from March to February.

  18. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    Grevillea robusta A. Cunn. ex R. Br. (Sil- ver Oak) of Proteaceae is a daintily lacy ornamental tree while young and growing into a mighty tree (45 m). Young shoots are silvery grey and the leaves are fern- like. Flowers are golden-yellow in one- sided racemes (10 cm). Fruit is a boat- shaped, woody follicle.

  19. Flowering Trees

    Indian Academy of Sciences (India)

    Baccaurea courtallensis Muell.-Arg. of Euphorbiaceae is an evergreen tree that is very attractive when in flower. Leaves are alternate. Male and female flowers are borne on separate trees. Inflorescences bearing several flowers arise in tufts on tubercles on the stem. Fruits are crimson red in colour. Seeds are covered.

  20. Improvement of isotope-based climate reconstructions in Patagonia through a better understanding of climate influences on isotopic fractionation in tree rings

    Science.gov (United States)

    Lavergne, Aliénor; Daux, Valérie; Villalba, Ricardo; Pierre, Monique; Stievenard, Michel; Srur, Ana Marina

    2017-02-01

    Very few studies of stable isotopes exist across the Andes in South America. This study is the first presenting annually resolved chronologies of both δ18 O and δ13 C in Nothofagus pumilio and Fitzroya cupressoides trees from Northern Patagonia. Interannual variability in δ18 O and δ13 C was assessed over the period 1952-2011. Based on these chronologies, we determined the primary climatic controls on stable isotopes and tree physiological responses to changes in atmospheric CO2 concentrations (ca), temperature and humidity. Changes in specific intrinsic water use efficiency (iWUE) were inferred from variations in δ13 C whereas the effects of CO2 increase on stomatal conductance were explored using δ18 O. Over the 60-year period, iWUE increased significantly (by ca. 25%) in coincidence with the rise of ca. The two species appear to have different strategies of gas-exchange. Whereas iWUE variations were likely driven by both stomatal conductance and photosynthetic assimilation rates in F. cupressoides, they were largely related to stomatal conductance in N. pumilio. After removing the low-frequency trends related to increasing ca, significant relationships between δ13 C and summer temperatures were recorded for both species. However, δ13 C variations in F. cupressoides were more strongly influenced by summer temperatures than in N. pumilio. Our results advocate for an indirect effect of summer temperatures on stable isotope ratios, which is mostly influenced by sunlight radiation in F. cupressoides and relative humidity/soil moisture in N. pumilio. δ13 C variations in F. cupressoides were spatially correlated to a large area south of 35°S in southern South America. These promising results encourage the use of δ13 C variations in F. cupressoides for reconstructing past variations in temperature and large-scale circulation indexes such as the Southern Annular Mode (SAM) in the Southern Hemisphere.

  1. Evolutionary origin of the Asteraceae capitulum: Insights from Calyceraceae.

    Science.gov (United States)

    Pozner, Raúl; Zanotti, Christian; Johnson, Leigh A

    2012-01-01

    Phylogenies based on molecular data are revealing that generalizations about complex morphological structures often obscure variation and developmental patterns important for understanding the evolution of forms, as is the case for inflorescence morphology within the well-supported MGCA clade (Menyanthaceae + Goodeniaceae + Calyceraceae + Asteraceae). While the basal families share a basic thyrsic/thyrsoid structure of their inflorescences, Asteraceae possesses a capitulum that is widely interpreted as a racemose, condensed inflorescence. Elucidating the poorly known inflorescence structure of Calyceraceae, sister to Asteraceae, should help clarify how the Asteraceae capitulum evolved from thyrsic/thyrsoid inflorescences. The early development and structure of the inflorescence of eight species (five genera) of Calyceraceae were studied by SEM, and patterns of evolutionary change were interpreted via phylogenetic character mapping. The basic inflorescence structure of Calyceraceae is a cephalioid (a very condensed botryoid/thyrsoid). Optimization of inflorescence characters on a DNA sequence-derived tree suggests that the Asteraceae capitulum derives from a simple cephalioid through two morphological changes: loss of the terminal flower and suppression of the cymose branching pattern in the peripheral branches. Widely understood as a condensed raceme, the Asteraceae capitulum is the evolutionary result of a very reduced, condensed thyrsoid. Starting from that point, evolution worked separately only on the racemose developmental control/pattern within Asteraceae and mainly on the cymose developmental control/pattern within Calyceraceae, producing head-like inflorescences in both groups but with very different diversification potential. We also discuss possible remnants of the ancestral cephalioid structure in some Asteraceae.

  2. VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

    Directory of Open Access Journals (Sweden)

    Andrew E. Webb

    2017-06-01

    Full Text Available Background Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each phase of these analyses can represent significant challenges, particularly when working with entire proteomes (all protein coding sequences in a genome from a large number of species. Methods We present VESPA, software capable of automating a selective pressure analysis using codeML in addition to the preparatory analyses and summary statistics. VESPA is written in python and Perl and is designed to run within a UNIX environment. Results We have benchmarked VESPA and our results show that the method is consistent, performs well on both large scale and smaller scale datasets, and produces results in line with previously published datasets. Discussion Large-scale gene family identification, sequence alignment, and phylogeny reconstruction are all important aspects of large-scale molecular evolutionary analyses. VESPA provides flexible software for simplifying these processes along with downstream selective pressure variation analyses. The software automatically interprets results from codeML and produces simplified summary files to assist the user in better understanding the results. VESPA may be found at the following website: http://www.mol-evol.org/VESPA.

  3. What genomic data can reveal about eco-evolutionary dynamics.

    Science.gov (United States)

    Rudman, Seth M; Barbour, Matthew A; Csilléry, Katalin; Gienapp, Phillip; Guillaume, Frederic; Hairston, Nelson G; Hendry, Andrew P; Lasky, Jesse R; Rafajlović, Marina; Räsänen, Katja; Schmidt, Paul S; Seehausen, Ole; Therkildsen, Nina O; Turcotte, Martin M; Levine, Jonathan M

    2018-01-01

    Recognition that evolution operates on the same timescale as ecological processes has motivated growing interest in eco-evolutionary dynamics. Nonetheless, generating sufficient data to test predictions about eco-evolutionary dynamics has proved challenging, particularly in natural contexts. Here we argue that genomic data can be integrated into the study of eco-evolutionary dynamics in ways that deepen our understanding of the interplay between ecology and evolution. Specifically, we outline five major questions in the study of eco-evolutionary dynamics for which genomic data may provide answers. Although genomic data alone will not be sufficient to resolve these challenges, integrating genomic data can provide a more mechanistic understanding of the causes of phenotypic change, help elucidate the mechanisms driving eco-evolutionary dynamics, and lead to more accurate evolutionary predictions of eco-evolutionary dynamics in nature.

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

    Science.gov (United States)

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

    2013-01-01

    Phylogenetic trees provide visual representations of ancestor-descendant relationships, a core concept of evolutionary theory. We introduced "tree thinking" into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted…

  5. Remembering the evolutionary Freud.

    Science.gov (United States)

    Young, Allan

    2006-03-01

    Throughout his career as a writer, Sigmund Freud maintained an interest in the evolutionary origins of the human mind and its neurotic and psychotic disorders. In common with many writers then and now, he believed that the evolutionary past is conserved in the mind and the brain. Today the "evolutionary Freud" is nearly forgotten. Even among Freudians, he is regarded to be a red herring, relevant only to the extent that he diverts attention from the enduring achievements of the authentic Freud. There are three ways to explain these attitudes. First, the evolutionary Freud's key work is the "Overview of the Transference Neurosis" (1915). But it was published at an inopportune moment, forty years after the author's death, during the so-called "Freud wars." Second, Freud eventually lost interest in the "Overview" and the prospect of a comprehensive evolutionary theory of psychopathology. The publication of The Ego and the Id (1923), introducing Freud's structural theory of the psyche, marked the point of no return. Finally, Freud's evolutionary theory is simply not credible. It is based on just-so stories and a thoroughly discredited evolutionary mechanism, Lamarckian use-inheritance. Explanations one and two are probably correct but also uninteresting. Explanation number three assumes that there is a fundamental difference between Freud's evolutionary narratives (not credible) and the evolutionary accounts of psychopathology that currently circulate in psychiatry and mainstream journals (credible). The assumption is mistaken but worth investigating.

  6. How to Prune Trees

    Science.gov (United States)

    Peter Bedker; Joseph O' Brien; Manfred Mielke

    2012-01-01

    The objective of pruning is to produce strong, healthy, attractive plants. By understanding how, when and why to prune, and by following a few simple principles, this objective can be achievedHow to Prune Trees (Revised 2012) Agency Publisher: Agriculture Dept., Forest Service, Northeastern Area State and Price forestry USA List Price:$4.00 Sale...

  7. Understanding Seasonal Dynamics of the Photo-Protective Xanthophyll Cycle Improves Remote Detection of Photosynthetic Phenology in Deciduous Trees and Evergreen Conifers

    Science.gov (United States)

    Ensminger, I.; Wong, C. Y.; Junker, L. V.; Bathena, Y.; Arain, M. A.; D'Odorico, P.

    2017-12-01

    The ability of plants to sequester carbon is highly variable over the course of the year and reflects seasonal variation in photosynthetic efficiency. This seasonal variation is most prominent during autumn, when leaves of deciduous tree species undergo senescence, which is associated with the downregulation of photosynthesis and a change of leaf color and leaf optical properties. Vegetation indices derived from remote sensing of leaf optical properties using e.g. spectral reflectance measurements are increasingly used to monitor and predict growing season length and seasonal variation in carbon sequestration. Here we compare leaf-level, canopy-level and drone based observations of leaf spectral reflectance measurements. We demonstrate that some of the widely used vegetation indices such as the normalized difference vegetation index (NDVI) and photochemical reflectance index (PRI) vary in their ability to adequately track the seasonal variation in photosynthetic efficiency and chlorophyll content. We further show that monitoring seasonal variation of photosynthesis using NDVI or PRI is particularly challenging in evergreen conifers, due to little seasonal variation in foliage. However, there is remarkable seasonal variation in leaf optical properties associated with changes in pools of xanthophyll cycle pigments and carotenoids that provide a promising way of monitoring photosynthetic phenology in evergreen conifers via leaf reflectance measurements.

  8. Evolutionary ecology of virus emergence.

    Science.gov (United States)

    Dennehy, John J

    2017-02-01

    The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment. © 2016 New York Academy of Sciences.

  9. Cancer research meets evolutionary biology.

    Science.gov (United States)

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

    2009-02-01

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

  10. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    shaped corolla. Fruit is large, ellipsoidal, green with a hard and smooth shell containing numerous flattened seeds, which are embedded in fleshy pulp. Calabash tree is commonly grown in the tropical gardens of the world as a botanical oddity.

  11. Electron Tree

    DEFF Research Database (Denmark)

    Appelt, Ane L; Rønde, Heidi S

    2013-01-01

    The photo shows a close-up of a Lichtenberg figure – popularly called an “electron tree” – produced in a cylinder of polymethyl methacrylate (PMMA). Electron trees are created by irradiating a suitable insulating material, in this case PMMA, with an intense high energy electron beam. Upon discharge......, during dielectric breakdown in the material, the electrons generate branching chains of fractures on leaving the PMMA, producing the tree pattern seen. To be able to create electron trees with a clinical linear accelerator, one needs to access the primary electron beam used for photon treatments. We...... appropriated a linac that was being decommissioned in our department and dismantled the head to circumvent the target and ion chambers. This is one of 24 electron trees produced before we had to stop the fun and allow the rest of the accelerator to be disassembled....

  12. The fault-tree compiler

    Science.gov (United States)

    Martensen, Anna L.; Butler, Ricky W.

    1987-01-01

    The Fault Tree Compiler Program is a new reliability tool used to predict the top event probability for a fault tree. Five different gate types are allowed in the fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N gates. The high level input language is easy to understand and use when describing the system tree. In addition, the use of the hierarchical fault tree capability can simplify the tree description and decrease program execution time. The current solution technique provides an answer precise (within the limits of double precision floating point arithmetic) to the five digits in the answer. The user may vary one failure rate or failure probability over a range of values and plot the results for sensitivity analyses. The solution technique is implemented in FORTRAN; the remaining program code is implemented in Pascal. The program is written to run on a Digital Corporation VAX with the VMS operation system.

  13. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 8; Issue 2. Evolutionary Biology Today - What do Evolutionary Biologists do? Amitabh Joshi. Series Article Volume 8 Issue 2 February 2003 pp 6-18. Fulltext. Click here to view fulltext PDF. Permanent link:

  14. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Amitabh Joshi studies and teaches evolutionary genetics and population ecology at the Jawaharlal. Nehru Centre for Advanced. Scientific Research,. Bangalore. His current research interests are in life- history evolution, the evolutionary genetics of biological clocks, and small population and meta population dynamics.

  15. Methodological problems in evolutionary biology. XII. Against evolutionary ethics.

    NARCIS (Netherlands)

    vd Steen, W.J.

    1999-01-01

    Evolutionary ethics has recently become popular again. Some of its representatives elaborate new attempts to derive ethics from evolutionary biology. The attempts, like previous ones, fail because they commit the naturalistic fallacy. Premises from evolutionary biology together with normative

  16. Core principles of evolutionary medicine: A Delphi study.

    Science.gov (United States)

    Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

    2018-01-01

    Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further.

  17. Mapping tree density at a global scale

    NARCIS (Netherlands)

    Crowther, T.W.; Glick, H.B.; Covey, K.R.; Bettigole, C.; Maynard, D.S.; Thomas, S.M.; Smith, J.R.; Hintler, G.; Duguid, M.C.; Amatulli, G.; Hengeveld, G.M.; Nabuurs, G.J.

    2015-01-01

    The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of

  18. Student Interpretations of Phylogenetic Trees in an Introductory Biology Course

    Science.gov (United States)

    Dees, Jonathan; Momsen, Jennifer L.; Niemi, Jarad; Montplaisir, Lisa

    2014-01-01

    Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa…

  19. Physiology and Genetics of Tree-Phytophage Interactions

    Science.gov (United States)

    Frances Lieutier; William J. Mattson; Michael R. Wagner

    1999-01-01

    Interactions between trees and phytophagous organisms represent an important fundamental process in the evolution of forest ecosystems. Through evolutionary time, the special traits of trees have lead the herbivore populations to differentiate and evolve in order to cope with the variability in natural resistance mechanisms of their hosts. Conversely, damage by...

  20. Evolutionary accounts of human behavioural diversity

    Science.gov (United States)

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

    2011-01-01

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

  1. Evolutionary and mechanistic theories of aging.

    Science.gov (United States)

    Hughes, Kimberly A; Reynolds, Rose M

    2005-01-01

    Senescence (aging) is defined as a decline in performance and fitness with advancing age. Senescence is a nearly universal feature of multicellular organisms, and understanding why it occurs is a long-standing problem in biology. Here we present a concise review of both evolutionary and mechanistic theories of aging. We describe the development of the general evolutionary theory, along with the mutation accumulation, antagonistic pleiotropy, and disposable soma versions of the evolutionary model. The review of the mechanistic theories focuses on the oxidative stress resistance, cellular signaling, and dietary control mechanisms of life span extension. We close with a discussion of how an approach that makes use of both evolutionary and molecular analyses can address a critical question: Which of the mechanisms that can cause variation in aging actually do cause variation in natural populations?

  2. Toward an integration of evolutionary biology and ecosystem science.

    Science.gov (United States)

    Matthews, Blake; Narwani, Anita; Hausch, Stephen; Nonaka, Etsuko; Peter, Hannes; Yamamichi, Masato; Sullam, Karen E; Bird, Kali C; Thomas, Mridul K; Hanley, Torrance C; Turner, Caroline B

    2011-07-01

    At present, the disciplines of evolutionary biology and ecosystem science are weakly integrated. As a result, we have a poor understanding of how the ecological and evolutionary processes that create, maintain, and change biological diversity affect the flux of energy and materials in global biogeochemical cycles. The goal of this article was to review several research fields at the interfaces between ecosystem science, community ecology and evolutionary biology, and suggest new ways to integrate evolutionary biology and ecosystem science. In particular, we focus on how phenotypic evolution by natural selection can influence ecosystem functions by affecting processes at the environmental, population and community scale of ecosystem organization. We develop an eco-evolutionary model to illustrate linkages between evolutionary change (e.g. phenotypic evolution of producer), ecological interactions (e.g. consumer grazing) and ecosystem processes (e.g. nutrient cycling). We conclude by proposing experiments to test the ecosystem consequences of evolutionary changes. © 2011 Blackwell Publishing Ltd/CNRS.

  3. Incorporating evolutionary principles into environmental management and policy

    DEFF Research Database (Denmark)

    Lankau, Richard; Jørgensen, Peter Søgaard; Harris, David J.

    2011-01-01

    As policymakers and managers work to mitigate the effects of rapid anthropogenic environmental changes, they need to consider organisms’ responses. In light of recent evidence that evolution can be quite rapid, this now includes evolutionary responses. Evolutionary principles have a long history...... in conservation biology, and the necessary next step for the field is to consider ways in which conservation policy makers and managers can proactively manipulate evolutionary processes to achieve their goals. In this review, we aim to illustrate the potential conservation benefits of an increased understanding...... of evolutionary history and prescriptive manipulation of three basic evolutionary factors: selection, variation, and gene flow. For each, we review and propose ways that policy makers and managers can use evolutionary thinking to preserve threatened species, combat pest species, or reduce undesirable evolutionary...

  4. Mapping tree density at a global scale.

    Science.gov (United States)

    Crowther, T W; Glick, H B; Covey, K R; Bettigole, C; Maynard, D S; Thomas, S M; Smith, J R; Hintler, G; Duguid, M C; Amatulli, G; Tuanmu, M-N; Jetz, W; Salas, C; Stam, C; Piotto, D; Tavani, R; Green, S; Bruce, G; Williams, S J; Wiser, S K; Huber, M O; Hengeveld, G M; Nabuurs, G-J; Tikhonova, E; Borchardt, P; Li, C-F; Powrie, L W; Fischer, M; Hemp, A; Homeier, J; Cho, P; Vibrans, A C; Umunay, P M; Piao, S L; Rowe, C W; Ashton, M S; Crane, P R; Bradford, M A

    2015-09-10

    The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

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

    Science.gov (United States)

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

    2014-03-01

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

  6. Part E: Evolutionary Computation

    DEFF Research Database (Denmark)

    2015-01-01

    of Computational Intelligence. First, comprehensive surveys of genetic algorithms, genetic programming, evolution strategies, parallel evolutionary algorithms are presented, which are readable and constructive so that a large audience might find them useful and – to some extent – ready to use. Some more general...... evolutionary algorithms, such as memetic algorithms, which have emerged as a very promising tool for solving many real-world problems in a multitude of areas of science and technology. Moreover, parallel evolutionary combinatorial optimization has been presented. Search operators, which are crucial in all...

  7. Evolutionary cost management in the nuclear industry

    International Nuclear Information System (INIS)

    Lombardi, C.G.; Mazzini, R.A.

    1986-01-01

    The reader is urged to consider the material in ''The Evolutionary Theory of Cost Management'' carefully before proceeding with the material in this paper. The recommendations in this paper flow from the revised line of thinking generated by the evolutionary approach. The suggestions will be difficult to accept in the absence of an understanding of the underlying theory. Although the authors briefly discuss some of the theory, it is nevertheless recommended that the reader develop a fuller understanding of the concepts by studying the prior paper

  8. Near-Minimal Node Control of Networked Evolutionary Games

    NARCIS (Netherlands)

    Riehl, James Robert; Cao, Ming

    2014-01-01

    We investigate a problem related to the controllability of networked evolutionary games, first presenting an algorithm that computes a near-minimal set of nodes to drive all nodes in a tree network to a desired strategy, and then briefly discussing an algorithm that works for arbitrary networks

  9. Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory

    Science.gov (United States)

    Ferriere, Regis; Legendre, Stéphane

    2013-01-01

    Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps. PMID:23209163

  10. Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory.

    Science.gov (United States)

    Ferriere, Regis; Legendre, Stéphane

    2013-01-19

    Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause 'evolutionary suicide'. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called 'evolutionary trapping'. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps.

  11. The complexity of deriving multi-labeled trees from bipartitions.

    Science.gov (United States)

    Huber, Katharina T; Lott, Martin; Moulton, Vincent; Spillner, Andreas

    2008-01-01

    Recently, multi-labeled trees have been used to help unravel the evolutionary origins of polyploid species. A multi-labeled tree is the same as a phylogenetic tree except that more than one leaf may be labeled by a single species, so that the leaf set of a multi-labeled tree can be regarded as a multiset. In contrast to phylogenetic trees, which can be efficiently encoded in terms of certain bipartitions of their leaf sets, we show that it is NP-hard to decide whether a collection of bipartitions of a multiset can be represented by a multi-labeled tree. Even so, we also show that it is possible to generalize to multi-labeled trees a well-known condition that characterizes when a collection of bipartitions encodes a phylogenetic tree. Using this generalization, we obtain a fixed-parameter algorithm for the above decision problem in terms of a parameter associated to the given multiset.

  12. Expansion of biological pathways based on evolutionary inference.

    Science.gov (United States)

    Li, Yang; Calvo, Sarah E; Gutman, Roee; Liu, Jun S; Mootha, Vamsi K

    2014-07-03

    The availability of diverse genomes makes it possible to predict gene function based on shared evolutionary history. This approach can be challenging, however, for pathways whose components do not exhibit a shared history but rather consist of distinct "evolutionary modules." We introduce a computational algorithm, clustering by inferred models of evolution (CLIME), which inputs a eukaryotic species tree, homology matrix, and pathway (gene set) of interest. CLIME partitions the gene set into disjoint evolutionary modules, simultaneously learning the number of modules and a tree-based evolutionary history that defines each module. CLIME then expands each module by scanning the genome for new components that likely arose under the inferred evolutionary model. Application of CLIME to ∼1,000 annotated human pathways and to the proteomes of yeast, red algae, and malaria reveals unanticipated evolutionary modularity and coevolving components. CLIME is freely available and should become increasingly powerful with the growing wealth of eukaryotic genomes. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Evolution, Science and Society: Evolutionary Biology and the National Research Agenda.

    Science.gov (United States)

    Futuyma, Douglas J.; Meagher, Thomas R.

    2001-01-01

    Discusses ways of advancing understanding of evolutionary biology which seeks to explain all the characteristics of organisms. Describes the goals of evolutionary biology, why it is important, and how it contributes to society and basic science. (ASK)

  14. Phylogenomics of palearctic Formica species suggests a single origin of temporary parasitism and gives insights to the evolutionary pathway toward slave-making behaviour.

    Science.gov (United States)

    Romiguier, Jonathan; Rolland, Jonathan; Morandin, Claire; Keller, Laurent

    2018-03-28

    The ants of the Formica genus are classical model species in evolutionary biology. In particular, Darwin used Formica as model species to better understand the evolution of slave-making, a parasitic behaviour where workers of another species are stolen to exploit their workforce. In his book "On the Origin of Species" (1859), Darwin first hypothesized that slave-making behaviour in Formica evolved in incremental steps from a free-living ancestor. The absence of a well-resolved phylogenetic tree of the genus prevent an assessment of whether relationships among Formica subgenera are compatible with this scenario. In this study, we resolve the relationships among the 4 palearctic Formica subgenera (Formica str. s., Coptoformica, Raptiformica and Serviformica) using a phylogenomic dataset of 945 genes for 16 species. We provide a reference tree resolving the relationships among the main Formica subgenera with high bootstrap supports. The branching order of our tree suggests that the free-living lifestyle is ancestral in the Formica genus and that parasitic colony founding could have evolved a single time, probably acting as a pre-adaptation to slave-making behaviour. This phylogenetic tree provides a solid backbone for future evolutionary studies in the Formica genus and slave-making behaviour.

  15. Flowering Trees

    Indian Academy of Sciences (India)

    branched evergreen shrub or small tree (6–7 m) with soft whitish-yellow wood. Branches are numerous and drooping. The leaves are elliptic-lanceolate and somewhat fleshy. Flowers are in loose axillary and terminal much-branched inflorescence, ...

  16. Flowering Trees

    Indian Academy of Sciences (India)

    narrow towards base. Flowers are large and attrac- tive, but emit unpleasant foetid smell. They appear in small numbers on erect terminal clusters and open at night. Stamens are numerous, pink or white. Style is slender and long, terminating in a small stigma. Fruit is green, ovoid and indistinctly lobed. Flowering Trees.

  17. ~{owering 'Trees

    Indian Academy of Sciences (India)

    Stamens are fused into a purple staminal tube that is toothed. Fruit is about 0.5 in. across, nearly globose, generally 5-seeded, green but yellow when ripe, quite smooth at first but wrinkled in drying, remaining long on the tree ajier ripening. The species is widely natural but occasionally cultivated for firewood as it grows very ...

