Approaches to Macroevolution: 1. General Concepts and Origin of Variation.

PubMed

Jablonski, David

2017-01-01

Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks (GRNs, used here in a broad sense incorporating not just the genetic circuitry per se but the factors controlling the timing and location of gene expression and repression), the non-linear relation between magnitude of genetic change and the phenotypic results, the evolutionary potential of co-opting existing GRNs, and developmental responsiveness to nongenetic signals (i.e. epigenetics and plasticity), all requiring modification of standard microevolutionary models, and rendering difficult any simple definition of evolutionary novelty. The developmental factors underlying macroevolution create anisotropic probabilities-i.e., an uneven density distribution-of evolutionary change around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. From this standpoint, "punctuated equilibrium" and "phyletic gradualism" simply represent two cells in a matrix of evolutionary models of phenotypic change, and the origin of trends and evolutionary novelty are not simply functions of ecological opportunity. Over long timescales, contingency becomes especially important, and can be viewed in terms of macroevolutionary lags (the temporal separation between the origin of a trait or clade and subsequent diversification); such lags can arise by several mechanisms: as geological or phylogenetic artifacts, or when diversifications require synergistic interactions among traits, or between traits and external events. The temporal and spatial patterns of the origins of evolutionary novelties are a challenge to macroevolutionary theory; individual events can be described retrospectively, but a general model relating development, genetics, and ecology is needed. An accompanying paper (Jablonski in Evol Biol 2017) reviews diversity dynamics and the sorting of variation, with some general conclusions.

Automated discovery of local search heuristics for satisfiability testing.

PubMed

Fukunaga, Alex S

2008-01-01

The development of successful metaheuristic algorithms such as local search for a difficult problem such as satisfiability testing (SAT) is a challenging task. We investigate an evolutionary approach to automating the discovery of new local search heuristics for SAT. We show that several well-known SAT local search algorithms such as Walksat and Novelty are composite heuristics that are derived from novel combinations of a set of building blocks. Based on this observation, we developed CLASS, a genetic programming system that uses a simple composition operator to automatically discover SAT local search heuristics. New heuristics discovered by CLASS are shown to be competitive with the best Walksat variants, including Novelty+. Evolutionary algorithms have previously been applied to directly evolve a solution for a particular SAT instance. We show that the heuristics discovered by CLASS are also competitive with these previous, direct evolutionary approaches for SAT. We also analyze the local search behavior of the learned heuristics using the depth, mobility, and coverage metrics proposed by Schuurmans and Southey.

Bellagio conference and book. Symbiosis as Source of Evolutionary Innovation: Speciation and Morphogenesis. Conference--June 25-30, 1989, Bellagio Conference Center, Italy

NASA Technical Reports Server (NTRS)

Margulis, L.; Fester, R.

1991-01-01

This conference at the Bellagio Conference Center, Italy, from June 25-30, 1989, provided a unique opportunity for evolutionary theorists and symbiosis biologists to cross the boundaries of their respective disciplines and share ideas. A major task was to address the adequacy of the prevailing neodarwinian concept of evolution with respect to the relative importance of symbiosis in the origin of morphological and evolutionary novelty.

Forelimb kinematics and motor patterns of swimming loggerhead sea turtles (Caretta caretta): are motor patterns conserved in the evolution of new locomotor strategies?

PubMed

Rivera, Angela R V; Wyneken, Jeanette; Blob, Richard W

2011-10-01

Novel functions in animals may evolve through changes in morphology, muscle activity or a combination of both. The idea that new functions or behavior can arise solely through changes in structure, without concurrent changes in the patterns of muscle activity that control movement of those structures, has been formalized as the neuromotor conservation hypothesis. In vertebrate locomotor systems, evidence for neuromotor conservation is found across evolutionary transitions in the behavior of terrestrial species, and in evolutionary transitions from terrestrial species to flying species. However, evolutionary transitions in the locomotion of aquatic species have received little comparable study to determine whether changes in morphology and muscle function were coordinated through the evolution of new locomotor behavior. To evaluate the potential for neuromotor conservation in an ancient aquatic system, we quantified forelimb kinematics and muscle activity during swimming in the loggerhead sea turtle, Caretta caretta. Loggerhead forelimbs are hypertrophied into wing-like flippers that produce thrust via dorsoventral forelimb flapping. We compared kinematic and motor patterns from loggerheads with previous data from the red-eared slider, Trachemys scripta, a generalized freshwater species exhibiting unspecialized forelimb morphology and anteroposterior rowing motions during swimming. For some forelimb muscles, comparisons between C. caretta and T. scripta support neuromotor conservation; for example, the coracobrachialis and the latissimus dorsi show similar activation patterns. However, other muscles (deltoideus, pectoralis and triceps) do not show neuromotor conservation; for example, the deltoideus changes dramatically from a limb protractor/elevator in sliders to a joint stabilizer in loggerheads. Thus, during the evolution of flapping in sea turtles, drastic restructuring of the forelimb was accompanied by both conservation and evolutionary novelty in limb motor patterns.

Horizontal gene transfer in parasitic plants.

PubMed

Davis, Charles C; Xi, Zhenxiang

2015-08-01

Horizontal gene transfer (HGT) between species has been a major focus of plant evolutionary research during the past decade. Parasitic plants, which establish a direct connection with their hosts, have provided excellent examples of how these transfers are facilitated via the intimacy of this symbiosis. In particular, phylogenetic studies from diverse clades indicate that parasitic plants represent a rich system for studying this phenomenon. Here, HGT has been shown to be astonishingly high in the mitochondrial genome, and appreciable in the nuclear genome. Although explicit tests remain to be performed, some transgenes have been hypothesized to be functional in their recipient species, thus providing a new perspective on the evolution of novelty in parasitic plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Testing inferences in developmental evolution: the forensic evidence principle.

PubMed

Larsson, Hans C E; Wagner, Günter P

2012-09-01

Developmental evolution (DE) examines the influence of developmental mechanisms on biological evolution. Here we consider the question: "what is the evidence that allows us to decide whether a certain developmental scenario for an evolutionary change is in fact "correct" or at least falsifiable?" We argue that the comparative method linked with what we call the "forensic evidence principle" (FEP) is sufficient to conduct rigorous tests of DE scenarios. The FEP states that different genetically mediated developmental causes of an evolutionary transformation will leave different signatures in the development of the derived character. Although similar inference rules have been used in practically every empirical science, we expand this approach here in two ways: (1) we justify the validity of this principle with reference to a well-known result from mathematical physics, known as the symmetry principle, and (2) propose a specific form of the FEP for DE: given two or more developmental explanations for a certain evolutionary event, say an evolutionary novelty, then the evidence discriminating between these hypotheses will be found in the most proximal internal drivers of the derived character. Hence, a detailed description of the ancestral and derived states, and their most proximal developmental drivers are necessary to discriminate between various evolutionary developmental hypotheses. We discuss how this stepwise order of testing is necessary, establishes a formal test, and how skipping this order of examination may violate a more accurate examination of DE. We illustrate the approach with an example from avian digit evolution. © 2012 Wiley Periodicals, Inc.

A Change in SHATTERPROOF Protein Lies at the Origin of a Fruit Morphological Novelty and a New Strategy for Seed Dispersal in Medicago Genus1[C][W

PubMed Central

Fourquin, Chloé; del Cerro, Carolina; Victoria, Filipe C.; Vialette-Guiraud, Aurélie; de Oliveira, Antonio C.; Ferrándiz, Cristina

2013-01-01

Angiosperms are the most diverse and numerous group of plants, and it is generally accepted that this evolutionary success owes in part to the diversity found in fruits, key for protecting the developing seeds and ensuring seed dispersal. Although studies on the molecular basis of morphological innovations are few, they all illustrate the central role played by transcription factors acting as developmental regulators. Here, we show that a small change in the protein sequence of a MADS-box transcription factor correlates with the origin of a highly modified fruit morphology and the change in seed dispersal strategies that occurred in Medicago, a genus belonging to the large legume family. This protein sequence modification alters the functional properties of the protein, affecting the affinities for other protein partners involved in high-order complexes. Our work illustrates that variation in coding regions can generate evolutionary novelties not based on gene duplication/subfunctionalization but by interactions in complex networks, contributing also to the current debate on the relative importance of changes in regulatory or coding regions of master regulators in generating morphological novelties. PMID:23640757