  18. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    quick-growing deciduous tree with a small crown. Branches are covered with dark conical prickles, which fall off after some time. The leaves are compound with three leaflets. Bright red or scarlet flowers which appear following leaf fall are in clusters at branch ends. Birds and bees visit flowers for nectar. Fruit is a cylindrical ...

  19. Flowering Trees

    Indian Academy of Sciences (India)

    deciduous tree with irregularly-shaped trunk, greyish-white scaly bark and milky latex. Leaves in opposite pairs are simple, oblong and whitish beneath. Flowers that occur in branched inflorescence are white, 2–. 3cm across and fragrant. Calyx is glandular inside. Petals bear numerous linear white scales, the corollary.

  20. Flowering Trees

    Indian Academy of Sciences (India)

    Muntingia calabura L. (Singapore cherry) of. Elaeocarpaceae is a medium size handsome ever- green tree. Leaves are simple and alternate with sticky hairs. Flowers are bisexual, bear numerous stamens, white in colour and arise in the leaf axils. Fruit is a berry, edible with several small seeds embedded in a fleshy pulp ...

  1. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    . (6-10m high) evergreen tree with a straight trunk and broad open crown. Leaves are clustered at the end of twigs. They are dark green, broadest near the rounded apex and tapering towards the base with a short stalk. Flowers are greenish or ...

  2. ~{owering 'Trees

    Indian Academy of Sciences (India)

    size (upto 40 ft. high) deciduous tree with thick trunk, large crown of spreading branches and furrowed greenish-brown bark. (picture shows a young specimen). Leaves are 10-20 in. long, twice compound bearing numerous dark- green ...

  3. Flowering Trees

    Indian Academy of Sciences (India)

    Guaiacum officinale L. (LIGNUM-VITAE) of Zygophyllaceae is a dense-crowned, squat, knobbly, rough and twisted medium-sized ev- ergreen tree with mottled bark. The wood is very hard and resinous. Leaves are compound. The leaflets are smooth, leathery, ovate-ellipti- cal and appear in two pairs. Flowers (about 1.5.

  4. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Caesalpinia coriaria (Jacq.) Willd. (THE AMERICAN SUMACH, DIVI-DIVI) of. Caesalpiniaceae is a small unarmed tree reaching up to 10 m in height with a spreading crown. Leaves are alternate and twice compound. The flowers are small, about 0.6 cm (enlarged 5 times here), greenish-yellow, fragrant and appear in dense ...

  5. Flowering Trees

    Indian Academy of Sciences (India)

    Canthium parviflorum Lam. of Rubiaceae is a large shrub that often grows into a small tree with conspicuous spines. Leaves are simple, in pairs at each node and are shiny. Inflorescence is an axillary few-flowered cymose fascicle. Flowers are small (less than 1 cm across), 4-merous and greenish-white. Fruit is ellipsoid ...

  6. Flowering Trees

    Indian Academy of Sciences (India)

    Diospyros peregrina (Gaertn.) Guercke Syn. Diospyros embryopteris Pers., Diospyros malabarica Desr. (PALE MOON EBONY, RIBER EBONY) of Ebenaceae is a small or mid-sized slow-growing evergreen tree with spreading branches that form a dense crown. The bark is smooth, thick, dark and flakes off in large shreds.

  7. Flowering Trees

    Indian Academy of Sciences (India)

    Andira inermis (wright) DC. , Dog Almond of Fabaceae is a handsome lofty evergreen tree. Leaves are alternate and pinnately compound with 4–7 pairs of leaflets. Flowers are fragrant and are borne on compact branched inflorescences. Fruit is ellipsoidal one-seeded drupe that is peculiar to members of this family.

  8. :Ffowering 'Trees-

    Indian Academy of Sciences (India)

    The tree is a host of lac insects which secrete a resinous substance that yields shellac or lac. A ruby-coloured gum known as Bengal Kino is collected from the incisions made in the bark. The wood, resistant to water, is used in water-well work. The seeds are used as anthelmintic and as an antidote for snake-bite.

  9. Flowering Trees

    Indian Academy of Sciences (India)

    Trincomali Wood of Tiliaceae is a tall evergreen tree with straight trunk, smooth brownish-grey bark and simple broad leaves. Inflorescence is much branched with white flowers. Stamens are many with golden yellow anthers. Fruit is a capsule with six spreading wings. Seeds bear short stiff hairs that cause skin irritation.

  10. Tree Mortality

    Science.gov (United States)

    Mark J. Ambrose

    2012-01-01

    Tree mortality is a natural process in all forest ecosystems. However, extremely high mortality also can be an indicator of forest health issues. On a regional scale, high mortality levels may indicate widespread insect or disease problems. High mortality may also occur if a large proportion of the forest in a particular region is made up of older, senescent stands....

  11. Flowering Trees

    Indian Academy of Sciences (India)

    Sterculia foetida L. (INDIAN ALMOND,. JAVA OLIVE) of Sterculiaceae is a tall deciduous tree reaching a height of 20 m with faintly ridged grey bark. The bole reaches up to 2m in girth. Branches are reddish, usually horizontal. Leaves are large, palmately compound (5–7 leaflets) and clustered at the branch ends. Flowers ...

  12. The cell biology of the endocytic system from an evolutionary perspective.

    Science.gov (United States)

    Wideman, Jeremy G; Leung, Ka Fai; Field, Mark C; Dacks, Joel B

    2014-04-01

    Evolutionary cell biology can afford an interdisciplinary comparative view that gives insights into both the functioning of modern cells and the origins of cellular systems, including the endocytic organelles. Here, we explore several recent evolutionary cell biology studies, highlighting investigations into the origin and diversity of endocytic systems in eukaryotes. Beginning with a brief overview of the eukaryote tree of life, we show how understanding the endocytic machinery in a select, but diverse, array of organisms provides insights into endocytic system origins and predicts the likely configuration in the last eukaryotic common ancestor (LECA). Next, we consider three examples in which a comparative approach yielded insight into the function of modern cellular systems. First, using ESCRT-0 as an example, we show how comparative cell biology can discover both lineage-specific novelties (ESCRT-0) as well as previously ignored ancient proteins (Tom1), likely of both evolutionary and functional importance. Second, we highlight the power of comparative cell biology for discovery of previously ignored but potentially ancient complexes (AP5). Finally, using examples from ciliates and trypanosomes, we show that not all organisms possess canonical endocytic pathways, but instead likely evolved lineage-specific mechanisms. Drawing from these case studies, we conclude that a comparative approach is a powerful strategy for advancing knowledge about the general mechanisms and functions of endocytic systems.

  13. Backbones of evolutionary history test biodiversity theory for microbes.

    Science.gov (United States)

    O'Dwyer, James P; Kembel, Steven W; Sharpton, Thomas J

    2015-07-07

    Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities.

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

    Science.gov (United States)

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

    2014-12-02

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

  15. Why an extended evolutionary synthesis is necessary.

    Science.gov (United States)

    Müller, Gerd B

    2017-10-06

    Since the last major theoretical integration in evolutionary biology-the modern synthesis (MS) of the 1940s-the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance systems, the '-omics' revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge about the factors responsible for evolutionary change. Some of these results are in agreement with the standard theory and others reveal different properties of the evolutionary process. A renewed and extended theoretical synthesis, advocated by several authors in this issue, aims to unite pertinent concepts that emerge from the novel fields with elements of the standard theory. The resulting theoretical framework differs from the latter in its core logic and predictive capacities. Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process. All these features stimulate research into new areas of evolutionary biology.

  16. New perspectives on the ecology of tree structure and tree communities through terrestrial laser scanning.

    Science.gov (United States)

    Malhi, Yadvinder; Jackson, Tobias; Patrick Bentley, Lisa; Lau, Alvaro; Shenkin, Alexander; Herold, Martin; Calders, Kim; Bartholomeus, Harm; Disney, Mathias I

    2018-04-06

    Terrestrial laser scanning (TLS) opens up the possibility of describing the three-dimensional structures of trees in natural environments with unprecedented detail and accuracy. It is already being extensively applied to describe how ecosystem biomass and structure vary between sites, but can also facilitate major advances in developing and testing mechanistic theories of tree form and forest structure, thereby enabling us to understand why trees and forests have the biomass and three-dimensional structure they do. Here we focus on the ecological challenges and benefits of understanding tree form, and highlight some advances related to capturing and describing tree shape that are becoming possible with the advent of TLS. We present examples of ongoing work that applies, or could potentially apply, new TLS measurements to better understand the constraints on optimization of tree form. Theories of resource distribution networks, such as metabolic scaling theory, can be tested and further refined. TLS can also provide new approaches to the scaling of woody surface area and crown area, and thereby better quantify the metabolism of trees. Finally, we demonstrate how we can develop a more mechanistic understanding of the effects of avoidance of wind risk on tree form and maximum size. Over the next few years, TLS promises to deliver both major empirical and conceptual advances in the quantitative understanding of trees and tree-dominated ecosystems, leading to advances in understanding the ecology of why trees and ecosystems look and grow the way they do.

  17. A Modeling Approach to Teaching Evolutionary Biology in High Schools.

    Science.gov (United States)

    Passmore, Cynthia; Stewart, Jim

    2002-01-01

    Describes the commitments and research that went into the design of a 9-week high school course in evolutionary biology designed to bring students to an understanding of the practice of evolutionary biology by engaging them in developing, elaborating, and using one of the discipline's most important explanatory models. (Contains 39 references.)…

  18. Evolutionary Ideas Held by Experienced South African Biology Teachers

    Science.gov (United States)

    Kyriacou, Xenia; de Beer, Josef; Ramnarain, Umesh

    2015-01-01

    With evolutionary biology relatively recently introduced into the South African school curriculum, the need arose to explore practising teachers' knowledge of the subject. A number of anticipated as well as unanticipated cognitive and affective barriers to the understanding of evolutionary biology were identified from a questionnaire with…

  19. Charisma as signal : An evolutionary perspective on charismatic leadership

    NARCIS (Netherlands)

    Grabo, Allen; Spisak, Brian R.; van Vugt, Mark

    2017-01-01

    We present an evolutionary perspective on charismatic leadership, arguing that charisma has evolved as a credible signal of a person's ability to solve a coordination challenge requiring urgent collective action from group members. We suggest that a better understanding of charisma's evolutionary

  20. Evolutionary Medicine: The Ongoing Evolution of Human Physiology and Metabolism.

    Science.gov (United States)

    Rühli, Frank; van Schaik, Katherine; Henneberg, Maciej

    2016-11-01

    The field of evolutionary medicine uses evolutionary principles to understand changes in human anatomy and physiology that have occurred over time in response to environmental changes. Through this evolutionary-based approach, we can understand disease as a consequence of anatomical and physiological "trade-offs" that develop to facilitate survival and reproduction. We demonstrate how diachronic study of human anatomy and physiology is fundamental for an increased understanding of human health and disease. ©2016 Int. Union Physiol. Sci./Am. Physiol. Soc.

  1. Evolutionary Biology Needs Wild Microbiomes.

    Science.gov (United States)

    Hird, Sarah M

    2017-01-01

    The microbiome is a vital component to the evolution of a host and much of what we know about the microbiome derives from studies on humans and captive animals. But captivity alters the microbiome and mammals have unique biological adaptations that affect their microbiomes (e.g., milk). Birds represent over 30% of known tetrapod diversity and possess their own suite of adaptations relevant to the microbiome. In a previous study, we showed that 59 species of birds displayed immense variation in their microbiomes and host (bird) taxonomy and ecology were most correlated with the gut microbiome. In this Frontiers Focused Review, I put those results in a broader context by discussing how collecting and analyzing wild microbiomes contributes to the main goals of evolutionary biology and the specific ways that birds are unique microbial hosts. Finally, I outline some of the methodological considerations for adding microbiome sampling to the research of wild animals and urge researchers to do so. To truly understand the evolution of a host, we need to understand the millions of microorganisms that inhabit it as well: evolutionary biology needs wild microbiomes.

  2. Evolutionary genetics: 150 years of natural selection

    Indian Academy of Sciences (India)

    The study of morphology, along with comparative anatomy, played an important role in the develop- ment of evolutionary thinking in the decades before and ... for our understanding of ageing but also for our attempts at intervention in the process of human ageing. Journal of Genetics, Vol. 87, No. 4, December 2008. 319 ...

  3. Urban Geography Evolving: Toward an Evolutionary Urban Geography

    Directory of Open Access Journals (Sweden)

    Weaver Russell C.

    2014-06-01

    Full Text Available Despite growing interest in the application of evolutionary concepts to research questions in human geography, the literature is largely characterised by metaphors or analogies that are disconnected from a broader evolutionary theoretical framework. This paper takes initial steps toward developing such a framework for the subfield of urban geography by defining critical elements and relationships from Darwinian and multilevel selection theories. It then synthesises those components in an application to the issues of urban blight and disorder, to demonstrate how an evolutionary understanding of urban spatial phenomena - an “evolutionary urban geography” - can produce new insights for managing complex processes.

  4. Paleoanthropology and evolutionary theory.

    Science.gov (United States)

    Tattersall, Ian

    2012-01-01

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

  5. On the use of cartographic projections in visualizing phylo-genetic tree space

    Directory of Open Access Journals (Sweden)

    Clement Mark

    2010-06-01

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

  6. Making evolutionary biology a basic science for medicine

    Science.gov (United States)

    Nesse, Randolph M.; Bergstrom, Carl T.; Ellison, Peter T.; Flier, Jeffrey S.; Gluckman, Peter; Govindaraju, Diddahally R.; Niethammer, Dietrich; Omenn, Gilbert S.; Perlman, Robert L.; Schwartz, Mark D.; Thomas, Mark G.; Stearns, Stephen C.; Valle, David

    2010-01-01

    New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease. PMID:19918069

  7. A framework for evolutionary systems biology.

    Science.gov (United States)

    Loewe, Laurence

    2009-02-24

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

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

    Science.gov (United States)

    Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito

    2014-11-11

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

  9. Molecular phylogeny of Blaberidae (Dictyoptera, Blattodea with implications for taxonomy and evolutionary studies

    Directory of Open Access Journals (Sweden)

    Frédéric Legendre

    2017-03-01

    Full Text Available In the present “tree-thinking” period, relying on accurate phylogenetic hypotheses is of paramount importance for biologists interested in an evolutionary perspective. In the Blaberidae cockroaches, a well-defined monophyletic family comprising several model species, no such phylogenetic tree is available despite several earlier contributions. Here, using six molecular markers (12S, 16S, 18S, 28S, COI and COII, we investigate the relationships of Blaberidae and compare our results with the traditional morphology-based classification. This resulted in a broad spectrum of situations, from congruent and well-supported hypotheses (e.g., the monophyly of Blaberidae, Oxyhaloinae and (Geoscapheiinae + Panesthiinae to incongruent and weakly supported results (e.g., polyphyly of Perisphaerinae. We emphasize that interesting and contrasted situations lie between the two extremities of this spectrum, especially concerning the genera Thanatophyllum Grandcolas, 1991, Phoetalia Stål, 1874, Laxta Walker, 1868 and Pronauphoeta Shelford, 1909. We also discuss the phylogenetic position of two incertae sedis genera (Eustegasta Gerstaecker, 1883 and Gynopeltis Gerstaecker, 1869. We conclude that in-depth signal analyses should be performed to better understand molecular evolution and its consequence on tree reconstruction for this group. As for phylogenetic relationships per se, new markers should be searched for, especially to decipher deeper relationships in Blaberidae.

  10. Evolutionary Statistical Procedures

    CERN Document Server

    Baragona, Roberto; Poli, Irene

    2011-01-01

    This proposed text appears to be a good introduction to evolutionary computation for use in applied statistics research. The authors draw from a vast base of knowledge about the current literature in both the design of evolutionary algorithms and statistical techniques. Modern statistical research is on the threshold of solving increasingly complex problems in high dimensions, and the generalization of its methodology to parameters whose estimators do not follow mathematically simple distributions is underway. Many of these challenges involve optimizing functions for which analytic solutions a

  11. Evolutionary change in continuous reaction norms

    DEFF Research Database (Denmark)

    Murren, Courtney J; Maclean, Heidi J; Diamond, Sarah E

    2014-01-01

    Understanding the evolution of reaction norms remains a major challenge in ecology and evolution. Investigating evolutionary divergence in reaction norm shapes between populations and closely related species is one approach to providing insights. Here we use a meta-analytic approach to compare...... or species. These results show that evolutionary divergence of curvature is common and should be considered an important aspect of plasticity, together with slope. Biological details about traits and environments, including cryptic variation expressed in novel environmental conditions, may be critical...

  12. Surface tree languages and parallel derivation trees

    NARCIS (Netherlands)

    Engelfriet, Joost

    1976-01-01

    The surface tree languages obtained by top-down finite state transformation of monadic trees are exactly the frontier-preserving homomorphic images of sets of derivation trees of ETOL systems. The corresponding class of tree transformation languages is therefore equal to the class of ETOL languages.

  13. Evolutionary Accessibility of Mutational Pathways

    Science.gov (United States)

    Franke, Jasper; Klözer, Alexander; de Visser, J. Arjan G. M.; Krug, Joachim

    2011-01-01

    Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways. For the trait under evolutionary selection (‘fitness’), measured values over all possible combinations of a set of mutations yield a fitness landscape that determines which mutational states can be reached from a given initial genotype. Understanding the accessibility properties of fitness landscapes is conceptually important in answering questions about the predictability and repeatability of evolutionary adaptation. Here we theoretically investigate accessibility of the globally optimal state on a wide variety of model landscapes, including landscapes with tunable ruggedness as well as neutral ‘holey’ landscapes. We define a mutational pathway to be accessible if it contains the minimal number of mutations required to reach the target genotype, and if fitness increases in each mutational step. Under this definition accessibility is high, in the sense that at least one accessible pathway exists with a substantial probability that approaches unity as the dimensionality of the fitness landscape (set by the number of mutational loci) becomes large. At the same time the number of alternative accessible pathways grows without bounds. We test the model predictions against an empirical 8-locus fitness landscape obtained for the filamentous fungus Aspergillus niger. By analyzing subgraphs of the full landscape containing different subsets of mutations, we are able to probe the mutational distance scale in the empirical data. The predicted effect of high accessibility is supported by the empirical data and is very robust, which we argue reflects the generic topology of sequence spaces. Together with the restrictive assumptions that lie in our definition of accessibility, this implies that the globally optimal configuration should be accessible to genome wide evolution, but the repeatability of evolutionary trajectories is limited owing to the presence of a

  14. Understanding search trees via statistical physics

    Indian Academy of Sciences (India)

    Sud,. Bât 100, 91405 Orsay Cedex, France. 2Laboratoire de Physique Theorique (UMR C5152 du CNRS), Université Paul Sabatier,. 31062 Toulouse Cedex, France. 3Center for Polymer Studies and Department of Physics, Boston University, ...

  15. Evolution in Mind: Evolutionary Dynamics, Cognitive Processes, and Bayesian Inference.

    Science.gov (United States)

    Suchow, Jordan W; Bourgin, David D; Griffiths, Thomas L

    2017-07-01

    Evolutionary theory describes the dynamics of population change in settings affected by reproduction, selection, mutation, and drift. In the context of human cognition, evolutionary theory is most often invoked to explain the origins of capacities such as language, metacognition, and spatial reasoning, framing them as functional adaptations to an ancestral environment. However, evolutionary theory is useful for understanding the mind in a second way: as a mathematical framework for describing evolving populations of thoughts, ideas, and memories within a single mind. In fact, deep correspondences exist between the mathematics of evolution and of learning, with perhaps the deepest being an equivalence between certain evolutionary dynamics and Bayesian inference. This equivalence permits reinterpretation of evolutionary processes as algorithms for Bayesian inference and has relevance for understanding diverse cognitive capacities, including memory and creativity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Transmissible cancers in an evolutionary context.

    Science.gov (United States)

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

    2016-07-01

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

  17. Democratizing evolutionary biology, lessons from insects.

    Science.gov (United States)

    Dunn, Robert R; Beasley, DeAnna E

    2016-12-01

    The engagement of the public in the scientific process is an old practice. Yet with recent advances in technology, the role of the citizen scientist in studying evolutionary processes has increased. Insects provide ideal models for understanding these evolutionary processes at large scales. This review highlights how insect-based citizen science has led to the expansion of specimen collections and reframed research questions in light of new observations and unexpected discoveries. Given the rapid expansion of human-modified (and inhabited) environments, the degree to which the public can participate in insect-based citizen science will allow us to track and monitor evolutionary trends at a global scale. Copyright © 2016. Published by Elsevier Inc.

  18. Molluscan Evolutionary Development

    DEFF Research Database (Denmark)

    Wanninger, Andreas Wilhelm Georg; Koop, Damien; Moshel-Lynch, Sharon

    2008-01-01

    Brought together by Winston F. Ponder and David R. Lindberg, thirty-six experts on the evolution of the Mollusca provide an up-to-date review of its evolutionary history. The Mollusca are the second largest animal phylum and boast a fossil record of over 540 million years. They exhibit remarkable...

  19. Origins of evolutionary transitions

    Indian Academy of Sciences (India)

    2014-03-15

    Mar 15, 2014 ... collectivist life forms have spread through the population, the situation – the terms of the evolutionary game – have changed. Where initially there ...... Kerr B and Godfrey-Smith P 2002 Individualist and multi-level perspectives on selection in structured populations. Biol. Philos. 17 477–517. Kirk DL 1998 ...

  20. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    IAS Admin

    After Maynard-Smith and Price [1] mathematically derived why a given behaviour or strategy was adopted by a certain proportion of the population at a given time, it was shown that a strategy which is currently stable in a population need not be stable in evolutionary time (across generations). Additionally it was sug-.

  1. Editorial overview: Evolutionary psychology

    NARCIS (Netherlands)

    Gangestad, S.W.; Tybur, J.M.

    2016-01-01

    Functional approaches in psychology - which ask what behavior is good for - are almost as old as scientific psychology itself. Yet sophisticated, generative functional theories were not possible until developments in evolutionary biology in the mid-20th century. Arising in the last three decades,

  2. Evolutionary trends in Heteroptera

    NARCIS (Netherlands)

    Cobben, R.H.

    1968-01-01

    1. This work, the first volume of a series dealing with evolutionary trends in Heteroptera, is concerned with the egg system of about 400 species. The data are presented systematically in chapters 1 and 2 with a critical review of the literature after each family.

    2. Chapter 3 evaluates facts

  3. Interfaces in evolutionary games

    Science.gov (United States)

    Kolotev, Sergei; Malyutin, Aleksandr; Burovski, Evgeni; Shchur, Lev

    2018-01-01

    We investigate geometrical aspects of a spatial evolutionary game. The game is based on the Prisoner’s dilemma. We analyze the geometrical structure of the space distribution of cooperators and defectors in the steady-state regime of evolution. We develop algorithm for the identification of the interfaces between clusters of cooperators and defectors, and measure fractal properties of the interfaces.

  4. Origins of evolutionary transitions

    Indian Academy of Sciences (India)

    2014-03-15

    Mar 15, 2014 ... was to define a major transition by identifying a pattern that is common across an otherwise diverse set of ... been many major evolutionary events that this definition of a transition excludes. The evolution of ...... fragmentation periodic, or brings it under endogenous con- trol. So the mechanisms are far from ...

  5. Evolutionary Developmental Psychology.

    Science.gov (United States)

    Geary, David C.; Bjorklund, David F.