What serial homologs can tell us about the origin of insect wings

PubMed Central

2017-01-01

Although the insect wing is a textbook example of morphological novelty, the origin of insect wings remains a mystery and is regarded as a chief conundrum in biology. Centuries of debates have culminated into two prominent hypotheses: the tergal origin hypothesis and the pleural origin hypothesis. However, between these two hypotheses, there is little consensus in regard to the origin tissue of the wing as well as the evolutionary route from the origin tissue to the functional flight device. Recent evolutionary developmental (evo-devo) studies have shed new light on the origin of insect wings. A key concept in these studies is “serial homology”. In this review, we discuss how the wing serial homologs identified in recent evo-devo studies have provided a new angle through which this century-old conundrum can be explored. We also review what we have learned so far from wing serial homologs and discuss what we can do to go beyond simply identifying wing serial homologs and delve further into the developmental and genetic mechanisms that have facilitated the evolution of insect wings. PMID:28357056

Understanding Innovation Engines: Automated Creativity and Improved Stochastic Optimization via Deep Learning.

PubMed

Nguyen, A; Yosinski, J; Clune, J

2016-01-01

The Achilles Heel of stochastic optimization algorithms is getting trapped on local optima. Novelty Search mitigates this problem by encouraging exploration in all interesting directions by replacing the performance objective with a reward for novel behaviors. This reward for novel behaviors has traditionally required a human-crafted, behavioral distance function. While Novelty Search is a major conceptual breakthrough and outperforms traditional stochastic optimization on certain problems, it is not clear how to apply it to challenging, high-dimensional problems where specifying a useful behavioral distance function is difficult. For example, in the space of images, how do you encourage novelty to produce hawks and heroes instead of endless pixel static? Here we propose a new algorithm, the Innovation Engine, that builds on Novelty Search by replacing the human-crafted behavioral distance with a Deep Neural Network (DNN) that can recognize interesting differences between phenotypes. The key insight is that DNNs can recognize similarities and differences between phenotypes at an abstract level, wherein novelty means interesting novelty. For example, a DNN-based novelty search in the image space does not explore in the low-level pixel space, but instead creates a pressure to create new types of images (e.g., churches, mosques, obelisks, etc.). Here, we describe the long-term vision for the Innovation Engine algorithm, which involves many technical challenges that remain to be solved. We then implement a simplified version of the algorithm that enables us to explore some of the algorithm's key motivations. Our initial results, in the domain of images, suggest that Innovation Engines could ultimately automate the production of endless streams of interesting solutions in any domain: for example, producing intelligent software, robot controllers, optimized physical components, and art.

Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms.

PubMed

Wang, Yupeng; Wang, Xiyin; Tang, Haibao; Tan, Xu; Ficklin, Stephen P; Feltus, F Alex; Paterson, Andrew H

2011-01-01

Both single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored. In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (WGD, tandem, proximal, DNA based transposed, retrotransposed and dispersed), and between positional orthologs. Both neo-functionalization and genetic redundancy appear to contribute to retention of duplicate genes. Genes resulting from WGD and tandem duplications diverge slowest in both coding sequences and gene expression, and contribute most to genetic redundancy, while other duplication modes contribute more to evolutionary novelty. WGD duplicates may more frequently be retained due to dosage amplification, while inferred transposon mediated gene duplications tend to reduce gene expression levels. The extent of expression divergence between duplicates is discernibly related to duplication modes, different WGD events, amino acid divergence, and putatively neutral divergence (time), but the contribution of each factor is heterogeneous among duplication modes. Gene loss may retard inter-species expression divergence. Members of different gene families may have non-random patterns of origin that are similar in Arabidopsis and rice, suggesting the action of pan-taxon principles of molecular evolution. Gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution.

Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms

PubMed Central

Wang, Yupeng; Wang, Xiyin; Tang, Haibao; Tan, Xu; Ficklin, Stephen P.; Feltus, F. Alex; Paterson, Andrew H.

2011-01-01

Background Both single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored. Results In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (WGD, tandem, proximal, DNA based transposed, retrotransposed and dispersed), and between positional orthologs. Both neo-functionalization and genetic redundancy appear to contribute to retention of duplicate genes. Genes resulting from WGD and tandem duplications diverge slowest in both coding sequences and gene expression, and contribute most to genetic redundancy, while other duplication modes contribute more to evolutionary novelty. WGD duplicates may more frequently be retained due to dosage amplification, while inferred transposon mediated gene duplications tend to reduce gene expression levels. The extent of expression divergence between duplicates is discernibly related to duplication modes, different WGD events, amino acid divergence, and putatively neutral divergence (time), but the contribution of each factor is heterogeneous among duplication modes. Gene loss may retard inter-species expression divergence. Members of different gene families may have non-random patterns of origin that are similar in Arabidopsis and rice, suggesting the action of pan-taxon principles of molecular evolution. Conclusion Gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution. PMID:22164235

On the Measurement of Ecological Novelty: Scale-Eating Pupfish Are Separated by 168 my from Other Scale-Eating Fishes

PubMed Central

Martin, Christopher H.; Wainwright, Peter C.