    2000-01-01

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

  6. Applications of Evolutionary Computation

    NARCIS (Netherlands)

    Mora, Antonio M.; Squillero, Giovanni; Di Chio, C; Agapitos, Alexandros; Cagnoni, Stefano; Cotta, Carlos; Fernández De Vega, F; Di Caro, G A; Drechsler, R.; Ekárt, A; Esparcia-Alcázar, Anna I.; Farooq, M; Langdon, W B; Merelo-Guervós, J.J.; Preuss, M; Richter, O.-M.H.; Silva, Sara; Sim$\\$~oes, A; Squillero, Giovanni; Tarantino, Ernesto; Tettamanzi, Andrea G B; Togelius, J; Urquhart, Neil; Uyar, A S; Yannakakis, G N; Smith, Stephen L; Caserta, Marco; Ramirez, Adriana; Voß, Stefan; Squillero, Giovanni; Burelli, Paolo; Mora, Antonio M.; Squillero, Giovanni; Jan, Mathieu; Matthias, M; Di Chio, C; Agapitos, Alexandros; Cagnoni, Stefano; Cotta, Carlos; Fernández De Vega, F; Di Caro, G A; Drechsler, R.; Ekárt, A; Esparcia-Alcázar, Anna I.; Farooq, M; Langdon, W B; Merelo-Guervós, J.J.; Preuss, M; Richter, O.-M.H.; Silva, Sara; Sim$\\$~oes, A; Squillero, Giovanni; Tarantino, Ernesto; Tettamanzi, Andrea G B; Togelius, J; Urquhart, Neil; Uyar, A S; Yannakakis, G N; Caserta, Marco; Ramirez, Adriana; Voß, Stefan; Squillero, Giovanni; Burelli, Paolo; Esparcia-Alcazar, Anna I; Silva, Sara; Agapitos, Alexandros; Cotta, Carlos; De Falco, Ivanoe; Cioppa, Antonio Della; Diwold, Konrad; Ekart, Aniko; Tarantino, Ernesto; Vega, Francisco Fernandez De; Burelli, Paolo; Sim, Kevin; Cagnoni, Stefano; Simoes, Anabela; Merelo, J.J.; Urquhart, Neil; Haasdijk, Evert; Zhang, Mengjie; Squillero, Giovanni; Eiben, A E; Tettamanzi, Andrea G B; Glette, Kyrre; Rohlfshagen, Philipp; Schaefer, Robert; Caserta, Marco; Ramirez, Adriana; Voß, Stefan

    2015-01-01

    The application of genetic and evolutionary computation to problems in medicine has increased rapidly over the past five years, but there are specific issues and challenges that distinguish it from other real-world applications. Obtaining reliable and coherent patient data, establishing the clinical

  7. Street tree structural differences and associated stormwater ...

    Science.gov (United States)

    Green infrastructure approaches leverage vegetation and soil to improve environmental quality. Municipal street trees are crucial components of urban green infrastructure because they provide stormwater interception benefits and other ecosystem services. Thus, it is important to understand the patterns and drivers of structural heterogeneity in urban street tree assemblages. In this study, we compared the forest structure of street trees across nine communities along both geographic and demographic gradients in metropolitan Cincinnati, Ohio, USA. Specifically, we used a two-part statistical model to compare both the proportion of sampled street segments containing zero trees, and basal area magnitude for street segments with trees. We made community-scale comparisons based on street tree management, socioeconomics, and geographic setting. Then, using modeled stormwater interception estimates from i-Tree Streets, we investigated the implications of heterogeneity in street tree assemblages for stormwater interception benefits. The forest structure of street trees varied across communities in relation to management practices, namely participation in the Tree City USA program. As a consequence of this structural difference, we observed a stark discrepancy in estimated stormwater interception between Tree City USA participants (128.7 m3/km street length) and non-participants (59.2 m3/km street length). While street tree assemblages did not vary by community poverty s

  8. Is evolutionary history repeatedly rewritten in light of new fossil discoveries?

    Science.gov (United States)

    Tarver, J E; Donoghue, P C J; Benton, M J

    2011-02-22

    Mass media and popular science journals commonly report that new fossil discoveries have 'rewritten evolutionary history'. Is this merely journalistic hyperbole or is our sampling of systematic diversity so limited that attempts to derive evolutionary history from these datasets are premature? We use two exemplars-catarrhine primates (Old World monkeys and apes) and non-avian dinosaurs-to investigate how the maturity of datasets can be assessed. Both groups have been intensively studied over the past 200 years and so should represent pinnacles in our knowledge of vertebrate systematic diversity. We test the maturity of these datasets by assessing the completeness of their fossil records, their susceptibility to changes in macroevolutionary hypotheses and the balance of their phylogenies through study time. Catarrhines have shown prolonged stability, with discoveries of new species being evenly distributed across the phylogeny, and thus have had little impact on our understanding of their fossil record, diversification and evolution. The reverse is true for dinosaurs, where the addition of new species has been non-random and, consequentially, their fossil record, tree shape and our understanding of their diversification is rapidly changing. The conclusions derived from these analyses are relevant more generally: the maturity of systematic datasets can and should be assessed before they are exploited to derive grand macroevolutionary hypotheses.

  9. The Evolutionary Basis of Risky Adolescent Behavior: Implications for Science, Policy, and Practice

    Science.gov (United States)

    Ellis, Bruce J.; Del Giudice, Marco; Dishion, Thomas J.; Figueredo, Aurelio Jose; Gray, Peter; Griskevicius, Vladas; Hawley, Patricia H.; Jacobs, W. Jake; James, Jenee; Volk, Anthony A.; Wilson, David Sloan

    2012-01-01

    This article proposes an evolutionary model of risky behavior in adolescence and contrasts it with the prevailing developmental psychopathology model. The evolutionary model contends that understanding the evolutionary functions of adolescence is critical to explaining why adolescents engage in risky behavior and that successful intervention…

  10. Never ending analysis of a century old evolutionary debate: unringing the urmetazoon bell

    Directory of Open Access Journals (Sweden)

    Bernd eSchierwater

    2016-02-01

    Full Text Available Our understanding of the early evolution of animals will be greatly improved if a final solution can be found to the evolutionary relationships between Porifera, Placozoa, Ctenophora, Cnidaria and Bilateria. There have been many recent attempts to solve this key issue at the base of the metazoan tree of life, and these have sparked heated discussions and highlighted fundamental analytical problems. We argue that solving this problem will necessitate analysis of disparate data types, including phylogenomic data, larger scale genomic characters, developmental data and morphological characters. At the least, morphological and developmental data must be used to cross-validate phylogenomic conclusions, but ideally solutions should be sought to the problems of combining disparate data sources with appropriate character weighting and algorithm choice.

  11. The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

    Science.gov (United States)

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between

  12. Evolutionary genetics: the Drosophila model

    Indian Academy of Sciences (India)

    Unknown

    In Evolutionary genetics: from molecules to morphology (ed. R. S. Singh and C. B. Krimbas), pp. 609–627. Cambridge Uni- versity Press, Cambridge. Houle D. 2001 Characters as the units of evolutionary change. In The character concept in evolutionary biology. (ed. G. P. Wagner), pp. 109–140. Academic Press, San Diego.

  13. Simple street tree sampling

    Science.gov (United States)

    David J. Nowak; Jeffrey T. Walton; James Baldwin; Jerry. Bond

    2015-01-01

    Information on street trees is critical for management of this important resource. Sampling of street tree populations provides an efficient means to obtain street tree population information. Long-term repeat measures of street tree samples supply additional information on street tree changes and can be used to report damages from catastrophic events. Analyses of...

  14. Programming macro tree transducers

    DEFF Research Database (Denmark)

    Bahr, Patrick; Day, Laurence E.

    2013-01-01

    A tree transducer is a set of mutually recursive functions transforming an input tree into an output tree. Macro tree transducers extend this recursion scheme by allowing each function to be defined in terms of an arbitrary number of accumulation parameters. In this paper, we show how macro tree ...

  15. Modular tree automata

    DEFF Research Database (Denmark)

    Bahr, Patrick

    2012-01-01

    Tree automata are traditionally used to study properties of tree languages and tree transformations. In this paper, we consider tree automata as the basis for modular and extensible recursion schemes. We show, using well-known techniques, how to derive from standard tree automata highly modular r...

  16. Quantum Mechanics predicts evolutionary biology.

    Science.gov (United States)

    Torday, J S

    2018-01-11

    Nowhere are the shortcomings of conventional descriptive biology more evident than in the literature on Quantum Biology. In the on-going effort to apply Quantum Mechanics to evolutionary biology, merging Quantum Mechanics with the fundamentals of evolution as the First Principles of Physiology-namely negentropy, chemiosmosis and homeostasis-offers an authentic opportunity to understand how and why physics constitutes the basic principles of biology. Negentropy and chemiosmosis confer determinism on the unicell, whereas homeostasis constitutes Free Will because it offers a probabilistic range of physiologic set points. Similarly, on this basis several principles of Quantum Mechanics also apply directly to biology. The Pauli Exclusion Principle is both deterministic and probabilistic, whereas non-localization and the Heisenberg Uncertainty Principle are both probabilistic, providing the long-sought after ontologic and causal continuum from physics to biology and evolution as the holistic integration recognized as consciousness for the first time. Copyright © 2018. Published by Elsevier Ltd.

  17. Simulating local adaptation to climate of forest trees with a Physio-Demo-Genetics model.

    Science.gov (United States)

    Oddou-Muratorio, Sylvie; Davi, Hendrik

    2014-04-01

    One challenge of evolutionary ecology is to predict the rate and mechanisms of population adaptation to environmental variations. The variations in most life history traits are shaped both by individual genotypic and by environmental variation. Forest trees exhibit high levels of genetic diversity, large population sizes, and gene flow, and they also show a high level of plasticity for life history traits. We developed a new Physio-Demo-Genetics model (denoted PDG) coupling (i) a physiological module simulating individual tree responses to the environment; (ii) a demographic module simulating tree survival, reproduction, and pollen and seed dispersal; and (iii) a quantitative genetics module controlling the heritability of key life history traits. We used this model to investigate the plastic and genetic components of the variations in the timing of budburst (TBB) along an elevational gradient of Fagus sylvatica (the European beech). We used a repeated 5 years climatic sequence to show that five generations of natural selection were sufficient to develop nonmonotonic genetic differentiation in the TBB along the local climatic gradient but also that plastic variation among different elevations and years was higher than genetic variation. PDG complements theoretical models and provides testable predictions to understand the adaptive potential of tree populations.

  18. Evolutionary constrained optimization

    CERN Document Server

    Deb, Kalyanmoy

    2015-01-01

    This book makes available a self-contained collection of modern research addressing the general constrained optimization problems using evolutionary algorithms. Broadly the topics covered include constraint handling for single and multi-objective optimizations; penalty function based methodology; multi-objective based methodology; new constraint handling mechanism; hybrid methodology; scaling issues in constrained optimization; design of scalable test problems; parameter adaptation in constrained optimization; handling of integer, discrete and mix variables in addition to continuous variables; application of constraint handling techniques to real-world problems; and constrained optimization in dynamic environment. There is also a separate chapter on hybrid optimization, which is gaining lots of popularity nowadays due to its capability of bridging the gap between evolutionary and classical optimization. The material in the book is useful to researchers, novice, and experts alike. The book will also be useful...

  19. Evolutionary patterns in coiled-coils.

    Science.gov (United States)

    Surkont, Jaroslaw; Pereira-Leal, Jose B

    2015-01-10

    Models of protein evolution are used to describe evolutionary processes, for phylogenetic analyses and homology detection. Widely used general models of protein evolution are biased toward globular domains and lack resolution to describe evolutionary processes for other protein types. As three-dimensional structure is a major constraint to protein evolution, specific models have been proposed for other types of proteins. Here, we consider evolutionary patterns in coiled-coil forming proteins. Coiled-coils are widespread structural domains, formed by a repeated motif of seven amino acids (heptad repeat). Coiled-coil forming proteins are frequently rods and spacers, structuring both the intracellular and the extracellular spaces that often form protein interaction interfaces. We tested the hypothesis that due to their specific structure the associated evolutionary constraints differ from those of globular proteins. We showed that substitution patterns in coiled-coil regions are different than those observed in globular regions, beyond the simple heptad repeat. Based on these substitution patterns we developed a coiled-coil specific (CC) model that in the context of phylogenetic reconstruction outperforms general models in tree likelihood, often leading to different topologies. For multidomain proteins containing both a coiled-coil region and a globular domain, we showed that a combination of the CC model and a general one gives higher likelihoods than a single model. Finally, we showed that the model can be used for homology detection to increase search sensitivity for coiled-coil proteins. The CC model, software, and other supplementary materials are available at http://www.evocell.org/cgl/resources (last accessed January 29, 2015). © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  20. Evolutionary Dynamics of Globalization

    OpenAIRE

    Naci Canpolat; Hüseyin Ozel

    2008-01-01

    The expansion of markets –globalization– was reversed during early 20th century and unfettered markets gave in to the welfare state and central planning. But the markets have been striking back since the early 1980s. Governments are withdrawn from economic activities, and many structural market reforms are implemented. Now the question is: Can the forces that market expansion create again reverse this expansion? This paper seeks an answer to this question by constructing an evolutionary game ...

  1. Evolutionary relationships and systematics of the alphaviruses.

    Science.gov (United States)

    Powers, A M; Brault, A C; Shirako, Y; Strauss, E G; Kang, W; Strauss, J H; Weaver, S C

    2001-11-01

    Partial E1 envelope glycoprotein gene sequences and complete structural polyprotein sequences were used to compare divergence and construct phylogenetic trees for the genus Alphavirus. Tree topologies indicated that the mosquito-borne alphaviruses could have arisen in either the Old or the New World, with at least two transoceanic introductions to account for their current distribution. The time frame for alphavirus diversification could not be estimated because maximum-likelihood analyses indicated that the nucleotide substitution rate varies considerably across sites within the genome. While most trees showed evolutionary relationships consistent with current antigenic complexes and species, several changes to the current classification are proposed. The recently identified fish alphaviruses salmon pancreas disease virus and sleeping disease virus appear to be variants or subtypes of a new alphavirus species. Southern elephant seal virus is also a new alphavirus distantly related to all of the others analyzed. Tonate virus and Venezuelan equine encephalitis virus strain 78V3531 also appear to be distinct alphavirus species based on genetic, antigenic, and ecological criteria. Trocara virus, isolated from mosquitoes in Brazil and Peru, also represents a new species and probably a new alphavirus complex.

  2. Asymmetric Evolutionary Games.

    Science.gov (United States)

    McAvoy, Alex; Hauert, Christoph

    2015-08-01

    Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.

  3. Asymmetric Evolutionary Games.

    Directory of Open Access Journals (Sweden)

    Alex McAvoy

    2015-08-01

    Full Text Available Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.

  4. City of Pittsburgh Trees

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Trees cared for and managed by the City of Pittsburgh Department of Public Works Forestry Division. Tree Benefits are calculated using the National Tree Benefit...

  5. Improved allometric models to estimate the aboveground biomass of tropical trees.

    Science.gov (United States)

    Chave, Jérôme; Réjou-Méchain, Maxime; Búrquez, Alberto; Chidumayo, Emmanuel; Colgan, Matthew S; Delitti, Welington B C; Duque, Alvaro; Eid, Tron; Fearnside, Philip M; Goodman, Rosa C; Henry, Matieu; Martínez-Yrízar, Angelina; Mugasha, Wilson A; Muller-Landau, Helene C; Mencuccini, Maurizio; Nelson, Bruce W; Ngomanda, Alfred; Nogueira, Euler M; Ortiz-Malavassi, Edgar; Pélissier, Raphaël; Ploton, Pierre; Ryan, Casey M; Saldarriaga, Juan G; Vieilledent, Ghislain

    2014-10-01

    Terrestrial carbon stock mapping is important for the successful implementation of climate change mitigation policies. Its accuracy depends on the availability of reliable allometric models to infer oven-dry aboveground biomass of trees from census data. The degree of uncertainty associated with previously published pantropical aboveground biomass allometries is large. We analyzed a global database of directly harvested trees at 58 sites, spanning a wide range of climatic conditions and vegetation types (4004 trees ≥ 5 cm trunk diameter). When trunk diameter, total tree height, and wood specific gravity were included in the aboveground biomass model as covariates, a single model was found to hold across tropical vegetation types, with no detectable effect of region or environmental factors. The mean percent bias and variance of this model was only slightly higher than that of locally fitted models. Wood specific gravity was an important predictor of aboveground biomass, especially when including a much broader range of vegetation types than previous studies. The generic tree diameter-height relationship depended linearly on a bioclimatic stress variable E, which compounds indices of temperature variability, precipitation variability, and drought intensity. For cases in which total tree height is unavailable for aboveground biomass estimation, a pantropical model incorporating wood density, trunk diameter, and the variable E outperformed previously published models without height. However, to minimize bias, the development of locally derived diameter-height relationships is advised whenever possible. Both new allometric models should contribute to improve the accuracy of biomass assessment protocols in tropical vegetation types, and to advancing our understanding of architectural and evolutionary constraints on woody plant development. © 2014 John Wiley & Sons Ltd.

  6. Michael Akam and the rise of evolutionary developmental biology.

    Science.gov (United States)

    Stern, David L; Dawes-Hoang, Rachel E

    2010-01-01

    Michael Akam has been awarded the 2007 Kowalevsky medal for his many research accomplishments in the area of evolutionary developmental biology. We highlight three tributaries of Michaels contribution to evolutionary developmental biology. First, he has made major contributions to our understanding of development of the fruit fly, Drosophila melanogaster. Second, he has maintained a consistent focus on several key problems in evolutionary developmental biology, including the evolving role of Hox genes in arthropods and, more recently, the evolution of segmentation mechanisms. Third, Michael has written a series of influential reviews that have integrated progress in developmental biology into an evolutionary perspective. Michael has also made a large impact on the field through his effective mentorship style, his selfless promotion of younger colleagues, and his leadership of the University Museum of Zoology at Cambridge and the European community of evolutionary developmental biologists.

  7. Applications of evolutionary computation in image processing and pattern recognition

    CERN Document Server

    Cuevas, Erik; Perez-Cisneros, Marco

    2016-01-01

    This book presents the use of efficient Evolutionary Computation (EC) algorithms for solving diverse real-world image processing and pattern recognition problems. It provides an overview of the different aspects of evolutionary methods in order to enable the reader in reaching a global understanding of the field and, in conducting studies on specific evolutionary techniques that are related to applications in image processing and pattern recognition. It explains the basic ideas of the proposed applications in a way that can also be understood by readers outside of the field. Image processing and pattern recognition practitioners who are not evolutionary computation researchers will appreciate the discussed techniques beyond simple theoretical tools since they have been adapted to solve significant problems that commonly arise on such areas. On the other hand, members of the evolutionary computation community can learn the way in which image processing and pattern recognition problems can be translated into an...

  8. SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

    Science.gov (United States)

    Beccati, Alan; Gerken, Jan; Quast, Christian; Yilmaz, Pelin; Glöckner, Frank Oliver

    2017-09-30

    Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself.

  9. Evolutionary theories of depression: a critical review.

    Science.gov (United States)

    Hagen, Edward H

    2011-12-01

    We critically review evolutionary theories of major depressive disorder (MDD). Because most instances of MDD appear to be caused by adversity, evolutionary theories of MDD generally propose that sadness and low mood evolved as beneficial responses to adversity, and that MDD is dysfunctional sadness and low mood. If so, MDD research should focus much more heavily on understanding the healthy functions of sadness and low mood to better understand how they dysfunction. A debate about the boundary between healthy sadness and MDD is then reviewed. In part, this debate turns on whether MDD's costliest symptoms could provide unknown benefits. Therefore, the review concludes by discussing 2 theories that explore possible benefits of prolonged anhedonia and suicidality.

  10. Estimating species trees from unrooted gene trees.

    Science.gov (United States)

    Liu, Liang; Yu, Lili

    2011-10-01

    In this study, we develop a distance method for inferring unrooted species trees from a collection of unrooted gene trees. The species tree is estimated by the neighbor joining (NJ) tree built from a distance matrix in which the distance between two species is defined as the average number of internodes between two species across gene trees, that is, average gene-tree internode distance. The distance method is named NJ(st) to distinguish it from the original NJ method. Under the coalescent model, we show that if gene trees are known or estimated correctly, the NJ(st) method is statistically consistent in estimating unrooted species trees. The simulation results suggest that NJ(st) and STAR (another coalescence-based method for inferring species trees) perform almost equally well in estimating topologies of species trees, whereas the Bayesian coalescence-based method, BEST, outperforms both NJ(st) and STAR. Unlike BEST and STAR, the NJ(st) method can take unrooted gene trees to infer species trees without using an outgroup. In addition, the NJ(st) method can handle missing data and is thus useful in phylogenomic studies in which data sets often contain missing loci for some individuals.

  11. A genome Tree of Life for the Fungi kingdom.

    Science.gov (United States)

    Choi, JaeJin; Kim, Sung-Hou

    2017-08-29

    Fungi belong to one of the largest and most diverse kingdoms of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information-based trees ("gene trees"), constructed commonly based on the degree of differences of proteins or DNA sequences of a small number of highly conserved genes common among the population by a multiple sequence alignment (MSA) method. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population depending on the subjective selection of the genes. Within the last decade, a large number of whole-genome sequences of fungi have become publicly available, which represent, at present, the most fundamental and complete information about each fungal organism. This presents an opportunity to infer kinship among fungi using a whole-genome information-based tree ("genome tree"). The method we used allows comparison of whole-genome information without MSA, and is a variation of a computational algorithm developed to find semantic similarities or plagiarism in two books, where we represent whole-genomic information of an organism as a book of words without spaces. The genome tree reveals several significant and notable differences from the gene trees, and these differences invoke new discussions about alternative narratives for the evolution of some of the currently accepted fungal groups.

  12. Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

    Science.gov (United States)

    Bapteste, Eric; Lopez, Philippe; Bouchard, Frédéric; Baquero, Fernando; McInerney, James O; Burian, Richard M

    2012-11-06

    All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

  13. Evolutionary patterns and processes

    DEFF Research Database (Denmark)

    Leonardi, Michela; Sanz, Pablo Librado; Der Sarkissian, Clio

    2017-01-01

    Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates......, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution-time, allowing a wealth of fundamental evolutionary...

  14. Molluscan Evolutionary Development

    DEFF Research Database (Denmark)

    Wanninger, Andreas Wilhelm Georg; Koop, Damien; Moshel-Lynch, Sharon

    2008-01-01

    Brought together by Winston F. Ponder and David R. Lindberg, thirty-six experts on the evolution of the Mollusca provide an up-to-date review of its evolutionary history. The Mollusca are the second largest animal phylum and boast a fossil record of over 540 million years. They exhibit remarkable...... anatomical diversity and include the bivalves (scallops, oysters, and clams), gastropods (limpets, snails, and slugs), and cephalopods (squid, cuttlefish, and octopus). This study treats each major taxon and supplies general information as well as overviews of evolution and phylogeny using data from...... different sources--morphological, ultrastructural, molecular, developmental, and from the fossil record....

  15. Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo, Evo-Eco and Evolutionary Transitions.

    Science.gov (United States)

    Watson, Richard A; Mills, Rob; Buckley, C L; Kouvaris, Kostas; Jackson, Adam; Powers, Simon T; Cox, Chris; Tudge, Simon; Davies, Adam; Kounios, Loizos; Power, Daniel

    2016-01-01

    The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term "evolutionary connectionism" to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary

  16. Understanding why we age and how: Evolutionary biology meets different model organisms and multi-level omics: Meeting report on "Comparative Biology of Aging," Roscoff, October 12-16, 2015.

    Science.gov (United States)

    Gilson, Eric; Bosch, Thomas C G

    2016-06-01

    The conference explored an extraordinary diversity of aging strategies in organisms ranging from short-lived species to "immortal" animals and plants. Research on the biological processes of aging is at the brink of a revolution with respect to our understanding of its underlying mechanisms as well as our ability to prevent and cure a wide variety of age-related pathologies. © 2016 WILEY Periodicals, Inc.

  17. Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes.

    Science.gov (United States)

    Ruane, Sara; Raxworthy, Christopher J; Lemmon, Alan R; Lemmon, Emily Moriarty; Burbrink, Frank T

    2015-10-12

    Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS. Here, we determine how a 5-locus Sanger dataset compares with a 377-locus anchored genomics dataset for understanding the evolutionary history of the pseudoxyrhophiine snake radiation centered in Madagascar. The Pseudoxyrhophiinae comprise ~86 % of Madagascar's serpent diversity, yet they are poorly known with respect to ecology, behavior, and systematics. Using the 377-locus NGS dataset and the summary statistics species-tree methods STAR and MP-EST, we estimated a well-supported species tree that provides new insights concerning intergeneric relationships for the pseudoxyrhophiines. We also compared how these and other methods performed with respect to estimating tree topology using datasets with varying numbers of loci. Using Sanger sequencing and an anchored phylogenomics approach, we sequenced datasets comprised of 5 and 377 loci, respectively, for 23 pseudoxyrhophiine taxa. For each dataset, we estimated phylogenies using both gene-tree (concatenation) and species-tree (STAR, MP-EST) approaches. We determined the similarity of resulting tree topologies from the different datasets using Robinson-Foulds distances. In addition, we examined how subsets of these data performed compared to the complete Sanger and anchored datasets for phylogenetic accuracy using the same tree inference methodologies, as well as the program *BEAST to determine if a full coalescent model for species tree estimation could generate robust results with fewer loci compared to the summary statistics species

  18. The evolutionary history of bears is characterized by gene flow across species.

    Science.gov (United States)

    Kumar, Vikas; Lammers, Fritjof; Bidon, Tobias; Pfenninger, Markus; Kolter, Lydia; Nilsson, Maria A; Janke, Axel

    2017-04-19

    Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.

  19. The evolutionary history of bears is characterized by gene flow across species

    Science.gov (United States)

    Kumar, Vikas; Lammers, Fritjof; Bidon, Tobias; Pfenninger, Markus; Kolter, Lydia; Nilsson, Maria A.; Janke, Axel

    2017-01-01

    Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow. PMID:28422140

  20. Urban tree growth modeling

    Science.gov (United States)

    E. Gregory McPherson; Paula J. Peper

    2012-01-01

    This paper describes three long-term tree growth studies conducted to evaluate tree performance because repeated measurements of the same trees produce critical data for growth model calibration and validation. Several empirical and process-based approaches to modeling tree growth are reviewed. Modeling is more advanced in the fields of forestry and...

  1. Keeping trees as assets

    Science.gov (United States)

    Kevin T. Smith

    2009-01-01

    Landscape trees have real value and contribute to making livable communities. Making the most of that value requires providing trees with the proper care and attention. As potentially large and long-lived organisms, trees benefit from commitment to regular care that respects the natural tree system. This system captures, transforms, and uses energy to survive, grow,...

  2. Multiple evolutionary mechanisms drive papillomavirus diversification.

    Science.gov (United States)

    Gottschling, Marc; Stamatakis, Alexandros; Nindl, Ingo; Stockfleth, Eggert; Alonso, Angel; Bravo, Ignacio G

    2007-05-01

    The circular, double-stranded 8-kb DNA genome of papillomaviruses (PVes) consists mainly of 4 large genes, E1, E2, L2, and L1. Approximately 150 papillomavirus genomes have been sequenced to date. We analyzed a representative sample of 53 PVes genomes using maximum likelihood, Bayesian inference, maximum parsimony, and distance-based methods both on nucleotide (nt) and on amino acid (aa) alignments. When the 4 genes were analyzed separately, aa-inferred phylogenies contradicted each other less than nt-inferred trees (judged by partition homogeneity tests). In particular, gene combinations including the L2 gene generated significant incongruence (P artifacts and insufficient taxon sampling, may contribute to the incomplete resolution of deep phylogenetic nodes. The molecular data globally supports a complex evolutionary scenario for PVes, which is driven by multiple mechanisms but not exclusively by coevolution with corresponding hosts.

  3. Evolutionary approaches to cultural and linguistic diversity.

    Science.gov (United States)

    Steele, James; Jordan, Peter; Cochrane, Ethan

    2010-12-12

    Evolutionary approaches to cultural change are increasingly influential, and many scientists believe that a 'grand synthesis' is now in sight. The papers in this Theme Issue, which derives from a symposium held by the AHRC Centre for the Evolution of Cultural Diversity (University College London) in December 2008, focus on how the phylogenetic tree-building and network-based techniques used to estimate descent relationships in biology can be adapted to reconstruct cultural histories, where some degree of inter-societal diffusion will almost inevitably be superimposed on any deeper signal of a historical branching process. The disciplines represented include the three most purely 'cultural' fields from the four-field model of anthropology (cultural anthropology, archaeology and linguistic anthropology). In this short introduction, some context is provided from the history of anthropology, and key issues raised by the papers are highlighted.

  4. Practical advantages of evolutionary computation

    Science.gov (United States)

    Fogel, David B.

    1997-10-01

    Evolutionary computation is becoming a common technique for solving difficult, real-world problems in industry, medicine, and defense. This paper reviews some of the practical advantages to using evolutionary algorithms as compared with classic methods of optimization or artificial intelligence. Specific advantages include the flexibility of the procedures, as well as their ability to self-adapt the search for optimum solutions on the fly. As desktop computers increase in speed, the application of evolutionary algorithms will become routine.

  5. Plant grafting: new mechanisms, evolutionary implications

    Directory of Open Access Journals (Sweden)

    Eliezer E Goldschmidt

    2014-12-01

    Full Text Available Grafting, an old plant propagation practice, is still widely used with fruit trees and in recent decades also with vegetables. Taxonomic proximity is a general prerequisite for successful graft-take and long-term survival of the grafted, composite plant. However, the mechanisms underlying interspecific graft incompatibility are as yet insufficiently understood. Hormonal signals, auxin in particular, are believed to play an important role in the wound healing and vascular regeneration within the graft union zone. Long-distance protein, mRNA and small RNA graft-transmissible signals currently emerge as novel mechanisms which regulate nutritional and developmental root/top relations and may play a pivotal role in grafting physiology. Grafting also has significant pathogenic projections. On one hand, stock to scion mechanical contact enables the spread of diseases, even without a complete graft union. But, on the other hand, grafting onto resistant rootstocks serves as a principal tool in the management of fruit tree plagues and vegetable soil-borne diseases. The ‘graft hybrid’ historic controversy has not yet been resolved. Recent evidence suggests that epigenetic modification of DNA-methylation patterns may account for certain graft-transformation phenomena. Root grafting is a wide spread natural phenomenon; both intraspecific and interspecific root grafts have been recorded. Root grafts have an evolutionary role in the survival of storm-hit forest stands as well as in the spread of devastating diseases. A more fundamental evolutionary role is hinted by recent findings that demonstrate plastid and nuclear genome transfer between distinct Nicotiana species in the graft union zone, within a tissue culture system. This has led to the formation of alloploid cells that, under laboratory conditions, gave rise to a novel, alloploid Nicotiana species, indicating that natural grafts may play a role in plant speciation. under certain circumstances.

  6. Plant grafting: new mechanisms, evolutionary implications.

    Science.gov (United States)

    Goldschmidt, Eliezer E

    2014-01-01

    Grafting, an old plant propagation practice, is still widely used with fruit trees and in recent decades also with vegetables. Taxonomic proximity is a general prerequisite for successful graft-take and long-term survival of the grafted, composite plant. However, the mechanisms underlying interspecific graft incompatibility are as yet insufficiently understood. Hormonal signals, auxin in particular, are believed to play an important role in the wound healing and vascular regeneration within the graft union zone. Incomplete and convoluted vascular connections impede the vital upward and downward whole plant transfer routes. Long-distance protein, mRNA and small RNA graft-transmissible signals currently emerge as novel mechanisms which regulate nutritional and developmental root/top relations and may play a pivotal role in grafting physiology. Grafting also has significant pathogenic projections. On one hand, stock to scion mechanical contact enables the spread of diseases, even without a complete graft union. But, on the other hand, grafting onto resistant rootstocks serves as a principal tool in the management of fruit tree plagues and vegetable soil-borne diseases. The 'graft hybrid' historic controversy has not yet been resolved. Recent evidence suggests that epigenetic modification of DNA-methylation patterns may account for certain graft-transformation phenomena. Root grafting is a wide spread natural phenomenon; both intraspecific and interspecific root grafts have been recorded. Root grafts have an evolutionary role in the survival of storm-hit forest stands as well as in the spread of devastating diseases. A more fundamental evolutionary role is hinted by recent findings that demonstrate plastid and nuclear genome transfer between distinct Nicotiana species in the graft union zone, within a tissue culture system. This has led to the formation of alloploid cells that, under laboratory conditions, gave rise to a novel, alloploid Nicotiana species, indicating

  7. Urban tree effects on fine particulate matter and human health

    Science.gov (United States)

    David J. Nowak

    2014-01-01

    Overall, city trees reduce particulate matter and provide substantial health benefits; but under certain conditions, they can locally increase particulate matter concentrations. Urban foresters need to understand how trees affect particulate matter so they can select proper species and create appropriate designs to improve air quality. This article details trees'...

  8. Genetic transformation of forest trees | Diouf | African Journal of ...

    African Journals Online (AJOL)

    In this review, the recent progress on genetic transformation of forest trees were discussed. Its described also, different applications of genetic engineering for improving forest trees or understanding the mechanisms governing genes expression in woody plants. Key words: Genetic transformation, transgenic forest trees, ...

  9. Classification and regression trees

    CERN Document Server

    Breiman, Leo; Olshen, Richard A; Stone, Charles J

    1984-01-01

    The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.

  10. Evolutionary problems in centrosome and centriole biology.

    Science.gov (United States)

    Ross, L; Normark, B B

    2015-05-01

    Centrosomes have been an enigma to evolutionary biologists. Either they have been the subject of ill-founded speculation or they have been ignored. Here, we highlight evolutionary paradoxes and problems of centrosome and centriole evolution and seek to understand them in the light of recent advances in centrosome biology. Most evolutionary accounts of centrosome evolution have been based on the hypothesis that centrosomes are replicators, independent of the nucleus and cytoplasm. It is now clear, however, that this hypothesis is not tenable. Instead, centrosomes are formed de novo each cell division, with the presence of an old centrosome regulating, but not essential for, the assembly of a new one. Centrosomes are the microtubule-organizing centres of cells. They can potentially affect sensory and motor characters (as the basal body of cilia), as well as the movements of chromosomes during cell division. This latter role does not seem essential, however, except in male meiosis, and the reasons for this remain unclear. Although the centrosome is absent in some taxa, when it is present, its structure is extraordinarily conserved: in most taxa across eukaryotes, it does not appear to evolve at all. And yet a few insect groups display spectacular hypertrophy of the centrioles. We discuss how this might relate to the unusual reproductive system found in these insects. Finally, we discuss why the fate of centrosomes in sperm and early embryos might differ between different groups of animals. © 2015 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

  11. Evolutionary explanations for natural language: criteria from evolutionary biology

    NARCIS (Netherlands)

    Zuidema, W.; de Boer, B.

    2008-01-01

    Theories of the evolutionary origins of language must be informed by empirical and theoretical results from a variety of different fields. Complementing recent surveys of relevant work from linguistics, animal behaviour and genetics, this paper surveys the requirements on evolutionary scenarios that

  12. Evolutionary history of LINE-1 in the major clades of placental mammals.

    Directory of Open Access Journals (Sweden)

    Paul D Waters

    2007-01-01

    Full Text Available LINE-1 constitutes an important component of mammalian genomes. It has a dynamic evolutionary history characterized by the rise, fall and replacement of subfamilies. Most data concerning LINE-1 biology and evolution are derived from the human and mouse genomes and are often assumed to hold for all placentals.To examine LINE-1 relationships, sequences from the 3' region of the reverse transcriptase from 21 species (representing 13 orders across Afrotheria, Xenarthra, Supraprimates and Laurasiatheria were obtained from whole genome sequence assemblies, or by PCR with degenerate primers. These sequences were aligned and analysed.Our analysis reflects accepted placental relationships suggesting mostly lineage-specific LINE-1 families. The data provide clear support for several clades including Glires, Supraprimates, Laurasiatheria, Boreoeutheria, Xenarthra and Afrotheria. Within the afrotherian LINE-1 (AfroLINE clade, our tree supports Paenungulata, Afroinsectivora and Afroinsectiphillia. Xenarthran LINE-1 (XenaLINE falls sister to AfroLINE, providing some support for the Atlantogenata (Xenarthra+Afrotheria hypothesis.LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics. Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches such as that to marsupials are shortened and/or broken up. Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

  13. On the evolutionary and biogeographic history of Saxifraga sect. Trachyphyllum (Gaud.) Koch (Saxifragaceae Juss.).

    Science.gov (United States)

    DeChaine, Eric G; Anderson, Stacy A; McNew, Jennifer M; Wendling, Barry M

    2013-01-01

    Arctic-alpine plants in the genus Saxifraga L. (Saxifragaceae Juss.) provide an excellent system for investigating the process of diversification in northern regions. Yet, sect. Trachyphyllum (Gaud.) Koch, which is comprised of about 8 to 26 species, has still not been explored by molecular systematists even though taxonomists concur that the section needs to be thoroughly re-examined. Our goals were to use chloroplast trnL-F and nuclear ITS DNA sequence data to circumscribe the section phylogenetically, test models of geographically-based population divergence, and assess the utility of morphological characters in estimating evolutionary relationships. To do so, we sequenced both genetic markers for 19 taxa within the section. The phylogenetic inferences of sect. Trachyphyllum using maximum likelihood and Bayesian analyses showed that the section is polyphyletic, with S. aspera L. and S bryoides L. falling outside the main clade. In addition, the analyses supported several taxonomic re-classifications to prior names. We used two approaches to test biogeographic hypotheses: i) a coalescent approach in Mesquite to test the fit of our reconstructed gene trees to geographically-based models of population divergence and ii) a maximum likelihood inference in Lagrange. These tests uncovered strong support for an origin of the clade in the Southern Rocky Mountains of North America followed by dispersal and divergence episodes across refugia. Finally we adopted a stochastic character mapping approach in SIMMAP to investigate the utility of morphological characters in estimating evolutionary relationships among taxa. We found that few morphological characters were phylogenetically informative and many were misleading. Our molecular analyses provide a foundation for the diversity and evolutionary relationships within sect. Trachyphyllum and hypotheses for better understanding the patterns and processes of divergence in this section, other saxifrages, and plants inhabiting

  14. On the evolutionary and biogeographic history of Saxifraga sect. Trachyphyllum (Gaud. Koch (Saxifragaceae Juss..

    Directory of Open Access Journals (Sweden)

    Eric G DeChaine

    Full Text Available Arctic-alpine plants in the genus Saxifraga L. (Saxifragaceae Juss. provide an excellent system for investigating the process of diversification in northern regions. Yet, sect. Trachyphyllum (Gaud. Koch, which is comprised of about 8 to 26 species, has still not been explored by molecular systematists even though taxonomists concur that the section needs to be thoroughly re-examined. Our goals were to use chloroplast trnL-F and nuclear ITS DNA sequence data to circumscribe the section phylogenetically, test models of geographically-based population divergence, and assess the utility of morphological characters in estimating evolutionary relationships. To do so, we sequenced both genetic markers for 19 taxa within the section. The phylogenetic inferences of sect. Trachyphyllum using maximum likelihood and Bayesian analyses showed that the section is polyphyletic, with S. aspera L. and S bryoides L. falling outside the main clade. In addition, the analyses supported several taxonomic re-classifications to prior names. We used two approaches to test biogeographic hypotheses: i a coalescent approach in Mesquite to test the fit of our reconstructed gene trees to geographically-based models of population divergence and ii a maximum likelihood inference in Lagrange. These tests uncovered strong support for an origin of the clade in the Southern Rocky Mountains of North America followed by dispersal and divergence episodes across refugia. Finally we adopted a stochastic character mapping approach in SIMMAP to investigate the utility of morphological characters in estimating evolutionary relationships among taxa. We found that few morphological characters were phylogenetically informative and many were misleading. Our molecular analyses provide a foundation for the diversity and evolutionary relationships within sect. Trachyphyllum and hypotheses for better understanding the patterns and processes of divergence in this section, other saxifrages, and

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

    Science.gov (United States)

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

    2016-12-01

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

  16. Different evolutionary pathways underlie the morphology of wrist bones in hominoids.

    Science.gov (United States)

    Kivell, Tracy L; Barros, Anna P; Smaers, Jeroen B

    2013-10-23

    The hominoid wrist has been a focus of numerous morphological analyses that aim to better understand long-standing questions about the evolution of human and hominoid hand use. However, these same analyses also suggest various scenarios of complex and mosaic patterns of morphological evolution within the wrist and potentially multiple instances of homoplasy that would benefit from require formal analysis within a phylogenetic context.We identify morphological features that principally characterize primate - and, in particular, hominoid (apes, including humans) - wrist evolution and reveal the rate, process and evolutionary timing of patterns of morphological change on individual branches of the primate tree of life. Linear morphological variables of five wrist bones - the scaphoid, lunate, triquetrum, capitate and hamate - are analyzed in a diverse sample of extant hominoids (12 species, 332 specimens), Old World (8 species, 43 specimens) and New World (4 species, 26 specimens) monkeys, fossil Miocene apes (8 species, 20 specimens) and Plio-Pleistocene hominins (8 species, 18 specimens). Results reveal a combination of parallel and synapomorphic morphology within haplorrhines, and especially within hominoids, across individual wrist bones. Similar morphology of some wrist bones reflects locomotor behaviour shared between clades (scaphoid, triquetrum and capitate) while others (lunate and hamate) indicate clade-specific synapomorphic morphology. Overall, hominoids show increased variation in wrist bone morphology compared with other primate clades, supporting previous analyses, and demonstrate several occurrences of parallel evolution, particularly between orangutans and hylobatids, and among hominines (extant African apes, humans and fossil hominins). Our analyses indicate that different evolutionary processes can underlie the evolution of a single anatomical unit (the wrist) to produce diversity in functional and morphological adaptations across individual wrist

  17. Public Reactions to New Street Tree Planting

    Directory of Open Access Journals (Sweden)

    Ruth A. Rae

    2010-01-01

    Full Text Available MillionTreesNYC, which has the goal of planting one million trees in New York City by 2017, is intended to make New York City a greener, more sustainable city and is part of the Mayor’s comprehensive long term strategic plan, PlaNYC. Through planting a tree at every suitable sidewalk location in the city, the City of New York is transforming blocks and communities, and providing a variety of environmental, social and aesthetic benefits. This article examines the large scale municipal planting of new street trees and the reaction by some of the pubic to this planting.Trees offer benefits to the city overall, but the public may not understand these benefits or the street tree planting process. Between 2007 and 2009, the Department of Parks & Recreation planted 53,235 new street trees, and received 4,108 items of correspondence from the public. The majority of this correspondence consisted of public comments about the City’s new street tree planting policies and processes including placement objections, maintenance concerns, reports of resultant damage from tree planting operations, requests for new street trees and reports of tree conditions.This study describes the operational policies that guide New York City's municipal street tree planting, and results of content and spatial analysis of the correspondence. Qualitative analysis of the correspondence revealed the public perceptions and concerns related to the MillionTreesNYC program. Spatial analysis explored the relationship between the planting locations of new street trees and the locations of the citizen correspondence.Public reactions to this large scale municipal planting are related to the dual public and private nature of the sidewalk, issues of territoriality, responsibility, aesthetics and place attachment. Correspondence volume was associated with the scale of the new street tree block planting program, and the effectiveness of NYC’s 311 Customer Service Center. The discussion

  18. Can live tree size-density relationships provide a mechanism for predicting down and dead tree resources?

    Science.gov (United States)

    Christopher Woodall; James Westfall

    2009-01-01

    Live tree size-density relationships in forests have long provided a framework for understanding stand dynamics. There has been little examination of the relationship between the size-density attributes of live and standing/down dead trees (e.g., number and mean tree size per unit area, such information could help in large-scale efforts to estimate dead wood resources...

  19. Occult hepatitis B infection: an evolutionary scenario

    Directory of Open Access Journals (Sweden)

    Lukashov Vladimir V

    2008-12-01

    Full Text Available Abstract Background Occult or latent hepatitis B virus (HBV infection is defined as infection with detectable HBV DNA and undetectable surface antigen (HBsAg in patients' blood. The cause of an overt HBV infection becoming an occult one is unknown. To gain insight into the mechanism of the development of occult infection, we compared the full-length HBV genome from a blood donor carrying an occult infection (d4 with global genotype D genomes. Results The phylogenetic analysis of polymerase, core and X protein sequences did not distinguish d4 from other genotype D strains. Yet, d4 surface protein formed the evolutionary outgroup relative to all other genotype D strains. Its evolutionary branch was the only one where accumulation of substitutions suggests positive selection (dN/dS = 1.3787. Many of these substitutiions accumulated specifically in regions encoding the core/surface protein interface, as revealed in a 3D-modeled protein complex. We identified a novel RNA splicing event (deleting nucleotides 2986-202 that abolishes surface protein gene expression without affecting polymerase, core and X-protein related functions. Genotype D strains differ in their ability to perform this 2986-202 splicing. Strains prone to 2986-202 splicing constitute a separate clade in a phylogenetic tree of genotype D HBVs. A single substitution (G173T that is associated with clade membership alters the local RNA secondary structure and is proposed to affect splicing efficiency at the 202 acceptor site. Conclusion We propose an evolutionary scenario for occult HBV infection, in which 2986-202 splicing generates intracellular virus particles devoid of surface protein, which subsequently accumulates mutations due to relaxation of coding constraints. Such viruses are deficient of autonomous propagation and cannot leave the host cell until it is lysed.

  20. Can't See the Forest: Using an Evolutionary Algorithm to Produce an Animated Artwork

    Science.gov (United States)

    Trist, Karen; Ciesielski, Vic; Barile, Perry

    We describe an artist's journey of working with an evolutionary algorithm to create an artwork suitable for exhibition in a gallery. Software based on the evolutionary algorithm produces animations which engage the viewer with a target image slowly emerging from a random collection of greyscale lines. The artwork consists of a grid of movies of eucalyptus tree targets. Each movie resolves with different aesthetic qualities, tempo and energy. The artist exercises creative control by choice of target and values for evolutionary and drawing parameters.

  1. On the accuracy of language trees.

    Directory of Open Access Journals (Sweden)

    Simone Pompei

    Full Text Available Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical, phonological, syntactic features or characters for many different languages: a set of parallel corpora whose compilation represents a paramount achievement in linguistics. From this perspective the reconstruction of language trees is an example of inverse problems: starting from present, incomplete and often noisy, information, one aims at inferring the most likely past evolutionary history. A fundamental issue in inverse problems is the evaluation of the inference made. A standard way of dealing with this question is to generate data with artificial models in order to have full access to the evolutionary process one is going to infer. This procedure presents an intrinsic limitation: when dealing with real data sets, one typically does not know which model of evolution is the most suitable for them. A possible way out is to compare algorithmic inference with expert classifications. This is the point of view we take here by conducting a thorough survey of the accuracy of reconstruction methods as compared with the Ethnologue expert classifications. We focus in particular on state-of-the-art distance-based methods for phylogeny reconstruction using worldwide linguistic databases. In order to assess the accuracy of the inferred trees we introduce and characterize two generalizations of standard definitions of distances between trees. Based on these scores we quantify the relative performances of the distance-based algorithms considered. Further we quantify how the completeness and the coverage of the available databases affect the accuracy of the reconstruction. Finally we draw some conclusions about where the accuracy of the reconstructions in historical linguistics stands and about the leading directions to improve

  2. Studies in evolutionary agroecology

    DEFF Research Database (Denmark)

    Wille, Wibke

    difference between optimal individual and optimal population performance increases with strong competition among individuals. Thus dense populations make ideal environments to exert forms of selection pressure deviating from natural selection. The first part of this study investigates the central hypothesis...... of Evolutionary Agroecology that the highest yielding individuals do not necessarily perform best as a population. The investment of resources into strategies and structures increasing individual competitive ability carries a cost. If a whole population consists of individuals investing resources to compete...... with each other, it will have a negative impact on the population performance. While high density results in strong competition, it also increases the potential for cooperation. The other aspect of this study has been to investigate the possibility of improving the yield and weed suppression potential...

  3. Evolutionary games under incompetence.

    Science.gov (United States)

    Kleshnina, Maria; Filar, Jerzy A; Ejov, Vladimir; McKerral, Jody C

    2018-02-26

    The adaptation process of a species to a new environment is a significant area of study in biology. As part of natural selection, adaptation is a mutation process which improves survival skills and reproductive functions of species. Here, we investigate this process by combining the idea of incompetence with evolutionary game theory. In the sense of evolution, incompetence and training can be interpreted as a special learning process. With focus on the social side of the problem, we analyze the influence of incompetence on behavior of species. We introduce an incompetence parameter into a learning function in a single-population game and analyze its effect on the outcome of the replicator dynamics. Incompetence can change the outcome of the game and its dynamics, indicating its significance within what are inherently imperfect natural systems.

  4. Microwave sensing of tree trunks

    Science.gov (United States)

    Jezova, Jana; Mertens, Laurence; Lambot, Sebastien

    2015-04-01

    The main subject of this research is the observation of the inner part of living tree trunks using ground-penetrating radar (GPR). Trees are everyday part of human life and therefore it is important to pay attention to the tree conditions. The most obvious consequence of the poor tree condition is dead or injury caused by falling tree. The trunk internal structure is divided into three main parts: heartwood, sapwood and bark, which make this medium highly anisotropic and heterogeneous. Furthermore, the properties of the wood are not only specie-dependent but also depend on genetic and on environmental conditions. In urban areas the main problem for the stability of the trees relies in the apparition of decays provoked by fungi, insect or birds. This results in cavities or decreasing of the support capacity of the tree. GPR has proved itself to be a very powerful electromagnetic tool for non-destructive detection of buried objects. Since the beginning of the 20th century it has been used in several different areas (archaeology, landmine detection, civil engineering, ...). GPR uses the principle of the scattering of the electromagnetic waves that are radiated from a transmitting antenna. Then the waves propagate through the medium and are reflected from the object and then they are received by a receiving antenna. The velocity of the scattered signal is determined primarily by the permittivity of the material. The optimal functionality of the GPR was investigated using the numerical simulation tool gprMax2D. This tool is based on a Finite-Difference Time-Domain (FDTD) numerical model. Subsequently, the GPR functionality was tested using the laboratory model of a decayed tree trunk. Afterwards, the results and lessons learnt in the simplified tests will be used in the processing of the real data and will help to achieve deeper understanding of them. The laboratory model of the tree trunk was made by plastic or carton pipes and filled by sand. Space inside the model

  5. Genealogical Trees of Scientific Papers.

    Science.gov (United States)

    Waumans, Michaël Charles; Bersini, Hugues

    2016-01-01

    Many results have been obtained when studying scientific papers citations databases in a network perspective. Articles can be ranked according to their current in-degree and their future popularity or citation counts can even be predicted. The dynamical properties of such networks and the observation of the time evolution of their nodes started more recently. This work adopts an evolutionary perspective and proposes an original algorithm for the construction of genealogical trees of scientific papers on the basis of their citation count evolution in time. The fitness of a paper now amounts to its in-degree growing trend and a "dying" paper will suddenly see this trend declining in time. It will give birth and be taken over by some of its most prevalent citing "offspring". Practically, this might be used to trace the successive published milestones of a research field.

  6. Were there evolutionary advantages to premenstrual syndrome?

    Science.gov (United States)

    Gillings, Michael R

    2014-09-01

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

  7. Improved Parametrized Complexity of Maximum Agreement Subtree and Maximum Compatible Tree problems

    OpenAIRE

    Berry, Vincent; Nicolas, François

    2006-01-01

    International audience; Given a set of evolutionary trees on a same set of taxa, the maximum agreement subtree problem (MAST), respectively maximum compatible tree problem (MCT), consists of finding a largest subset of taxa such that all input trees restricted to these taxa are isomorphic, respectively compatible. These problems have several applications in phylogenetics such as the computation of a consensus of phylogenies obtained from different datasets, the identification of species subje...

  8. Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees.

    Science.gov (United States)

    Kalaghatgi, Prabhav; Pfeifer, Nico; Lengauer, Thomas

    2016-10-01

    The widely used model for evolutionary relationships is a bifurcating tree with all taxa/observations placed at the leaves. This is not appropriate if the taxa have been densely sampled across evolutionary time and may be in a direct ancestral relationship, or if there is not enough information to fully resolve all the branching points in the evolutionary tree. In this article, we present a fast distance-based agglomeration method called family-joining (FJ) for constructing so-called generally labeled trees in which taxa may be placed at internal vertices and the tree may contain polytomies. FJ constructs such trees on the basis of pairwise distances and a distance threshold. We tested three methods for threshold selection, FJ-AIC, FJ-BIC, and FJ-CV, which minimize Akaike information criterion, Bayesian information criterion, and cross-validation error, respectively. When compared with related methods on simulated data, FJ-BIC was among the best at reconstructing the correct tree across a wide range of simulation scenarios. FJ-BIC was applied to HIV sequences sampled from individuals involved in a known transmission chain. The FJ-BIC tree was found to be compatible with almost all transmission events. On average, internal branches in the FJ-BIC tree have higher bootstrap support than branches in the leaf-labeled bifurcating tree constructed using RAxML. 36% and 25% of the internal branches in the FJ-BIC tree and RAxML tree, respectively, have bootstrap support greater than 70%. To the best of our knowledge the method presented here is the first attempt at modeling evolutionary relationships using generally labeled trees. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  9. Evolutionary design assistants for architecture

    Directory of Open Access Journals (Sweden)

    N. Onur Sönmez

    2015-04-01

    existing literature and the proposals and applications of the thesis; secondly, proposals for descriptive and prescriptive models, mappings, summary illustrations, task structures, decomposition schemes, and integratory frameworks; and finally, experimental applications of these proposals. This tripartite progression allows an evaluation of each proposal both conceptually and practically; thereby, enabling a progressive improvement of the understanding regarding the research question, while producing concrete outputs on the way. Besides theoretical and interpretative examinations, the thesis investigates its subject through a set of practical and speculative proposals, which function as both research instruments and the outputs of the study. The first main output of the study is the “design_proxy” approach (d_p, which is an integrated approach for draft making design assistants. It is an outcome of both theoretical examinations and experimental applications, and proposes an integration of, (1 flexible and relaxed task definitions and representations (instead of strict formalisms, (2 intuitive interfaces that make use of usual design media, (3 evaluation of solution proposals through their similarity to given examples, and (4 a dynamic evolutionary approach for solution generation. The design_proxy approach may be useful for AD researchers that aim at developing practical design assistants, as has been examined and demonstrated with the two applications, i.e., design_proxy.graphics and design_proxy.layout. The second main output, the “Interleaved Evolutionary Algorithm” (IEA, or Interleaved EA is a novel evolutionary algorithm proposed and used as the underlying generative mechanism of design_proxybased design assistants. The Interleaved EA is a dynamic, adaptive, and multi-objective EA, in which one of the objectives leads the evolution until its fitness progression stagnates; in the sense that the settings and fitness values of this objective is used for most

  10. Fault tree handbook

    International Nuclear Information System (INIS)

    Haasl, D.F.; Roberts, N.H.; Vesely, W.E.; Goldberg, F.F.

    1981-01-01

    This handbook describes a methodology for reliability analysis of complex systems such as those which comprise the engineered safety features of nuclear power generating stations. After an initial overview of the available system analysis approaches, the handbook focuses on a description of the deductive method known as fault tree analysis. The following aspects of fault tree analysis are covered: basic concepts for fault tree analysis; basic elements of a fault tree; fault tree construction; probability, statistics, and Boolean algebra for the fault tree analyst; qualitative and quantitative fault tree evaluation techniques; and computer codes for fault tree evaluation. Also discussed are several example problems illustrating the basic concepts of fault tree construction and evaluation

  11. Topics of Evolutionary Computation 2001

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    This booklet contains the student reports from the course: Topics of Evolutionary Computation, Fall 2001, given by Thiemo Krink, Rene Thomsen and Rasmus K. Ursem......This booklet contains the student reports from the course: Topics of Evolutionary Computation, Fall 2001, given by Thiemo Krink, Rene Thomsen and Rasmus K. Ursem...

  12. Fixation Time for Evolutionary Graphs

    Science.gov (United States)

    Nie, Pu-Yan; Zhang, Pei-Ai

    Evolutionary graph theory (EGT) is recently proposed by Lieberman et al. in 2005. EGT is successful for explaining biological evolution and some social phenomena. It is extremely important to consider the time of fixation for EGT in many practical problems, including evolutionary theory and the evolution of cooperation. This study characterizes the time to asymptotically reach fixation.

  13. Evolutionary dynamics in structured populations

    Science.gov (United States)

    Nowak, Martin A.; Tarnita, Corina E.; Antal, Tibor

    2010-01-01

    Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces. PMID:20008382

  14. Open Issues in Evolutionary Robotics.

    Science.gov (United States)

    Silva, Fernando; Duarte, Miguel; Correia, Luís; Oliveira, Sancho Moura; Christensen, Anders Lyhne

    2016-01-01

    One of the long-term goals in evolutionary robotics is to be able to automatically synthesize controllers for real autonomous robots based only on a task specification. While a number of studies have shown the applicability of evolutionary robotics techniques for the synthesis of behavioral control, researchers have consistently been faced with a number of issues preventing the widespread adoption of evolutionary robotics for engineering purposes. In this article, we review and discuss the open issues in evolutionary robotics. First, we analyze the benefits and challenges of simulation-based evolution and subsequent deployment of controllers versus evolution on real robotic hardware. Second, we discuss specific evolutionary computation issues that have plagued evolutionary robotics: (1) the bootstrap problem, (2) deception, and (3) the role of genomic encoding and genotype-phenotype mapping in the evolution of controllers for complex tasks. Finally, we address the absence of standard research practices in the field. We also discuss promising avenues of research. Our underlying motivation is the reduction of the current gap between evolutionary robotics and mainstream robotics, and the establishment of evolutionary robotics as a canonical approach for the engineering of autonomous robots.

  15. Contemporary issues in evolutionary biology

    Indian Academy of Sciences (India)

    We are delighted to bring to the readers, a set of peer-reviewed papers on evolutionary biology, published as a special issue of the Journal of Genetics. These papers emanated from ruminations upon and discussions at the Foundations of. Evolutionary Theory: the Ongoing Synthesis meeting at Coorg, India, in February ...

  16. Accelerating Bayesian inference for evolutionary biology models.

    Science.gov (United States)

    Meyer, Xavier; Chopard, Bastien; Salamin, Nicolas

    2017-03-01

    Bayesian inference is widely used nowadays and relies largely on Markov chain Monte Carlo (MCMC) methods. Evolutionary biology has greatly benefited from the developments of MCMC methods, but the design of more complex and realistic models and the ever growing availability of novel data is pushing the limits of the current use of these methods. We present a parallel Metropolis-Hastings (M-H) framework built with a novel combination of enhancements aimed towards parameter-rich and complex models. We show on a parameter-rich macroevolutionary model increases of the sampling speed up to 35 times with 32 processors when compared to a sequential M-H process. More importantly, our framework achieves up to a twentyfold faster convergence to estimate the posterior probability of phylogenetic trees using 32 processors when compared to the well-known software MrBayes for Bayesian inference of phylogenetic trees. https://bitbucket.org/XavMeyer/hogan. nicolas.salamin@unil.ch. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  17. Teaching Teaching & Understanding Understanding

    DEFF Research Database (Denmark)

    2006-01-01

    "Teaching Teaching & Understanding Understanding" is a 19-minute award-winning short-film about teaching at university and higher-level educational institutions. It is based on the "Constructive Alignment" theory developed by Prof. John Biggs. The film delivers a foundation for understanding what...

  18. Predicting loss of evolutionary history: Where are we?

    Science.gov (United States)

    Veron, Simon; Davies, T Jonathan; Cadotte, Marc W; Clergeau, Philippe; Pavoine, Sandrine

    2017-02-01

    The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic

  19. A Simple General Model of Evolutionary Dynamics

    Science.gov (United States)

    Thurner, Stefan

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

  20. New weighting methods for phylogenetic tree reconstruction using multiple loci.

    Science.gov (United States)

    Misawa, Kazuharu; Tajima, Fumio

    2012-08-01

    Efficient determination of evolutionary distances is important for the correct reconstruction of phylogenetic trees. The performance of the pooled distance required for reconstructing a phylogenetic tree can be improved by applying large weights to appropriate distances for reconstructing phylogenetic trees and small weights to inappropriate distances. We developed two weighting methods, the modified Tajima-Takezaki method and the modified least-squares method, for reconstructing phylogenetic trees from multiple loci. By computer simulations, we found that both of the new methods were more efficient in reconstructing correct topologies than the no-weight method. Hence, we reconstructed hominoid phylogenetic trees from mitochondrial DNA using our new methods, and found that the levels of bootstrap support were significantly increased by the modified Tajima-Takezaki and by the modified least-squares method.

  1. Evolutionary Explanations of Eating Disorders

    Directory of Open Access Journals (Sweden)

    Igor Kardum

    2008-12-01

    Full Text Available This article reviews several most important evolutionary mechanisms that underlie eating disorders. The first part clarifies evolutionary foundations of mental disorders and various mechanisms leading to their development. In the second part selective pressures and evolved adaptations causing contemporary epidemic of obesity as well as differences in dietary regimes and life-style between modern humans and their ancestors are described. Concerning eating disorders, a number of current evolutionary explanations of anorexia nervosa are presented together with their main weaknesses. Evolutionary explanations of eating disorders based on the reproductive suppression hypothesis and its variants derived from kin selection theory and the model of parental manipulation were elaborated. The sexual competition hypothesis of eating disorder, adapted to flee famine hypothesis as well as explanation based on the concept of social attention holding power and the need to belonging were also explained. The importance of evolutionary theory in modern conceptualization and research of eating disorders is emphasized.

  2. How competition affects evolutionary rescue

    Science.gov (United States)

    Osmond, Matthew Miles; de Mazancourt, Claire

    2013-01-01

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

  3. Why count trees? Volunteer motivations and experiences with tree monitoring in New York City

    Science.gov (United States)

    Michelle L. Johnson; Lindsay K. Campbell; Erika S. Svendsen; Philip. Silva

    2018-01-01

    Volunteer programs can benefit from a deeper understanding of the motivations and experiences of people engaged in citizen science. Research to date has studied motivations of citizen scientists and tree-planting volunteers. Less work has focused on tree-monitoring volunteers, a role that is rapidly increasing as more cities involve the public in monitoring the urban...

  4. The Concept of Cosmic Tree in Armenian and Iranian Cosmologies

    Science.gov (United States)

    Farmanyan, S. V.; Mickaelian, A. M.

    2016-09-01

    Cosmic Tree or Tree of Life is a common motif in various world theologies, mythologies, and philosophies. In the present study we focus on Armenian and Iranian Cosmic Tree. In ancient Armenia, the Tree of Life (Կենաց Ծառ) is a religious symbol and is drawn on walls of fortresses and carved on the armour of warriors. According to ancient Armenians the center of the Universe is located at the crown of the tree or the column, which is the closest to the sky. We explore the idea of cosmic tree in the riddles, prayers, medieval rituals and miniatures. In the riddles, the tree mostly symbolizes the celestial phenomena (Sun, Stars, and Heavens), different units of time (years, months, weeks, days, and seasons), the people, Jerusalem, the apostles and Jesus Christ. The branches of the tree were equally divided on the right and left sides of the stem, with each branch having one leaf, and one leaf on the apex of the tree. Servants stood on each side of the tree with one of their hands up as if they are taking care of the tree. In pre-Islamic Persian mythology, the Gaokerena world tree is a large, sacred Haoma tree which bears all seeds. Ahriman created a frog to invade the tree and destroy it, aiming at preventing all trees from growing on the Earth. As a reaction, God (Ahura Mazda) created two kar fish staring at the frog to guard the tree. The concept of world tree in Persian Mythology is very closely related to the concept of the Tree of Life. Another related issue in ancient mythology of Iran is the myth of Mashya and Mashyane, two trees who were the ancestors of all living beings. This myth can be considered as a prototype for the creation myth where living beings are created by Gods (who have human forms). We come to the conclusion that in both cultures, no matter of the present different religions, the perception of Cosmic Tree is interconnected to the life on our planet and served as a metaphor for common descent in the evolutionary sense.

  5. Covering tree with stars

    DEFF Research Database (Denmark)

    Baumbach, Jan; Guo, Jian-Ying; Ibragimov, Rashid

    2013-01-01

    We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting...... tree is isomorphic to T? We prove that in the general setting, CST is NP-complete, which implies that the tree edit distance considered here is also NP-hard, even when both input trees having diameters bounded by 10. We also show that, when the number of distinct stars is bounded by a constant k, CTS...

  6. Covering tree with stars

    DEFF Research Database (Denmark)

    Baumbach, Jan; Guo, Jiong; Ibragimov, Rashid

    2015-01-01

    We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting...... tree is isomorphic to T? We prove that in the general setting, CST is NP-complete, which implies that the tree edit distance considered here is also NP-hard, even when both input trees having diameters bounded by 10. We also show that, when the number of distinct stars is bounded by a constant k, CTS...

  7. Evolutionary dynamics under interactive diversity

    Science.gov (United States)

    Su, Qi; Li, Aming; Wang, Long

    2017-10-01

    As evidenced by many cases in human societies, individuals often make different behavior decisions in different interactions, and adaptively adjust their behavior in changeable interactive scenarios. However, up to now, how such diverse interactive behavior affects cooperation dynamics has still remained unknown. Here we develop a general framework of interactive diversity, which models individuals’ separated behavior against distinct opponents and their adaptive adjustment in response to opponents’ strategies, to explore the evolution of cooperation. We find that interactive diversity enables individuals to reciprocate every single opponent, and thus sustains large-scale reciprocal interactions. Our work witnesses an impressive boost of cooperation for a notably extensive range of parameters and for all pairwise games. These results are robust against well-mixed and various networked populations, and against degree-normalized and cumulative payoff patterns. From the perspective of network dynamics, distinguished from individuals competing for nodes in most previous work, in this paper, the system evolves in the form of behavior disseminating along edges. We propose a theoretical method based on evolution of edges, which predicts well both the frequency of cooperation and the compact cooperation clusters. Our thorough investigation clarifies the positive role of interactive diversity in resolving social dilemmas and highlights the significance of understanding evolutionary dynamics from the viewpoint of edge dynamics.

  8. Flourishing: An Evolutionary Concept Analysis.

    Science.gov (United States)

    Agenor, Christine; Conner, Norma; Aroian, Karen

    2017-11-01

    Mental health is an important measure of public health (WHO, 2004); however, nursing practice and research continues to prioritize mental illness, rather than well-being (Wand, 2011). Flourishing is a recent concept in the field of well-being. The term has been used sparingly in nursing practice and research, and conceptual clarification is needed to promote comprehensive understanding of the phenomenon. The purpose of this study is to critically analyze flourishing, assess the maturity of the concept, and provide recommendations for future research, education, and practice. The concept of flourishing was analyzed using the evolutionary approach to concept analysis (Rodgers, 2000). A search for articles on flourishing within the context of well-being was conducted through CINAHL, MEDLINE, and PsycINFO. A sample of 32 articles and 1 book was reviewed. Data were reviewed for concept attributes, antecedents, consequences, surrogate terms and related concepts. Four models of flourishing were identified with six overlapping attributes: meaning, positive relationships, engagement, competence, positive emotion, and self-esteem. Limited longitudinal and predictive studies have been conducted, but there is evidence for several antecedents and outcomes of flourishing. Research is ongoing primarily in psychology and sociology and is lacking in other disciplines. The concept of flourishing is immature; however, evidence is building for related concepts. A lack of consistent terminology regarding flourishing prevents knowledge development of flourishing as a distinct concept. Further multidisciplinary research is needed to establish standard operational and conceptual definitions and develop effective interventions.

  9. PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

    Directory of Open Access Journals (Sweden)

    Pontarotti Pierre

    2009-09-01

    Full Text Available Abstract Background To effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be recognized within the trees, so that associated information can be extracted. Results Here, we present a new software library, PhyloPattern, for automating tree manipulations and analysis. PhyloPattern includes three main modules, which address essential tasks in high-throughput phylogenetic tree analysis: node annotation, pattern matching, and tree comparison. PhyloPattern thus allows the programmer to focus on: i the use of predefined or user defined annotation functions to perform immediate or deferred evaluation of node properties, ii the search for user-defined patterns in large phylogenetic trees, iii the pairwise comparison of trees by dynamically generating patterns from one tree and applying them to the other. Conclusion PhyloPattern greatly simplifies and accelerates the work of the computer scientist in the evolutionary biology field. The library has been used to automatically identify phylogenetic evidence for domain shuffling or gene loss events in the evolutionary histories of protein sequences. However any workflow that relies on phylogenetic tree analysis, could be automated with PhyloPattern.

  10. The Tree of Life on Earth

    Science.gov (United States)

    Stahl, D. A.

    2002-12-01

    Similar biochemistry and a common genetic code unite all life on earth and speak to a common origin. However, the nature of the "family tree," encompassing all life forms in a single genealogy, has only recently begun to be understood. It was only with the advent of molecular biology and methods for sequencing proteins and nucleic acids that ancient patterns of relationship could be discerned. The basis for establishing evolutionary relationships was found in the DNA, RNA, and proteins that determine each organism's biochemistry. Common sequence patterns in today's organisms - either in the order of amino acids in proteins or the four bases making up DNA or RNA - was recognized to derive from features of ancestral molecules preserved over evolutionary time. This approach to genealogical reconstruction, called molecular phylogeny, has led to the construction of a single "Tree of Life," and revealed that all of today's life (bacteria, protozoa, plants, animals, fungi) has emerged from three primary lines of descent. Properties of the most "deeply rooted" organisms then yield important clues about conditions on the early Earth. These analyses have also revealed that the greater part of the evolutionary diversity of our planet, represented by the microorganisms, has yet to be characterized.

  11. Molecular phylogeny of Myriapoda provides insights into evolutionary patterns of the mode in post-embryonic development

    Science.gov (United States)

    Miyazawa, Hideyuki; Ueda, Chiaki; Yahata, Kensuke; Su, Zhi-Hui

    2014-01-01

    Myriapoda, a subphylum of Arthropoda, comprises four classes, Chilopoda, Diplopoda, Pauropoda, and Symphyla. While recent molecular evidence has shown that Myriapoda is monophyletic, the internal phylogeny, which is pivotal for understanding the evolutionary history of myriapods, remains unresolved. Here we report the results of phylogenetic analyses and estimations of divergence time and ancestral state of myriapods. Phylogenetic analyses were performed based on three nuclear protein-coding genes determined from 19 myriapods representing the four classes (17 orders) and 11 outgroup species. The results revealed that Symphyla whose phylogenetic position has long been debated is the sister lineage to all other myriapods, and that the interordinal relationships within classes were consistent with traditional classifications. Ancestral state estimation based on the tree topology suggests that myriapods evolved from an ancestral state that was characterized by a hemianamorphic mode of post-embryonic development and had a relatively low number of body segments and legs. PMID:24535281

  12. Using Evolutionary Theory to Guide Mental Health Research.

    Science.gov (United States)

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

    2016-03-01

    Evolutionary approaches to medicine can shed light on the origins and etiology of disease. Such an approach may be especially useful in psychiatry, which frequently addresses conditions with heterogeneous presentation and unknown causes. We review several previous applications of evolutionary theory that highlight the ways in which psychiatric conditions may persist despite and because of natural selection. One lesson from the evolutionary approach is that some conditions currently classified as disorders (because they cause distress and impairment) may actually be caused by functioning adaptations operating "normally" (as designed by natural selection). Such conditions suggest an alternative illness model that may generate alternative intervention strategies. Thus, the evolutionary approach suggests that psychiatry should sometimes think differently about distress and impairment. The complexity of the human brain, including normal functioning and potential for dysfunctions, has developed over evolutionary time and has been shaped by natural selection. Understanding the evolutionary origins of psychiatric conditions is therefore a crucial component to a complete understanding of etiology. © The Author(s) 2016.

  13. Fast Image Texture Classification Using Decision Trees

    Science.gov (United States)

    Thompson, David R.

    2011-01-01

    Texture analysis would permit improved autonomous, onboard science data interpretation for adaptive navigation, sampling, and downlink decisions. These analyses would assist with terrain analysis and instrument placement in both macroscopic and microscopic image data products. Unfortunately, most state-of-the-art texture analysis demands computationally expensive convolutions of filters involving many floating-point operations. This makes them infeasible for radiation- hardened computers and spaceflight hardware. A new method approximates traditional texture classification of each image pixel with a fast decision-tree classifier. The classifier uses image features derived from simple filtering operations involving integer arithmetic. The texture analysis method is therefore amenable to implementation on FPGA (field-programmable gate array) hardware. Image features based on the "integral image" transform produce descriptive and efficient texture descriptors. Training the decision tree on a set of training data yields a classification scheme that produces reasonable approximations of optimal "texton" analysis at a fraction of the computational cost. A decision-tree learning algorithm employing the traditional k-means criterion of inter-cluster variance is used to learn tree structure from training data. The result is an efficient and accurate summary of surface morphology in images. This work is an evolutionary advance that unites several previous algorithms (k-means clustering, integral images, decision trees) and applies them to a new problem domain (morphology analysis for autonomous science during remote exploration). Advantages include order-of-magnitude improvements in runtime, feasibility for FPGA hardware, and significant improvements in texture classification accuracy.

  14. The human dark side: evolutionary psychology and original sin.

    Science.gov (United States)

    Lee, Joseph; Theol, M

    2014-04-01

    Human nature has a dark side, something important to religions. Evolutionary psychology has been used to illuminate the human shadow side, although as a discipline it has attracted criticism. This article seeks to examine the evolutionary psychology's understanding of human nature and to propose an unexpected dialog with an enduring account of human evil known as original sin. Two cases are briefly considered: murder and rape. To further the exchange, numerous theoretical and methodological criticisms and replies of evolutionary psychology are explored jointly with original sin. Evolutionary psychology can partner with original sin since they share some theoretical likenesses and together they offer insights into the nature of what it means to be human.

  15. Yule-generated trees constrained by node imbalance.

    Science.gov (United States)

    Disanto, Filippo; Schlizio, Anna; Wiehe, Thomas

    2013-11-01

    The Yule process generates a class of binary trees which is fundamental to population genetic models and other applications in evolutionary biology. In this paper, we introduce a family of sub-classes of ranked trees, called Ω-trees, which are characterized by imbalance of internal nodes. The degree of imbalance is defined by an integer 0 ≤ ω. For caterpillars, the extreme case of unbalanced trees, ω = 0. Under models of neutral evolution, for instance the Yule model, trees with small ω are unlikely to occur by chance. Indeed, imbalance can be a signature of permanent selection pressure, such as observable in the genealogies of certain pathogens. From a mathematical point of view it is interesting to observe that the space of Ω-trees maintains several statistical invariants although it is drastically reduced in size compared to the space of unconstrained Yule trees. Using generating functions, we study here some basic combinatorial properties of Ω-trees. We focus on the distribution of the number of subtrees with two leaves. We show that expectation and variance of this distribution match those for unconstrained trees already for very small values of ω. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Taxonomic colouring of phylogenetic trees of protein sequences

    Directory of Open Access Journals (Sweden)

    Andrade-Navarro Miguel A

    2006-02-01

    Full Text Available Abstract Background Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the species associated to those sequences. However, there is no online tool to facilitate this interpretation, for example, by automatically attaching taxonomic information to the nodes of a tree, or by interactively colouring the branches of a tree according to any combination of taxonomic divisions. This is especially problematic if the tree contains on the order of hundreds of sequences, which, given the accelerated increase in the size of the protein sequence databases, is a situation that is becoming common. Results We have developed PhyloView, a web based tool for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree. Provided that the tree contains SwissProt, SpTrembl, or GenBank protein identifiers, the tool retrieves the taxonomic information from the corresponding database. A colour picker displays a summary of the findings and allows the user to associate colours to the leaves of the tree according to any number of taxonomic partitions. Then, the colours are propagated to the branches of the tree. Conclusion PhyloView can be used at http://www.ogic.ca/projects/phyloview/. A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address.

  17. Evolutionary analysis of the TPP-dependent enzyme family.

    Science.gov (United States)

    Costelloe, Seán J; Ward, John M; Dalby, Paul A

    2008-01-01

    The evolutionary relationships of the thiamine pyrophosphate (TPP)-dependent family of enzymes was investigated by generation of a neighbor joining phylogenetic tree using sequences from the conserved pyrophosphate (PP) and pyrimidine (Pyr) binding domains of 17 TPP-dependent enzymes. This represents the most comprehensive analysis of TPP-dependent enzyme evolution to date. The phylogeny was shown to be robust by comparison with maximum likelihood trees generated for each individual enzyme and also broadly confirms the evolutionary history proposed recently from structural comparisons alone (Duggleby 2006). The phylogeny is most parsimonious with the TPP enzymes having arisen from a homotetramer which subsequently diverged into an alpha(2)beta(2) heterotetramer. The relationship between the PP- and Pyr-domains and the recruitment of additional protein domains was examined using the transketolase C-terminal (TKC)-domain as an example. This domain has been recruited by several members of the family and yet forms no part of the active site and has unknown function. Removal of the TKC-domain was found to increase activity toward beta-hydroxypyruvate and glycolaldehyde. Further truncations of the Pyr-domain yielded several variants with retained activity. This suggests that the influence of TKC-domain recruitment on the evolution of the mechanism and specificity of transketolase (TK) has been minor, and that the smallest functioning unit of TK comprises the PP- and Pyr-domains, whose evolutionary histories extend to all TPP-dependent enzymes.

  18. Trees and highway safety.

    Science.gov (United States)

    2011-03-01

    To minimize the severity of run-off-road collisions of vehicles with trees, departments of transportation (DOTs) : commonly establish clear zones for trees and other fixed objects. Caltrans clear zone on freeways is 30 feet : minimum (40 feet pref...

  19. Resolving the evolutionary relationships of molluscs with phylogenomic tools.

    Science.gov (United States)

    Smith, Stephen A; Wilson, Nerida G; Goetz, Freya E; Feehery, Caitlin; Andrade, Sónia C S; Rouse, Greg W; Giribet, Gonzalo; Dunn, Casey W

    2011-10-26

    Molluscs (snails, octopuses, clams and their relatives) have a great disparity of body plans and, among the animals, only arthropods surpass them in species number. This diversity has made Mollusca one of the best-studied groups of animals, yet their evolutionary relationships remain poorly resolved. Open questions have important implications for the origin of Mollusca and for morphological evolution within the group. These questions include whether the shell-less, vermiform aplacophoran molluscs diverged before the origin of the shelled molluscs (Conchifera) or lost their shells secondarily. Monoplacophorans were not included in molecular studies until recently, when it was proposed that they constitute a clade named Serialia together with Polyplacophora (chitons), reflecting the serial repetition of body organs in both groups. Attempts to understand the early evolution of molluscs become even more complex when considering the large diversity of Cambrian fossils. These can have multiple dorsal shell plates and sclerites or can be shell-less but with a typical molluscan radula and serially repeated gills. To better resolve the relationships among molluscs, we generated transcriptome data for 15 species that, in combination with existing data, represent for the first time all major molluscan groups. We analysed multiple data sets containing up to 216,402 sites and 1,185 gene regions using multiple models and methods. Our results support the clade Aculifera, containing the three molluscan groups with spicules but without true shells, and they support the monophyly of Conchifera. Monoplacophora is not the sister group to other Conchifera but to Cephalopoda. Strong support is found for a clade that comprises Scaphopoda (tusk shells), Gastropoda and Bivalvia, with most analyses placing Scaphopoda and Gastropoda as sister groups. This well-resolved tree will constitute a framework for further studies of mollusc evolution, development and anatomy.

  20. Evolutionary Tracks for Betelgeuse

    Science.gov (United States)

    Dolan, Michelle M.; Mathews, Grant J.; Lam, Doan Duc; Quynh Lan, Nguyen; Herczeg, Gregory J.; Dearborn, David S. P.

    2016-03-01

    We have constructed a series of nonrotating quasi-hydrostatic evolutionary models for the M2 Iab supergiant Betelgeuse (α Orionis). Our models are constrained by multiple observed values for the temperature, luminosity, surface composition, and mass loss for this star, along with the parallax distance and high-resolution imagery that determines its radius. We have then applied our best-fit models to analyze the observed variations in surface luminosity and the size of detected surface bright spots as the result of up-flowing convective material from regions of high temperature in the surface convective zone. We also attempt to explain the intermittently observed periodic variability in a simple radial linear adiabatic pulsation model. Based on the best fit to all observed data, we suggest a best progenitor mass estimate of {20}-3+5 {M}⊙ and a current age from the start of the zero-age main sequence of 8.0-8.5 Myr based on the observed ejected mass while on the giant branch.

  1. Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

    Directory of Open Access Journals (Sweden)

    Lespinet Olivier

    2007-11-01

    Full Text Available Abstract Background Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. Results We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing bona fide orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs, and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms. Conclusion The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene

  2. Social traits, social networks and evolutionary biology.

    Science.gov (United States)

    Fisher, D N; McAdam, A G

    2017-12-01

    effects) provides the potential to understand how entire networks of social interactions in populations influence phenotypes and predict how these traits may evolve. By theoretical integration of social network analysis and quantitative genetics, we hope to identify areas of compatibility and incompatibility and to direct research efforts towards the most promising areas. Continuing this synthesis could provide important insights into the evolution of traits expressed in a social context and the evolutionary consequences of complex and nuanced social phenotypes. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  3. Decision-Tree Program

    Science.gov (United States)

    Buntine, Wray

    1994-01-01

    IND computer program introduces Bayesian and Markov/maximum-likelihood (MML) methods and more-sophisticated methods of searching in growing trees. Produces more-accurate class-probability estimates important in applications like diagnosis. Provides range of features and styles with convenience for casual user, fine-tuning for advanced user or for those interested in research. Consists of four basic kinds of routines: data-manipulation, tree-generation, tree-testing, and tree-display. Written in C language.

  4. Industrial Applications of Evolutionary Algorithms

    CERN Document Server

    Sanchez, Ernesto; Tonda, Alberto

    2012-01-01

    This book is intended as a reference both for experienced users of evolutionary algorithms and for researchers that are beginning to approach these fascinating optimization techniques. Experienced users will find interesting details of real-world problems, and advice on solving issues related to fitness computation, modeling and setting appropriate parameters to reach optimal solutions. Beginners will find a thorough introduction to evolutionary computation, and a complete presentation of all evolutionary algorithms exploited to solve different problems. The book could fill the gap between the

  5. On the Existence of Evolutionary Learning Equilibriums

    Directory of Open Access Journals (Sweden)

    Masudul Alam Choudhury

    2011-12-01

    Full Text Available The usual kinds of Fixed-Point Theorems formalized on the existence of competitive equilibrium that explain much of economic theory at the core of economics can operate only on bounded and closed sets with convex mappings. But these conditions are hardly true of the real world of economic and financial complexities and perturbations. The category of learning sets explained by continuous fields of interactive, integrative and evolutionary behaviour caused by dynamic preferences at the individual and institutional and social levels cannot maintain the assumption of closed, bounded and convex sets. Thus learning sets and multi-system inter-temporal relations explained by pervasive complementarities and  participation between variables and entities, and evolution by learning, have evolutionary equilibriums. Such a study requires a new methodological approach. This paper formalizes such a methodology for evolutionary equilibriums in learning spaces. It briefly points out the universality of learning equilibriums in all mathematical structures. For a particular case though, the inter-systemic interdependence between sustainable development and ethics and economics in the specific understanding of learning domain is pointed out.

  6. Toward a general evolutionary theory of oncogenesis.

    Science.gov (United States)

    Ewald, Paul W; Swain Ewald, Holly A

    2013-01-01

    We propose an evolutionary framework, the barrier theory of cancer, which is based on the distinction between barriers to oncogenesis and restraints. Barriers are defined as mechanisms that prevent oncogenesis. Restraints, which are more numerous, inhibit but do not prevent oncogenesis. Processes that compromise barriers are essential causes of cancer; those that interfere with restraints are exacerbating causes. The barrier theory is built upon the three evolutionary processes involved in oncogenesis: natural selection acting on multicellular organisms to mold barriers and restraints, natural selection acting on infectious organisms to abrogate these protective mechanisms, and oncogenic selection which is responsible for the evolution of normal cells into cancerous cells. The barrier theory is presented as a first step toward the development of a general evolutionary theory of cancer. Its attributes and implications for intervention are compared with those of other major conceptual frameworks for understanding cancer: the clonal diversification model, the stem cell theory and the hallmarks of cancer. The barrier theory emphasizes the practical value of distinguishing between essential and exacerbating causes. It also stresses the importance of determining the scope of infectious causation of cancer, because individual pathogens can be responsible for multiple essential causes in infected cells.

  7. An evolutionary ecology of individual differences

    Science.gov (United States)

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

    2014-01-01

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

  8. Expanding from discrete Cartesian to permutation Gene-pool Optimal Mixing Evolutionary Algorithms

    NARCIS (Netherlands)

    P.A.N. Bosman (Peter); N.H. Luong (Ngoc Hoang); D. Thierens (Dirk)

    2016-01-01

    textabstractThe recently introduced Gene-pool Optimal Mixing Evolutionary Algorithm (GOMEA) family, which includes the Linkage Tree Genetic Algorithm (LTGA), has been shown to scale excellently on a variety of discrete, Cartesian-space, optimization problems. This paper shows that GOMEA can quite

  9. Winter Birch Trees

    Science.gov (United States)

    Sweeney, Debra; Rounds, Judy

    2011-01-01

    Trees are great inspiration for artists. Many art teachers find themselves inspired and maybe somewhat obsessed with the natural beauty and elegance of the lofty tree, and how it changes through the seasons. One such tree that grows in several regions and always looks magnificent, regardless of the time of year, is the birch. In this article, the…

  10. Total well dominated trees

    DEFF Research Database (Denmark)

    Finbow, Arthur; Frendrup, Allan; Vestergaard, Preben D.

    cardinality then G is a total well dominated graph. In this paper we study composition and decomposition of total well dominated trees. By a reversible process we prove that any total well dominated tree can both be reduced to and constructed from a family of three small trees....

  11. Macro tree transducers

    NARCIS (Netherlands)

    Engelfriet, Joost; Vogler, Heiko

    1985-01-01

    Macro tree transducers are a combination of top-down tree transducers and macro grammars. They serve as a model for syntax-directed semantics in which context information can be handled. In this paper the formal model of macro tree transducers is studied by investigating typical automata theoretical

  12. Tree communities of white-sand and terra-firme forests of the upper Rio Negro

    NARCIS (Netherlands)

    Stropp, J.; Sleen, van der J.P.; Assunção, P.A.; Silva, da A.L.; Steege, ter H.

    2011-01-01

    The high tree diversity and vast extent of Amazonian forests challenge our understanding of how tree species abundance and composition varies across this region. Information about these parameters, usually obtained from tree inventories plots, is essential for revealing patterns of tree diversity.

  13. TreePics: visualizing trees with pictures

    Directory of Open Access Journals (Sweden)

    Nicolas Puillandre

    2017-09-01

    Full Text Available While many programs are available to edit phylogenetic trees, associating pictures with branch tips in an efficient and automatic way is not an available option. Here, we present TreePics, a standalone software that uses a web browser to visualize phylogenetic trees in Newick format and that associates pictures (typically, pictures of the voucher specimens to the tip of each branch. Pictures are visualized as thumbnails and can be enlarged by a mouse rollover. Further, several pictures can be selected and displayed in a separate window for visual comparison. TreePics works either online or in a full standalone version, where it can display trees with several thousands of pictures (depending on the memory available. We argue that TreePics can be particularly useful in a preliminary stage of research, such as to quickly detect conflicts between a DNA-based phylogenetic tree and morphological variation, that may be due to contamination that needs to be removed prior to final analyses, or the presence of species complexes.

  14. Evolutionary Origin of Euglena.

    Science.gov (United States)

    Zakryś, Bożena; Milanowski, Rafał; Karnkowska, Anna

    2017-01-01

    Euglenids (Excavata, Discoba, Euglenozoa, Euglenida) is a group of free-living, single-celled flagellates living in the aquatic environments. The uniting and unique morphological feature of euglenids is the presence of a cell covering called the pellicle. The morphology and organization of the pellicle correlate well with the mode of nutrition and cell movement. Euglenids exhibit diverse modes of nutrition, including phagotrophy and photosynthesis. Photosynthetic species (Euglenophyceae) constitute a single subclade within euglenids. Their plastids embedded by three membranes arose as the result of a secondary endosymbiosis between phagotrophic eukaryovorous euglenid and the Pyramimonas-related green alga. Within photosynthetic euglenids three evolutionary lineages can be distinguished. The most basal lineage is formed by one mixotrophic species, Rapaza viridis. Other photosynthetic euglenids are split into two groups: predominantly marine Eutreptiales and freshwater Euglenales. Euglenales are divided into two families: Phacaceae, comprising three monophyletic genera (Discoplastis, Lepocinclis, Phacus) and Euglenaceae with seven monophyletic genera (Euglenaformis, Euglenaria, Colacium, Cryptoglena, Strombomonas, Trachelomonas, Monomorphina) and polyphyletic genus Euglena. For 150 years researchers have been studying Euglena based solely on morphological features what resulted in hundreds of descriptions of new taxa and many artificial intra-generic classification systems. In spite of the progress towards defining Euglena, it still remains polyphyletic and morphologically almost undistinguishable from members of the recently described genus Euglenaria; members of both genera have cells undergoing metaboly (dynamic changes in cell shape), large chloroplasts with pyrenoids and monomorphic paramylon grains. Model organisms Euglena gracilis Klebs, the species of choice for addressing fundamental questions in eukaryotic biochemistry, cell and molecular biology, is a

  15. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

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

  16. Evolutionary biology in biodiversity science, conservation, and policy: a call to action.

    Science.gov (United States)

    Hendry, Andrew P; Lohmann, Lúcia G; Conti, Elena; Cracraft, Joel; Crandall, Keith A; Faith, Daniel P; Häuser, Christoph; Joly, Carlos A; Kogure, Kazuhiro; Larigauderie, Anne; Magallón, Susana; Moritz, Craig; Tillier, Simon; Zardoya, Rafael; Prieur-Richard, Anne-Hélène; Walther, Bruno A; Yahara, Tetsukazu; Donoghue, Michael J

    2010-05-01

    Evolutionary biologists have long endeavored to document how many species exist on Earth, to understand the processes by which biodiversity waxes and wanes, to document and interpret spatial patterns of biodiversity, and to infer evolutionary relationships. Despite the great potential of this knowledge to improve biodiversity science, conservation, and policy, evolutionary biologists have generally devoted limited attention to these broader implications. Likewise, many workers in biodiversity science have underappreciated the fundamental relevance of evolutionary biology. The aim of this article is to summarize and illustrate some ways in which evolutionary biology is directly relevant. We do so in the context of four broad areas: (1) discovering and documenting biodiversity, (2) understanding the causes of diversification, (3) evaluating evolutionary responses to human disturbances, and (4) implications for ecological communities, ecosystems, and humans. We also introduce bioGENESIS, a new project within DIVERSITAS launched to explore the potential practical contributions of evolutionary biology. In addition to fostering the integration of evolutionary thinking into biodiversity science, bioGENESIS provides practical recommendations to policy makers for incorporating evolutionary perspectives into biodiversity agendas and conservation. We solicit your involvement in developing innovative ways of using evolutionary biology to better comprehend and stem the loss of biodiversity.

  17. Defining fitness in evolutionary models

    Indian Academy of Sciences (India)

    jgen/087/04/0339-0348. Keywords. fitness; invasion exponent; adaptive dynamics; game theory; Lyapunov exponent; invasibility; Malthusian parameter. Abstract. The analysis of evolutionary models requires an appropriate definition for fitness.

  18. Evolutionary Processes and Mental Deficiency

    Science.gov (United States)

    Spitz, Herman H.

    1973-01-01

    The author hypothesizes that central nervous system damage of deficiency associated with mental retardation affects primarily those cortical processes which developed at a late stage in man's evolutionary history. (Author)

  19. Evolutionary computation for reinforcement learning

    NARCIS (Netherlands)

    Whiteson, S.; Wiering, M.; van Otterlo, M.

    2012-01-01

    Algorithms for evolutionary computation, which simulate the process of natural selection to solve optimization problems, are an effective tool for discovering high-performing reinforcement-learning policies. Because they can automatically find good representations, handle continuous action spaces,

  20. Evolutionary computation for trading systems

    OpenAIRE

    Kaucic, Massimiliano

    2008-01-01

    2007/2008 Evolutionary computations, also called evolutionary algorithms, consist of several heuristics, which are able to solve optimization tasks by imitating some aspects of natural evolution. They may use different levels of abstraction, but they are always working on populations of possible solutions for a given task. The basic idea is that if only those individuals of a population which meet a certain selection criteria reproduce, while the remaining individuals die, the ...

  1. Freud: the first evolutionary psychologist?

    Science.gov (United States)

    LeCroy, D

    2000-04-01

    An evolutionary perspective on attachment theory and psychoanalytic theory brings these two fields together in interesting ways. Application of the evolutionary principle of parent-offspring conflict to attachment theory suggests that attachment styles represent context-sensitive, evolved (adaptive) behaviors. In addition, an emphasis on offspring counter-strategies to adult reproductive strategies leads to consideration of attachment styles as overt manifestations of psychodynamic mediating processes, including the defense mechanisms of repression and reaction formation.

  2. Ancestral trees for modeling stem cell lineages genetically rather than functionally: understanding mutation accumulation and distinguishing the restrictive cancer stem cell propagation theory and the unrestricted cell propagation theory of human tumorigenesis.

    Science.gov (United States)

    Shibata, Darryl K; Kern, Scott E

    2008-01-01

    Cancer stem cells either could be rare or common in tumors, constituting the major distinction between the two fundamentally opposed theoretical models of tumor progression: A newer and restrictive stem cell propagation model, in which the stem cells are a small and special minority of the tumor cells, and a standard older model, an unrestricted cell proliferation theory, in which many or most tumor cells are capable of indefinite generations of cell division. Stem cells of tumors are difficult to quantitate using functional assays, and the validity of the most common assays is seriously questioned. Nonetheless, stem cells are an essential component of any tumorigenesis model. Alternative approaches to studying tumor stem cells should be explored. Cell populations can be conceived of as having a genealogy, a relationship of cells to their ancestral lineage, from the zygote to the adult cells or neoplasms. Models using ancestral trees thus offer an anatomic and genetic means to "observe" stem cells independent of artificial conditions. Ancestral trees broaden our attention backward along a lineage, to the zygote stage, and thereby add insight into how the mutations of tumors accumulate. It is possible that a large fraction of mutations in a tumor originate from normal, endogenous, replication errors (nearly all being passenger mutations) occurring prior to the emergence of the first transformed cell. Trees can be constructed from experimental measurements - molecular clocks - of real human tissues and tumors. Detailed analysis of single-cell methylation patterns, heritable yet slightly plastic, now can provide this information in the necessary depth. Trees based on observations of molecular clocks may help us to distinguish between competing theories regarding the proliferative properties among cells of actual human tumors, to observe subtle and difficult phenomena such as the extinction of stem lineages, and to address the origins and rates of mutations in various

  3. The evolutionary approach to understand human low fertility phenomenon

    Science.gov (United States)

    Cernak, Jozef

    2017-05-01

    Is it possible to reverse the low total fertility rate (TFR) in the developed world? Using a hypothetical model of population we have analysed the decline of the TFR which have took place in the background of ongoing global economic changes, and a liberalization process after the end of the Cold War. These phenomena have affected more that 110 millions of inhabitants of Central Europe and the Baltics and approximately 80 millions of inhabitants in Germany. The model has features of complex and evolving system of interacting individuals, and it enables to investigate a broad spectrum of input factors on individual decisions to limit the offspring. In the case of the TFR global economy that will stimulate series of self-regulations of demographic processes and evolution toward the safe TFR > 2.1. The changes should stimulate more uniform spatial distribution of wealth, capital and usage. They will increase a number of self-sufficient and cooperative territories, to decrease the income inequality, to decrease labour and social mobilities. Societies should investigate the impacts of economic regulations and actions on the TFR trends in advance and take into account a biological nature of women more responsible.

  4. Understanding national and international safeguards: an evolutionary process

    International Nuclear Information System (INIS)

    Higinbotham, W.A.

    1983-01-01

    Domestic and international safeguards have been evolving and will continue to evolve. in the case of the United States, the concern was to protect the classified materials, at first. Then attention focussed on material accounting, then on measures to promptly detect theft by individuals with access, and later on physical protection to ward-off armed terrorists. The objective of the IAEA has always been to provide assurance that nuclear materials are not being diverted from the peaceful facilities that are under safeguards. The evolution has taken place in deciding how to provide this assurance, and in the definition of specific safeguards goals. In both cases the technology needed to meet the goals has improved due to R and D and to experience. A plea is made for more cooperation betwen those who develop and manage the policies, those who develop safeguards techniques, and those who are subject to national and IAEA safeguards. Some illustrations of the evolution of policies, inadequate coordination and general progress are given

  5. Understanding Life : The Evolutionary Dynamics of Complexity and Semiosis

    Science.gov (United States)

    Loeckenhoff, Helmut K.

    2010-11-01

    Post-Renaissance sciences created different cultures. To establish an epistemological base, Physics were separated from the Mental domain. Consciousness was excluded from science. Life Sciences were left in between e.g. LaMettrie's `man—machine' (1748) and 'vitalism' [e.g. Bergson 4]. Causative thinking versus intuitive arguing limited strictly comprehensive concepts. First ethology established a potential shared base for science, proclaiming the `biology paradigm' in the middle of the 20th century. Initially procured by Cybernetics and Systems sciences, `constructivist' models prepared a new view on human perception and thus also of scientific `objectivity when introducing the `observer'. In sequel Computer sciences triggered the ICT revolution. In turn ICT helped to develop Chaos and Complexity sciences, Non-linear Mathematics and its spin-offs in the formal sciences [Spencer-Brown 49] as e.g. (proto-)logics. Models of life systems, as e.g. Anticipatory Systems, integrated epistemology with mathematics and Anticipatory Computing [Dubois 11, 12, 13, 14] connecting them with Semiotics. Seminal ideas laid in the turn of the 19th to the 20th century [J. v. Uexküll 53] detected the co-action and co-evolvement of environments and life systems. Bio-Semiotics ascribed purpose, intent and meaning as essential qualities of life. The concepts of Systems Biology and Qualitative Research enriched and develop also anthropologies and humanities. Brain research added models of (higher) consciousness. An avant-garde is contemplating a science including consciousness as one additional base. New insights from the extended qualitative approach led to re-conciliation of basic assumptions of scientific inquiry, creating the `epistemological turn'. Paradigmatically, resting on macro- micro- and recently on nano-biology, evolution biology sired fresh scripts of evolution [W. Wieser 60,61]. Its results tie to hypotheses describing the emergence of language, of the human mind and of culture [e.g. R. Logan 34]. The different but related approaches are yet but loosely connected. Recent efforts search for a shared foundation e.g. in a set of Transdisciplinary base models [Loeckenhoff 30, 31]. The domain of pure mental constructions as ideologies/religions and spiritual phenomena will be implied.

  6. Evolutionary Information System Development

    DEFF Research Database (Denmark)

    Kristensen, Jan

    This paper offers advice to companies and professionals that implement e-commerce systems in business organizations. Implementing e-commerce systems is different from traditional IT implementation and thus requires a new set of tools and skills. The need for a novel approach is illustrated...... and necessary items that must be taken into account are pointed out by narrating two stories of e-commerce implementation processes in wholesale companies. The empirical evidence suggests the following: Managing the continued development on an operational level requires operational insight and understanding...... of business priorities. On a more theoretical level this suggests that we must revise our current understanding of systems development to cope....

  7. Evolutionary biology and life histories

    Directory of Open Access Journals (Sweden)

    Brown, C. R.

    2004-06-01

    Full Text Available The demographic processes that drive the spread of populations through environments and in turn determine the abundance of organisms are the same demographic processes that drive the spread of genes through populations and in turn determine gene frequencies and fitness. Conceptually, marked similarities exist in the dynamic processes underlying population ecology and those underlying evolutionary biology. Central to an understanding of both disciplines is life history and its component demographic rates, such as survival, fecundity, and age of first breeding, and biologists from both fields have a vested interest in good analytical machinery for the estimation and analysis of these demographic rates. In the EURING conferences, we have been striving since the mid 1980s to promote a quantitative understanding of demographic rates through interdisciplinary collaboration between ecologists and statisticians. From the ecological side, the principal impetus has come from population biology, and in particular from wildlife biology, but the importance of good quantitative insights into demographic processes has long been recognized by a number of evolutionary biologists (e.g., Nichols & Kendall, 1995; Clobert, 1995; Cooch et al., 2002. In organizing this session, we have aimed to create a forum for those committed to gaining the best possible understanding of evolutionary processes through the application of modern quantitative methods for the collection and interpretation of data on marked animal populations. Here we present a short overview of the material presented in the session on evolutionary biology and life histories. In a plenary talk, Brown & Brown (2004 explored how mark–recapture methods have allowed a better understanding of the evolution of group–living and alternative reproductive tactics in colonial cliff swallows (Petrochelidon pyrrhonota. By estimating the number of transient birds passing through colonies of different sizes, they

  8. Evolutionary adaptations: theoretical and practical implications for visual ergonomics.

    Science.gov (United States)

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

    2014-01-01

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

  9. The evolutionary paradox and the missing heritability of schizophrenia.

    Science.gov (United States)

    van Dongen, Jenny; Boomsma, Dorret I

    2013-03-01

    Schizophrenia is one of the most detrimental common psychiatric disorders, occurring at a prevalence of approximately 1%, and characterized by increased mortality and reduced reproduction, especially in men. The heritability has been estimated around 70% and the genome-wide association meta-analyses conducted by the Psychiatric Genomics Consortium have been successful at identifying an increasing number of risk loci. Various theories have been proposed to explain why genetic variants that predispose to schizophrenia persist in the population, despite the fitness reduction in affected individuals, a question known as the evolutionary paradox. In this review, we consider evolutionary perspectives of schizophrenia and of the empirical evidence that may support these perspectives. Proposed evolutionary explanations include balancing selection, fitness trade-offs, fluctuating environments, sexual selection, mutation-selection balance and genomic conflicts. We address the expectations about the genetic architecture of schizophrenia that are predicted by different evolutionary scenarios and discuss the implications for genetic studies. Several potential sources of "missing" heritability, including gene-environment interactions, epigenetic variation, and rare genetic variation are examined from an evolutionary perspective. A better understanding of evolutionary history may provide valuable clues to the genetic architecture of schizophrenia and other psychiatric disorders, which is highly relevant to genetic studies that aim to detect genetic risk variants. Copyright © 2013 Wiley Periodicals, Inc.

  10. Infinite populations and counterfactual frequencies in evolutionary theory.

    Science.gov (United States)

    Abrams, Marshall

    2006-06-01

    One finds intertwined with ideas at the core of evolutionary theory claims about frequencies in counterfactual and infinitely large populations of organisms, as well as in sets of populations of organisms. One also finds claims about frequencies in counterfactual and infinitely large populations--of events--at the core of an answer to a question concerning the foundations of evolutionary theory. The question is this: to what do the numerical probabilities found throughout evolutionary theory correspond? The answer in question says that evolutionary probabilities are 'hypothetical frequencies' (including what are sometimes called 'long-run frequencies' and 'long-run propensities'). In this paper, I review two arguments against hypothetical frequencies. The arguments have implications for the interpretation of evolutionary probabilities, but more importantly, they seem to raise problems for biologists' claims about frequencies in counterfactual or infinite populations of organisms and sets of populations of organisms. I argue that when properly understood, claims about frequencies in large and infinite populations of organisms and sets of populations are not threatened by the arguments. Seeing why gives us a clearer understanding of the nature of counterfactual and infinite population claims and probability in evolutionary theory.

  11. Domestication as a model system for the extended evolutionary synthesis.

    Science.gov (United States)

    Zeder, Melinda A

    2017-10-06

    One of the challenges in evaluating arguments for extending the conceptual framework of evolutionary biology involves the identification of a tractable model system that allows for an assessment of the core assumptions of the extended evolutionary synthesis (EES). The domestication of plants and animals by humans provides one such case study opportunity. Here, I consider domestication as a model system for exploring major tenets of the EES. First I discuss the novel insights that niche construction theory (NCT, one of the pillars of the EES) provides into the domestication processes, particularly as they relate to five key areas: coevolution, evolvability, ecological inheritance, cooperation and the pace of evolutionary change. This discussion is next used to frame testable predictions about initial domestication of plants and animals that contrast with those grounded in standard evolutionary theory, demonstrating how these predictions might be tested in multiple regions where initial domestication took place. I then turn to a broader consideration of how domestication provides a model case study consideration of the different ways in which the core assumptions of the EES strengthen and expand our understanding of evolution, including reciprocal causation, developmental processes as drivers of evolutionary change, inclusive inheritance, and the tempo and rate of evolutionary change.

  12. Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.

    Science.gov (United States)

    Kordi, Misagh; Bansal, Mukul S

    2017-06-01

    Duplication-Transfer-Loss (DTL) reconciliation is a powerful method for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation seeks to reconcile gene trees with species trees by postulating speciation, duplication, transfer, and loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. In practice, however, gene trees are often non-binary due to uncertainty in the gene tree topologies, and DTL reconciliation with non-binary gene trees is known to be NP-hard. In this paper, we present the first exact algorithms for DTL reconciliation with non-binary gene trees. Specifically, we (i) show that the DTL reconciliation problem for non-binary gene trees is fixed-parameter tractable in the maximum degree of the gene tree, (ii) present an exponential-time, but in-practice efficient, algorithm to track and enumerate all optimal binary resolutions of a non-binary input gene tree, and (iii) apply our algorithms to a large empirical data set of over 4700 gene trees from 100 species to study the impact of gene tree uncertainty on DTL-reconciliation and to demonstrate the applicability and utility of our algorithms. The new techniques and algorithms introduced in this paper will help biologists avoid incorrect evolutionary inferences caused by gene tree uncertainty.

  13. Reconstruction of certain phylogenetic networks from their tree-average distances.

    Science.gov (United States)

    Willson, Stephen J

    2013-10-01

    Trees are commonly utilized to describe the evolutionary history of a collection of biological species, in which case the trees are called phylogenetic trees. Often these are reconstructed from data by making use of distances between extant species corresponding to the leaves of the tree. Because of increased recognition of the possibility of hybridization events, more attention is being given to the use of phylogenetic networks that are not necessarily trees. This paper describes the reconstruction of certain such networks from the tree-average distances between the leaves. For a certain class of phylogenetic networks, a polynomial-time method is presented to reconstruct the network from the tree-average distances. The method is proved to work if there is a single reticulation cycle.

  14. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree.

    Science.gov (United States)

    Karafet, Tatiana M; Mendez, Fernando L; Meilerman, Monica B; Underhill, Peter A; Zegura, Stephen L; Hammer, Michael F

    2008-05-01

    Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

  15. Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae).

    Science.gov (United States)

    Daïnou, K; Mahy, G; Duminil, J; Dick, C W; Doucet, J-L; Donkpégan, A S L; Pluijgers, M; Sinsin, B; Lejeune, P; Hardy, O J

    2014-07-01

    The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically.

  16. Grand challenges in evolutionary and population genetics: The importance of integrating epigenetics, genomics, modeling, and experimentation

    Science.gov (United States)

    Samuel A. Cushman

    2014-01-01

    This is a time of explosive growth in the fields of evolutionary and population genetics, with whole genome sequencing and bioinformatics driving a transformative paradigm shift (Morozova and Marra, 2008). At the same time, advances in epigenetics are thoroughly transforming our understanding of evolutionary processes and their implications for populations, species and...

  17. Biochemistry and evolutionary biology: Two disciplines that need ...

    Indian Academy of Sciences (India)

    Biochemical information has been crucial for the development of evolutionary biology. On the one hand, the sequence information now appearing is producing a huge increase in the amount of data available for phylogenetic analysis; on the other hand, and perhaps more fundamentally, it allows understanding of the ...

  18. Contemporary climate change and terrestrial invertebrates : Evolutionary versus plastic changes

    NARCIS (Netherlands)

    Schilthuizen, Menno; Kellermann, Vanessa

    To forecast the responses of species to future climate change, an understanding of the ability of species to adapt to long-term shifts in temperature is crucial. We present a review on evolutionary adaptation and phenotypic plasticity of temperature-related traits in terrestrial invertebrates. The

  19. Polemics and Synthesis: Ernst Mayr and Evolutionary Biology

    Indian Academy of Sciences (India)

    A hundred years is but an instant in evolutionary time; however during his life that spanned a century, Ernst Mayr (1904-2005) made outstanding contributions to our understanding of the pat- tern and process of evolution. An ornithologist and systematist by training, Mayr embraced Darwinism and championed the cause of.

  20. Can Evolutionary Principles Explain Patterns of Family Violence?

    Science.gov (United States)

    Archer, John

    2013-01-01

    The article's aim is to evaluate the application of the evolutionary principles of kin selection, reproductive value, and resource holding power to the understanding of family violence. The principles are described in relation to specific predictions and the mechanisms underlying these. Predictions are evaluated for physical violence perpetrated…

  1. Evolutionary responses to climate change in a range expanding plant

    NARCIS (Netherlands)

    Macel, Mirka; Dostálek, Tomás; Esch, Sonja; Bucharová, Anna; van Dam, Nicole M.; Tielbörger, Katja; Verhoeven, Koen J. F.; Münzbergová, Zuzana

    2017-01-01

    To understand the biological effects of climate change, it is essential to take into account species' evolutionary responses to their changing environments. Ongoing climate change is resulting in species shifting their geographical distribution ranges poleward. We tested whether a successful range

  2. Evolutionary inevitability of sexual antagonism.

    Science.gov (United States)

    Connallon, Tim; Clark, Andrew G

    2014-02-07

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

  3. Measuring (bio)physical tree properties using accelerometers

    Science.gov (United States)

    van Emmerik, Tim; Steele-Dunne, Susan; Hut, Rolf; Gentine, Pierre; Selker, John; van de Giesen, Nick

    2017-04-01

    Trees play a crucial role in the water, carbon and nitrogen cycle on local, regional and global scales. Understanding the exchange of heat, water, and CO2 between trees and the atmosphere is important to assess the impact of drought, deforestation and climate change. Unfortunately, ground measurements of tree dynamics are often expensive, or difficult due to challenging environments. We demonstrate the potential of measuring (bio)physical properties of trees using robust and affordable acceleration sensors. Tree sway is dependent on e.g. mass and wind energy absorption of the tree. By measuring tree acceleration we can relate the tree motion to external loads (e.g. precipitation), and tree (bio)physical properties (e.g. mass). Using five months of acceleration data of 19 trees in the Brazilian Amazon, we show that the frequency spectrum of tree sway is related to mass, precipitation, and canopy drag. This presentation aims to show the concept of using accelerometers to measure tree dynamics, and we acknowledge that the presented example applications is not an exhaustive list. Further analyses are the scope of current research, and we hope to inspire others to explore additional applications.

  4. The valuative tree

    CERN Document Server

    Favre, Charles

    2004-01-01

    This volume is devoted to a beautiful object, called the valuative tree and designed as a powerful tool for the study of singularities in two complex dimensions. Its intricate yet manageable structure can be analyzed by both algebraic and geometric means. Many types of singularities, including those of curves, ideals, and plurisubharmonic functions, can be encoded in terms of positive measures on the valuative tree. The construction of these measures uses a natural tree Laplace operator of independent interest.

  5. Evolution in health and medicine Sackler colloquium: Making evolutionary biology a basic science for medicine.

    Science.gov (United States)

    Nesse, Randolph M; Bergstrom, Carl T; Ellison, Peter T; Flier, Jeffrey S; Gluckman, Peter; Govindaraju, Diddahally R; Niethammer, Dietrich; Omenn, Gilbert S; Perlman, Robert L; Schwartz, Mark D; Thomas, Mark G; Stearns, Stephen C; Valle, David

    2010-01-26

    New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease.

  6. National assessment of Tree City USA participation

    Science.gov (United States)

    Tree City USA is a national program that recognizes municipal commitment to community forestry. In return for meeting program requirements, Tree City USA participants expect social, economic, and/or environmental benefits. Understanding the geographic distribution and socioeconomic characteristics of Tree City USA communities at the national scale can offer insights into the motivations or barriers to program participation, and provide context for community forestry research at finer scales. In this study, researchers assessed patterns in Tree City USA participation for all U.S. communities with more than 2,500 people according to geography, community population size, and socioeconomic characteristics, such as income, education, and race. Nationally, 23.5% of communities studied were Tree City USA participants, and this accounted for 53.9% of the total population in these communities. Tree City USA participation rates varied substantially by U.S. region, but in each region participation rates were higher in larger communities, and long-term participants tended to be larger communities than more recent enrollees. In logistic regression models, owner occupancy rates were significant negative predictors of Tree City USA participation, education and percent white population were positive predictors in many U.S. regions, and inconsistent patterns were observed for income and population age. The findings indicate that communities with smaller populations, lower educat

  7. Urban tree effects on soil organic carbon.

    Directory of Open Access Journals (Sweden)

    Jill L Edmondson

    Full Text Available Urban trees sequester carbon into biomass and provide many ecosystem service benefits aboveground leading to worldwide tree planting schemes. Since soils hold ∼75% of ecosystem organic carbon, understanding the effect of urban trees on soil organic carbon (SOC and soil properties that underpin belowground ecosystem services is vital. We use an observational study to investigate effects of three important tree genera and mixed-species woodlands on soil properties (to 1 m depth compared to adjacent urban grasslands. Aboveground biomass and belowground ecosystem service provision by urban trees are found not to be directly coupled. Indeed, SOC enhancement relative to urban grasslands is genus-specific being highest under Fraxinus excelsior and Acer spp., but similar to grasslands under Quercus robur and mixed woodland. Tree cover type does not influence soil bulk density or C∶N ratio, properties which indicate the ability of soils to provide regulating ecosystem services such as nutrient cycling and flood mitigation. The trends observed in this study suggest that genus selection is important to maximise long-term SOC storage under urban trees, but emerging threats from genus-specific pathogens must also be considered.

  8. A theory of game trees, based on solution trees

    NARCIS (Netherlands)

    W.H.L.M. Pijls (Wim); A. de Bruin (Arie); A. Plaat (Aske)

    1996-01-01

    textabstractIn this paper a complete theory of game tree algorithms is presented, entirely based upon the notion of a solution tree. Two types of solution trees are distinguished: max and min solution trees respectively. We show that most game tree algorithms construct a superposition of a max and a

  9. Phosphorus nutrition of mycorrhizal trees.

    Science.gov (United States)

    Plassard, C; Dell, B

    2010-09-01

    Globally, phosphorus (P) limits productivity of trees in many forests and plantations especially in highly weathered, acidic or calcareous profiles. Most trees form mycorrhizal associations which are prevalent in the organic and mineral soil horizons. This review critically examines mechanisms that enhance the acquisition of P by tree roots. Mycorrhizal roots have a greater capacity to take up phosphate (Pi) from the soil solution than non-mycorrhizal root tips. Factors that contribute to this include the extent of extraradical hyphal penetration of soil and the physiology and biochemistry of the fungal/soil and fungal/plant interfaces. Ectomycorrhizal (ECM) trees are likely to benefit from association with basidiomycetes that possess several high-affinity Pi transporters that are expressed in extraradical hyphae and whose expression is enhanced by P deficiency. To understand fully the role of these putative transporters in the symbiosis, data regarding their localization, Pi transport capacities and regulation are required. Some ECM fungi are able to effect release of Pi from insoluble mineral P through excretion of low-molecular-weight organic anions such as oxalate, but the relative contribution of insoluble P dissolution in situ remains to be quantified. How the production of oxalate is regulated by nitrogen remains a key question to be answered. Lastly, phosphatase release from mycorrhizas is likely to play a significant role in the acquisition of Pi from labile organic forms of P (Po). As labile forms of Po can constitute the major fraction of the total P in some tropical and temperate soils, a greater understanding of the forms of Po available to the phosphatases is warranted.

  10. D2-tree

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Sioutas, Spyros; Pantazos, Kostas

    2015-01-01

    We present a new overlay, called the Deterministic Decentralized tree (D2-tree). The D2-tree compares favorably to other overlays for the following reasons: (a) it provides matching and better complexities, which are deterministic for the supported operations; (b) the management of nodes (peers......-balancing scheme of elements into nodes is deterministic and general enough to be applied to other hierarchical tree-based overlays. This load-balancing mechanism is based on an innovative lazy weight-balancing mechanism, which is interesting in its own right....

  11. Morocco - Fruit Tree Productivity

    Data.gov (United States)

    Millennium Challenge Corporation — Date Tree Irrigation Project: The specific objectives of this evaluation are threefold: - Performance evaluation of project activities, like the mid-term evaluation,...

  12. The evolutionary psychology of hunger.

    Science.gov (United States)

    Al-Shawaf, Laith

    2016-10-01

    An evolutionary psychological perspective suggests that emotions can be understood as coordinating mechanisms whose job is to regulate various psychological and physiological programs in the service of solving an adaptive problem. This paper suggests that it may also be fruitful to approach hunger from this coordinating mechanism perspective. To this end, I put forward an evolutionary task analysis of hunger, generating novel a priori hypotheses about the coordinating effects of hunger on psychological processes such as perception, attention, categorization, and memory. This approach appears empirically fruitful in that it yields a bounty of testable new hypotheses. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Evolutionary Aesthetics and Print Advertising

    Directory of Open Access Journals (Sweden)

    Kamil Luczaj

    2015-06-01

    Full Text Available The article analyzes the extent to which predictions based on the theory of evolutionary aesthetics are utilized by the advertising industry. The purpose of a comprehensive content analysis of print advertising is to determine whether the items indicated by evolutionists such as animals, flowers, certain types of landscapes, beautiful humans, and some colors are part of real advertising strategies. This article has shown that many evolutionary hypotheses (although not all of them are supported by empirical data. Along with these hypotheses, some inferences from Bourdieu’s cultural capital theory were tested. It turned out that advertising uses both biological schemata and cultural patterns to make an image more likable.

  14. Diversity-Guided Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    2002-01-01

    Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few...... algorithms have used a measure to guide the search. The diversity-guided evolutionary algorithm (DGEA) uses the wellknown distance-to-average-point measure to alternate between phases of exploration (mutation) and phases of exploitation (recombination and selection). The DGEA showed remarkable results...

  15. Applied evolutionary theories for engineering of secondary metabolic pathways.

    Science.gov (United States)

    Bachmann, Brian O

    2016-12-01

    An expanded definition of 'secondary metabolism' is emerging. Once the exclusive provenance of naturally occurring organisms, evolved over geological time scales, secondary metabolism increasingly encompasses molecules generated via human engineered biocatalysts and biosynthetic pathways. Many of the tools and strategies for enzyme and pathway engineering can find origins in evolutionary theories. This perspective presents an overview of selected proposed evolutionary strategies in the context of engineering secondary metabolism. In addition to the wealth of biocatalysts provided via secondary metabolic pathways, improving the understanding of biosynthetic pathway evolution will provide rich resources for methods to adapt to applied laboratory evolution. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Phylogenetic tests for evolutionary innovation: the problematic link between key innovations and exceptional diversification.

    Science.gov (United States)

    Rabosky, Daniel L

    2017-12-05

    Evolutionary innovation contributes to the spectacular diversity of species and phenotypes across the tree of life. 'Key innovations' are widely operationalized within evolutionary biology as traits that facilitate increased diversification rates, such that lineages bearing the traits ultimately contain more species than closely related lineages lacking the focal trait. In this article, I briefly review the inference, analysis and interpretation of evolutionary innovation on phylogenetic trees. I argue that differential rates of lineage diversification should not be used as the basis for key innovation tests, despite the statistical tractability of such approaches. Under traditional interpretations of the macroevolutionary 'adaptive zone', we should not necessarily expect key innovations to confer faster diversification rates upon lineages that possess them relative to their extant sister clades. I suggest that a key innovation is a trait that allows a lineage to interact with the environment in a fundamentally different way and which, as a result, increases the total diversification-but not necessarily the diversification rate-of the parent clade. Considered alone, branching patterns in phylogenetic trees are poorly suited to the inference of evolutionary innovation due to their inherently low information content with respect to the processes that produce them. However, phylogenies may be important for identifying transformational shifts in ecological and morphological space that are characteristic of innovation at the macroevolutionary scale.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'. © 2017 The Author(s).

  17. Allometric Convergence in Savanna Trees and Implications for the Use of Plant Scaling Models in Variable Ecosystems

    Science.gov (United States)

    Tredennick, Andrew T.; Bentley, Lisa Patrick; Hanan, Niall P.

    2013-01-01

    Theoretical models of allometric scaling provide frameworks for understanding and predicting how and why the morphology and function of organisms vary with scale. It remains unclear, however, if the predictions of ‘universal’ scaling models for vascular plants hold across diverse species in variable environments. Phenomena such as competition and disturbance may drive allometric scaling relationships away from theoretical predictions based on an optimized tree. Here, we use a hierarchical Bayesian approach to calculate tree-specific, species-specific, and ‘global’ (i.e. interspecific) scaling exponents for several allometric relationships using tree- and branch-level data harvested from three savanna sites across a rainfall gradient in Mali, West Africa. We use these exponents to provide a rigorous test of three plant scaling models (Metabolic Scaling Theory (MST), Geometric Similarity, and Stress Similarity) in savanna systems. For the allometric relationships we evaluated (diameter vs. length, aboveground mass, stem mass, and leaf mass) the empirically calculated exponents broadly overlapped among species from diverse environments, except for the scaling exponents for length, which increased with tree cover and density. When we compare empirical scaling exponents to the theoretical predictions from the three models we find MST predictions are most consistent with our observed allometries. In those situations where observations are inconsistent with MST we find that departure from theory corresponds with expected tradeoffs related to disturbance and competitive interactions. We hypothesize savanna trees have greater length-scaling exponents than predicted by MST due to an evolutionary tradeoff between fire escape and optimization of mechanical stability and internal resource transport. Future research on the drivers of systematic allometric variation could reconcile the differences between observed scaling relationships in variable ecosystems and those

  18. Allometric convergence in savanna trees and implications for the use of plant scaling models in variable ecosystems.

    Directory of Open Access Journals (Sweden)

    Andrew T Tredennick

    Full Text Available Theoretical models of allometric scaling provide frameworks for understanding and predicting how and why the morphology and function of organisms vary with scale. It remains unclear, however, if the predictions of 'universal' scaling models for vascular plants hold across diverse species in variable environments. Phenomena such as competition and disturbance may drive allometric scaling relationships away from theoretical predictions based on an optimized tree. Here, we use a hierarchical Bayesian approach to calculate tree-specific, species-specific, and 'global' (i.e. interspecific scaling exponents for several allometric relationships using tree- and branch-level data harvested from three savanna sites across a rainfall gradient in Mali, West Africa. We use these exponents to provide a rigorous test of three plant scaling models (Metabolic Scaling Theory (MST, Geometric Similarity, and Stress Similarity in savanna systems. For the allometric relationships we evaluated (diameter vs. length, aboveground mass, stem mass, and leaf mass the empirically calculated exponents broadly overlapped among species from diverse environments, except for the scaling exponents for length, which increased with tree cover and density. When we compare empirical scaling exponents to the theoretical predictions from the three models we find MST predictions are most consistent with our observed allometries. In those situations where observations are inconsistent with MST we find that departure from theory corresponds with expected tradeoffs related to disturbance and competitive interactions. We hypothesize savanna trees have greater length-scaling exponents than predicted by MST due to an evolutionary tradeoff between fire escape and optimization of mechanical stability and internal resource transport. Future research on the drivers of systematic allometric variation could reconcile the differences between observed scaling relationships in variable ecosystems and

  19. Are trees long-lived?

    Science.gov (United States)

    Kevin T. Smith

    2009-01-01

    Trees and tree care can capture the best of people's motivations and intentions. Trees are living memorials that help communities heal at sites of national tragedy, such as Oklahoma City and the World Trade Center. We mark the places of important historical events by the trees that grew nearby even if the original tree, such as the Charter Oak in Connecticut or...

  20. Evolutionary divergence of chloroplast FAD synthetase proteins

    Directory of Open Access Journals (Sweden)

    Arilla-Luna Sonia

    2010-10-01

    Full Text Available Abstract Background Flavin adenine dinucleotide synthetases (FADSs - a group of bifunctional enzymes that carry out the dual functions of riboflavin phosphorylation to produce flavin mononucleotide (FMN and its subsequent adenylation to generate FAD in most prokaryotes - were studied in plants in terms of sequence, structure and evolutionary history. Results Using a variety of bioinformatics methods we have found that FADS enzymes localized to the chloroplasts, which we term as plant-like FADS proteins, are distributed across a variety of green plant lineages and constitute a divergent protein family clearly of cyanobacterial origin. The C-terminal module of these enzymes does not contain the typical riboflavin kinase active site sequence, while the N-terminal module is broadly conserved. These results agree with a previous work reported by Sandoval et al. in 2008. Furthermore, our observations and preliminary experimental results indicate that the C-terminus of plant-like FADS proteins may contain a catalytic activity, but different to that of their prokaryotic counterparts. In fact, homology models predict that plant-specific conserved residues constitute a distinct active site in the C-terminus. Conclusions A structure-based sequence alignment and an in-depth evolutionary survey of FADS proteins, thought to be crucial in plant metabolism, are reported, which will be essential for the correct annotation of plant genomes and further structural and functional studies. This work is a contribution to our understanding of the evolutionary history of plant-like FADS enzymes, which constitute a new family of FADS proteins whose C-terminal module might be involved in a distinct catalytic activity.

  1. Differential effects of landscape-level environmental features on genetic structure in three codistributed tree species in Central America.

    Science.gov (United States)

    Poelchau, Monica F; Hamrick, J L

    2012-10-01

    Landscape genetic studies use spatially explicit population genetic information to determine the physical and environmental causes of population genetic structure on regional scales. Comparative studies that identify common barriers to gene flow across multiple species within a community are important to both understand the evolutionary trajectories of populations and prioritize habitat conservation. Here, we use a comparative landscape genetic approach to ask whether gradients in temperature or precipitation seasonality structure genetic variation across three codistributed tree species in Central America, or whether a simpler (geographic distance) or more complex, species-specific environmental niche model is necessary to individually explain population genetic structure. Using descriptive statistics and causal modelling, we find that different factors best explain genetic distance in each of the three species: environmental niche distance in Bursera simaruba, geographic distance in Ficus insipida and historical barriers to gene flow or cryptic reproductive barriers for Brosimum alicastrum. This study confirms suggestions from previous studies of Central American tree species that imply that population genetic structure of trees in this region is determined by complex interactions of both historical and current barriers to gene flow. © 2012 Blackwell Publishing Ltd.

  2. GM trees with increased resistance to herbivores: trait efficiency and their potential to promote tree growth

    Directory of Open Access Journals (Sweden)

    Joakim eHjältén

    2015-05-01

    Full Text Available Climate change, as well as a more intensive forestry, is expected to increase the risk of damage by pests and pathogens on trees, which can already be a severe problem in tree plantations. Recent development of biotechnology theoretically allows for resistance enhancement that could help reduce these risks but we still lack a comprehensive understanding of benefits and tradeoffs with pest resistant GM (genetically modified trees. We synthesized the current knowledge on the effectiveness of GM forest trees with increased resistance to herbivores. There is ample evidence that induction of exogenous Bacillus thuringiensis genes reduce performance of target pests whereas upregulation of endogenous resistance traits e.g. phenolics, generates variable results. Our review identified very few studies estimating the realized benefits in tree growth of GM trees in the field. This is concerning as the realized benefit with insect resistant GM plants seems to be context-dependent and likely manifested only if herbivore pressure is sufficiently high. Future studies of secondary pest species and resistance evolution in pest to GM trees should be prioritized. But most importantly we need more long-term field tests to evaluate the benefits and risks with pest resistant GM trees.

  3. Decision Tree Phytoremediation

    Science.gov (United States)

    1999-12-01

    8 2.4 Irrigation, Agronomic Inputs, and...documents will provide the reader in-depth background on the science and engineering mechanisms of phytoremediation. Using the decision tree and the...ITRC – Phytoremediation Decision Tree December 1999 8 • Contaminant levels • Plant selection • Treatability • Irrigation, agronomic

  4. Structural Equation Model Trees

    Science.gov (United States)

    Brandmaier, Andreas M.; von Oertzen, Timo; McArdle, John J.; Lindenberger, Ulman

    2013-01-01

    In the behavioral and social sciences, structural equation models (SEMs) have become widely accepted as a modeling tool for the relation between latent and observed variables. SEMs can be seen as a unification of several multivariate analysis techniques. SEM Trees combine the strengths of SEMs and the decision tree paradigm by building tree…

  5. Uncovering dynamic fault trees

    NARCIS (Netherlands)

    Junges, Sebastian; Guck, Dennis; Katoen, Joost P.; Stoelinga, Mariëlle Ida Antoinette

    Fault tree analysis is a widespread industry standard for assessing system reliability. Standard (static) fault trees model the failure behaviour of systems in dependence of their component failures. To overcome their limited expressive power, common dependability patterns, such as spare management,

  6. Matching Subsequences in Trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li

    2009-01-01

    Given two rooted, labeled trees P and T the tree path subsequence problem is to determine which paths in P are subsequences of which paths in T. Here a path begins at the root and ends at a leaf. In this paper we propose this problem as a useful query primitive for XML data, and provide new...

  7. Individual tree control

    Science.gov (United States)

    Harvey A. Holt

    1989-01-01

    Controlling individual unwanted trees in forest stands is a readily accepted method for improving the value of future harvests. The practice is especially important in mixed hardwood forests where species differ considerably in value and within species individual trees differ in quality. Individual stem control is a mechanical or chemical weeding operation that...

  8. Trees and Climate Change

    OpenAIRE

    Dettenmaier, Megan; Kuhns, Michael; Unger, Bethany; McAvoy, Darren

    2017-01-01

    This fact sheet describes the complex relationship between forests and climate change based on current research. It explains ways that trees can mitigate some of the risks associated with climate change. It details the impacts that forests are having on the changing climate and discuss specific ways that trees can be used to reduce or counter carbon emissions directly and indirectly.

  9. The tree BVOC index

    Science.gov (United States)

    J.R. Simpson; E.G. McPherson

    2011-01-01

    Urban trees can produce a number of benefits, among them improved air quality. Biogenic volatile organic compounds (BVOCs) emitted by some species are ozone precursors. Modifying future tree planting to favor lower-emitting species can reduce these emissions and aid air management districts in meeting federally mandated emissions reductions for these compounds. Changes...

  10. Environment determines evolutionary trajectory in a constrained phenotypic space.

    Science.gov (United States)

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

    2017-03-27

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

  11. Buried Treasure: Evolutionary Perspectives on Microbial Iron Piracy.

    Science.gov (United States)

    Barber, Matthew F; Elde, Nels C

    2015-11-01

    Host-pathogen interactions provide valuable systems for the study of evolutionary genetics and natural selection. The sequestration of essential iron has emerged as a crucial innate defense system termed nutritional immunity, leading pathogens to evolve mechanisms of 'iron piracy' to scavenge this metal from host proteins. This battle for iron carries numerous consequences not only for host-pathogen evolution but also microbial community interactions. Here we highlight recent and potential future areas of investigation on the evolutionary implications of microbial iron piracy in relation to molecular arms races, host range, competition, and virulence. Applying evolutionary genetic approaches to the study of microbial iron acquisition could also provide new inroads for understanding and combating infectious disease. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Evolutionary systems biology: what it is and why it matters.

    Science.gov (United States)

    Soyer, Orkun S; O'Malley, Maureen A

    2013-08-01

    Evolutionary systems biology (ESB) is a rapidly growing integrative approach that has the core aim of generating mechanistic and evolutionary understanding of genotype-phenotype relationships at multiple levels. ESB's more specific objectives include extending knowledge gained from model organisms to non-model organisms, predicting the effects of mutations, and defining the core network structures and dynamics that have evolved to cause particular intracellular and intercellular responses. By combining mathematical, molecular, and cellular approaches to evolution, ESB adds new insights and methods to the modern evolutionary synthesis, and offers ways in which to enhance its explanatory and predictive capacities. This combination of prediction and explanation marks ESB out as a research manifesto that goes further than its two contributing fields. Here, we summarize ESB via an analysis of characteristic research examples and exploratory questions, while also making a case for why these integrative efforts are worth pursuing. © 2013 WILEY Periodicals, Inc.

  13. The application of statistical physics to evolutionary biology.

    Science.gov (United States)

    Sella, Guy; Hirsh, Aaron E

    2005-07-05

    A number of fundamental mathematical models of the evolutionary process exhibit dynamics that can be difficult to understand analytically. Here we show that a precise mathematical analogy can be drawn between certain evolutionary and thermodynamic systems, allowing application of the powerful machinery of statistical physics to analysis of a family of evolutionary models. Analytical results that follow directly from this approach include the steady-state distribution of fixed genotypes and the load in finite populations. The analogy with statistical physics also reveals that, contrary to a basic tenet of the nearly neutral theory of molecular evolution, the frequencies of adaptive and deleterious substitutions at steady state are equal. Finally, just as the free energy function quantitatively characterizes the balance between energy and entropy, a free fitness function provides an analytical expression for the balance between natural selection and stochastic drift.

  14. From Songlines to genomes: Prehistoric assisted migration of a rain forest tree by Australian Aboriginal people.

    Directory of Open Access Journals (Sweden)

    Maurizio Rossetto

    Full Text Available Prehistoric human activities have contributed to the dispersal of many culturally important plants. The study of these traditional interactions can alter the way we perceive the natural distribution and dynamics of species and communities. Comprehensive research on native crops combining evolutionary and anthropological data is revealing how ancient human populations influenced their distribution. Although traditional diets also included a suite of non-cultivated plants that in some cases necessitated the development of culturally important technical advances such as the treatment of toxic seed, empirical evidence for their deliberate dispersal by prehistoric peoples remains limited. Here we integrate historic and biocultural research involving Aboriginal people, with chloroplast and nuclear genomic data to demonstrate Aboriginal-mediated dispersal of a non-cultivated rainforest tree.We assembled new anthropological evidence of use and deliberate dispersal of Castanospermum australe (Fabaceae, a non-cultivated culturally important riparian tree that produces toxic but highly nutritious water-dispersed seed. We validated cultural evidence of recent human-mediated dispersal by revealing genomic homogeneity across extensively dissected habitat, multiple catchments and uneven topography in the southern range of this species. We excluded the potential contribution of other dispersal mechanisms based on the absence of suitable vectors and current distributional patterns at higher elevations and away from water courses, and by analyzing a comparative sample from northern Australia.Innovative studies integrating evolutionary and anthropological data will continue to reveal the unexpected impact that prehistoric people have had on current vegetation patterns. A better understanding of how traditional practices shaped species' distribution and assembly will directly inform cultural heritage management strategies, challenge "natural" species distribution

  15. Conceptual foundations of evolutionary thought

    Indian Academy of Sciences (India)

    2017-07-04

    Jul 4, 2017 ... Home; Journals; Journal of Genetics; Volume 96; Issue 3. Conceptual foundations of evolutionary thought. K. P. MOHANAN. Perspectives Volume 96 Issue 3 July 2017 pp 401-412. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/jgen/096/03/0401-0412. Abstract ...

  16. Evolutionary robotics–A review

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... In evolutionary robotics, a suitable robot control system is developed automatically through evolution due to the interactions between the robot and its environment. It is a complicated task, as the robot and the environment constitute a highly dynamical system. Several methods have been tried by various ...

  17. Haldane and modern evolutionary genetics

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 96; Issue 5. Haldane and modern evolutionary genetics. BRIAN CHARLESWORTH. HALDANE AT 125 Volume 96 Issue 5 November 2017 pp 773-782. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/jgen/096/05/0773-0782. Keywords.

  18. Scalable Computing for Evolutionary Genomics

    NARCIS (Netherlands)

    Prins, J.C.P.; Belhachemi, D.; Möller, S.; Smant, G.

    2012-01-01

    Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving

  19. Evolutionary Biology Research in India

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 10. Evolutionary Biology Research in India. Information and Announcements Volume 5 Issue 10 October 2000 pp 102-104. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/005/10/0102-0104 ...

  20. Realism, Relativism, and Evolutionary Psychology

    NARCIS (Netherlands)

    Derksen, M.

    Against recent attempts to forge a reconciliation between constructionism and realism, I contend that, in psychology at least, stirring up conflict is a more fruitful strategy. To illustrate this thesis, I confront a school of psychology with strong realist leanings, evolutionary psychology, with

  1. Cryptic eco-evolutionary dynamics.

    Science.gov (United States)

    Kinnison, Michael T; Hairston, Nelson G; Hendry, Andrew P

    2015-12-01

    Natural systems harbor complex interactions that are fundamental parts of ecology and evolution. These interactions challenge our inclinations and training to seek the simplest explanations of patterns in nature. Not least is the likelihood that some complex processes might be missed when their patterns look similar to predictions for simpler mechanisms. Along these lines, theory and empirical evidence increasingly suggest that environmental, ecological, phenotypic, and genetic processes can be tightly intertwined, resulting in complex and sometimes surprising eco-evolutionary dynamics. The goal of this review is to temper inclinations to unquestioningly seek the simplest explanations in ecology and evolution, by recognizing that some eco-evolutionary outcomes may appear very similar to purely ecological, purely evolutionary, or even null expectations, and thus be cryptic. We provide theoretical and empirical evidence for observational biases and mechanisms that might operate among the various links in eco-evolutionary feedbacks to produce cryptic patterns. Recognition that cryptic dynamics can be associated with outcomes like stability, resilience, recovery, or coexistence in a dynamically changing world provides added impetus for finding ways to study them. © 2015 New York Academy of Sciences.

  2. Darwinian foundations for evolutionary economics

    NARCIS (Netherlands)

    Stoelhorst, J.W.

    2008-01-01

    This paper engages with the methodological debate on the contribution of Darwinism to Veblen's (1898) evolutionary research program for economics. I argue that ontological continuity, generalized Darwinism, and multi-level selection are necessary building blocks for an explanatory framework that can

  3. Evolutionary Psychology and Intelligence Research

    Science.gov (United States)

    Kanazawa, Satoshi

    2010-01-01

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

  4. Diversity-Guided Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    2002-01-01

    Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few algorit...

  5. Testing evolutionary theories of menopause.

    Science.gov (United States)

    Shanley, Daryl P; Sear, Rebecca; Mace, Ruth; Kirkwood, Thomas B L

    2007-12-07

    Why do women cease fertility rather abruptly through menopause at an age well before generalized senescence renders child rearing biologically impossible? The two main evolutionary hypotheses are that menopause serves either (i) to protect mothers from rising age-specific maternal mortality risks, thereby protecting their highly dependent younger children from death if the mother dies or (ii) to provide post-reproductive grandmothers who enhance their inclusive fitness by helping to care and provide for their daughters' children. Recent theoretical work indicates that both factors together are necessary if menopause is to provide an evolutionary advantage. However, these ideas need to be tested using detailed data from actual human life histories lived under reasonably 'natural' conditions; for obvious reasons, such data are extremely scarce. We here describe a study based on a remarkably complete dataset from The Gambia. The data provided quantitative estimates for key parameters for the theoretical model, which were then used to assess the actual effects on fitness. Empirically based numerical analysis of this nature is essential if the enigma of menopause is to be explained satisfactorily in evolutionary terms. Our results point to the distinctive (and perhaps unique) role of menopause in human evolution and provide important support for the hypothesized evolutionary significance of grandmothers.

  6. Defining fitness in evolutionary models

    Indian Academy of Sciences (India)

    2008-12-23

    Dec 23, 2008 ... The analysis of evolutionary models requires an appropriate definition for fitness. ..... of dimorphism for dormancy in plants (Cohen 1966). .... yses have assumed nonoverlapping generations (i.e. no age- structure). The solution to defining fitness when the environ- ment is spatially variable and there is a ...

  7. Evolutionary dynamics of mammalian karyotypes

    Directory of Open Access Journals (Sweden)

    Carlo Alberto Redi

    2012-12-01

    Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....

  8. Euryhalinity in an evolutionary context

    Science.gov (United States)

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

    2013-01-01

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

  9. Ernst Mayr and Evolutionary Biology

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 7. Polemics and Synthesis: Ernst Mayr and Evolutionary Biology. Renee M Borges. General Article Volume 10 Issue 7 July 2005 pp 21-33. Fulltext. Click here to view fulltext PDF. Permanent link:

  10. Evolutionary Biology Research in India

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 10. Evolutionary Biology Research in India. Information and Announcements Volume 5 Issue 10 October 2000 pp 102-104. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/005/10/0102-0104 ...

  11. Evolutionary robotics – A review

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    to solve this problem. This paper provides a survey on some of these important studies carried out in the recent past. Keywords. Evolutionary robotics; genetic ... neural network (NN) (Kosko 1994), to study the interaction between evolution and learning. .... After GA-based learning of the neural controller, the navigation.

  12. Environmental tritium in trees

    International Nuclear Information System (INIS)

    Brown, R.M.

    1979-01-01

    The distribution of environmental tritium in the free water and organically bound hydrogen of trees growing in the vicinity of the Chalk River Nuclear Laboratories (CRNL) has been studied. The regional dispersal of HTO in the atmosphere has been observed by surveying the tritium content of leaf moisture. Measurement of the distribution of organically bound tritium in the wood of tree ring sequences has given information on past concentrations of HTO taken up by trees growing in the CRNL Liquid Waste Disposal Area. For samples at background environmental levels, cellulose separation and analysis was done. The pattern of bomb tritium in precipitation of 1955-68 was observed to be preserved in the organically bound tritium of a tree ring sequence. Reactor tritium was discernible in a tree growing at a distance of 10 km from CRNL. These techniques provide convenient means of monitoring dispersal of HTO from nuclear facilities. (author)

  13. Coded Splitting Tree Protocols

    DEFF Research Database (Denmark)

    Sørensen, Jesper Hemming; Stefanovic, Cedomir; Popovski, Petar

    2013-01-01

    This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... instance is terminated prematurely and subsequently iterated. The combined set of leaves from all the tree instances can then be viewed as a graph code, which is decodable using belief propagation. The main design problem is determining the order of splitting, which enables successful decoding as early...... as possible. Evaluations show that the proposed protocol provides considerable gains over the standard tree splitting protocol applying SIC. The improvement comes at the expense of an increased feedback and receiver complexity....

  14. Language trees not equal gene trees.

    Science.gov (United States)

    Steele, James; Kandler, Anne

    2010-09-01

    Darwin saw similarities between the evolution of species and the evolution of languages, and it is now widely accepted that similarities between related languages can often be interpreted in terms of a bifurcating descent history ('phylogenesis'). Such interpretations are supported when the distributions of shared and unshared traits (for example, in terms of etymological roots for elements of basic vocabulary) are analysed using tree-building techniques and found to be well-explained by a phylogenetic model. In this article, we question the demographic assumption which is sometimes made when a tree-building approach has been taken to a set of cultures or languages, namely that the resulting tree is also representative of a bifurcating population history. Using historical census data relating to Gaelic- and English-speaking inhabitants of Sutherland (Highland Scotland), we have explored the dynamics of language death due to language shift, representing the extreme case of lack of congruence between the genetic and the culture-historical processes. Such cases highlight the important role of selective cultural migration (or shifting between branches) in determining the extinction rates of different languages on such trees.

  15. Why do trees die? Characterizing the drivers of background tree mortality

    Science.gov (United States)

    Das, Adrian J.; Stephenson, Nathan L.; Davis, Kristin P.

    2016-01-01

    The drivers of background tree mortality rates—the typical low rates of tree mortality found in forests in the absence of acute stresses like drought—are central to our understanding of forest dynamics, the effects of ongoing environmental changes on forests, and the causes and consequences of geographical gradients in the nature and strength of biotic interactions. To shed light on factors contributing to background tree mortality, we analyzed detailed pathological data from 200,668 tree-years of observation and 3,729 individual tree deaths, recorded over a 13-yr period in a network of old-growth forest plots in California's Sierra Nevada mountain range. We found that: (1) Biotic mortality factors (mostly insects and pathogens) dominated (58%), particularly in larger trees (86%). Bark beetles were the most prevalent (40%), even though there were no outbreaks during the study period; in contrast, the contribution of defoliators was negligible. (2) Relative occurrences of broad classes of mortality factors (biotic, 58%; suppression, 51%; and mechanical, 25%) are similar among tree taxa, but may vary with tree size and growth rate. (3) We found little evidence of distinct groups of mortality factors that predictably occur together on trees. Our results have at least three sets of implications. First, rather than being driven by abiotic factors such as lightning or windstorms, the “ambient” or “random” background mortality that many forest models presume to be independent of tree growth rate is instead dominated by biotic agents of tree mortality, with potentially critical implications for forecasting future mortality. Mechanistic models of background mortality, even for healthy, rapidly growing trees, must therefore include the insects and pathogens that kill trees. Second, the biotic agents of tree mortality, instead of occurring in a few predictable combinations, may generally act opportunistically and with a relatively large degree of independence from

  16. Evolutionary biology today and the call for an extended synthesis.

    Science.gov (United States)

    Futuyma, Douglas J

    2017-10-06

    Evolutionary theory has been extended almost continually since the evolutionary synthesis (ES), but except for the much greater importance afforded genetic drift, the principal tenets of the ES have been strongly supported. Adaptations are attributable to the sorting of genetic variation by natural selection, which remains the only known cause of increase in fitness. Mutations are not adaptively directed, but as principal authors of the ES recognized, the material (structural) bases of biochemistry and development affect the variety of phenotypic variations that arise by mutation and recombination. Against this historical background, I analyse major propositions in the movement for an 'extended evolutionary synthesis'. 'Niche construction' is a new label for a wide variety of well-known phenomena, many of which have been extensively studied, but (as with every topic in evolutionary biology) some aspects may have been understudied. There is no reason to consider it a neglected 'process' of evolution. The proposition that phenotypic plasticity may engender new adaptive phenotypes that are later genetically assimilated or accommodated is theoretically plausible; it may be most likely when the new phenotype is not truly novel, but is instead a slight extension of a reaction norm already shaped by natural selection in similar environments. However, evolution in new environments often compensates for maladaptive plastic phenotypic responses. The union of population genetic theory with mechanistic understanding of developmental processes enables more complete understanding by joining ultimate and proximate causation; but the latter does not replace or invalidate the former. Newly discovered molecular phenomena have been easily accommodated in the past by elaborating orthodox evolutionary theory, and it appears that the same holds today for phenomena such as epigenetic inheritance. In several of these areas, empirical evidence is needed to evaluate enthusiastic speculation

  17. Mitochondria and the evolutionary roots of cancer

    International Nuclear Information System (INIS)

    Davila, Alfonso F; Zamorano, Pedro

    2013-01-01

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

  18. Evolutionary dynamics of cooperation in neutral populations

    Science.gov (United States)

    Szolnoki, Attila; Perc, Matjaž

    2018-01-01

    Cooperation is a difficult proposition in the face of Darwinian selection. Those that defect have an evolutionary advantage over cooperators who should therefore die out. However, spatial structure enables cooperators to survive through the formation of homogeneous clusters, which is the hallmark of network reciprocity. Here we go beyond this traditional setup and study the spatiotemporal dynamics of cooperation in a population of populations. We use the prisoner's dilemma game as the mathematical model and show that considering several populations simultaneously gives rise to fascinating spatiotemporal dynamics and pattern formation. Even the simplest assumption that strategies between different populations are payoff-neutral with one another results in the spontaneous emergence of cyclic dominance, where defectors of one population become prey of cooperators in the other population, and vice versa. Moreover, if social interactions within different populations are characterized by significantly different temptations to defect, we observe that defectors in the population with the largest temptation counterintuitively vanish the fastest, while cooperators that hang on eventually take over the whole available space. Our results reveal that considering the simultaneous presence of different populations significantly expands the complexity of evolutionary dynamics in structured populations, and it allows us to understand the stability of cooperation under adverse conditions that could never be bridged by network reciprocity alone.

  19. Mitochondria and the evolutionary roots of cancer

    Science.gov (United States)

    Davila, Alfonso F.; Zamorano, Pedro

    2013-04-01

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

  20. Evolutionary origin of rhizobium Nod factor signaling

    Science.gov (United States)

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

    2011-01-01

    For over two decades now, it is known that the nodule symbiosis between legume plants and nitrogen fixing rhizobium bacteria is set in motion by the bacterial signal molecule named nodulation (Nod) factor.1 Upon Nod factor perception a signaling cascade is activated that is also essential for endomycorrhizal symbiosis (Fig. 1). This suggests that rhizobium co-opted the evolutionary far more ancient mycorrhizal signaling pathway in order to establish an endosymbiotic interaction with legumes.2 As arbuscular mycorrhizal fungi of the Glomeromycota phylum can establish a symbiosis with the vast majority of land plants, it is most probable that this signaling cascade is wide spread in the plant kingdom.3 However, Nod factor perception generally is considered to be unique to legumes. Two recent breakthroughs on the evolutionary origin of rhizobium Nod factor signaling demonstrate that this is not the case.4,5 The purification of Nod factor-like molecules excreted by the mycorrhizal fungus Glomus intraradices and the role of the LysM-type Nod factor receptor PaNFP in the non-legume Parasponia andersonii provide novel understanding on the evolution of rhizobial Nod factor signaling. PMID:21904113