2013-01-01

The colonization of new adaptive zones is widely recognized as one of the hallmarks of adaptive radiation. However, the adoption of novel resources during this process is rarely distinguished from phenotypic change because morphology is a common proxy for ecology. How can we quantify ecological novelty independent of phenotype? Our study is split into two parts: we first document a remarkable example of ecological novelty, scale-eating (lepidophagy), within a rapidly-evolving adaptive radiation of Cyprinodon pupfishes on San Salvador Island, Bahamas. This specialized predatory niche is known in several other fish groups, but is not found elsewhere among the 1,500 species of atherinomorphs. Second, we quantify this ecological novelty by measuring the time-calibrated phylogenetic distance in years to the most closely-related species with convergent ecology. We find that scale-eating pupfish are separated by 168 million years of evolution from the nearest scale-eating fish. We apply this approach to a variety of examples and highlight the frequent decoupling of ecological novelty from phenotypic divergence. We observe that novel ecology is not always tightly correlated with rates of phenotypic or species diversification, particularly within recent adaptive radiations, necessitating the use of additional measures of ecological novelty independent of phenotype. PMID:23976994

Evo-devo and accounting for Darwin's endless forms

PubMed Central

Brakefield, Paul M.

2011-01-01

Evo-devo has led to dramatic advances in our understanding of how the processes of development can contribute to explaining patterns of evolutionary diversification that underlie the endless forms of animal life on the Earth. This is increasingly the case not only for the origins of evolutionary novelties that permit new functions and open up new adaptive zones, but also for the processes of evolutionary tinkering that occur within the subsequent radiations of related species. Evo-devo has time and again yielded spectacular examples of Darwin's notions of common ancestry and of descent with modification. It has also shown that the evolution of endless forms is more about the evolution of the regulatory machinery of ancient genes than the origin and elaboration of new genes. Evolvability, especially with respect to the capacity of a developmental system to evolve and to generate the variation in form for natural selection to screen, has become a pivotal focus of evo-devo. As a consequence, a balancing of the concept of endless forms in morphospace with a greater awareness of the potential for developmental constraints and bias is becoming more general. The prospect of parallel horizons opening up for the evolution of behaviour is exciting; in particular, does Sean Carroll's phrase referring to old genes learning new tricks in the evolution of endless forms apply equally as well to patterns of diversity and disparity in behavioural trait-space? PMID:21690125

Evo-devo and accounting for Darwin's endless forms.

PubMed

Brakefield, Paul M

2011-07-27

Evo-devo has led to dramatic advances in our understanding of how the processes of development can contribute to explaining patterns of evolutionary diversification that underlie the endless forms of animal life on the Earth. This is increasingly the case not only for the origins of evolutionary novelties that permit new functions and open up new adaptive zones, but also for the processes of evolutionary tinkering that occur within the subsequent radiations of related species. Evo-devo has time and again yielded spectacular examples of Darwin's notions of common ancestry and of descent with modification. It has also shown that the evolution of endless forms is more about the evolution of the regulatory machinery of ancient genes than the origin and elaboration of new genes. Evolvability, especially with respect to the capacity of a developmental system to evolve and to generate the variation in form for natural selection to screen, has become a pivotal focus of evo-devo. As a consequence, a balancing of the concept of endless forms in morphospace with a greater awareness of the potential for developmental constraints and bias is becoming more general. The prospect of parallel horizons opening up for the evolution of behaviour is exciting; in particular, does Sean Carroll's phrase referring to old genes learning new tricks in the evolution of endless forms apply equally as well to patterns of diversity and disparity in behavioural trait-space?

Multiple ancient origins of neoteny in Lycidae (Coleoptera): consequences for ecology and macroevolution

PubMed Central

Bocak, Ladislav; Bocakova, Milada; Hunt, Toby; Vogler, Alfried P

2008-01-01

Neoteny, the maintenance of larval features in sexually mature adults, is a radical way of generating evolutionary novelty through shifts in relative timing of developmental programmes. While controlled by the environment in facultative neotenics, retention of larval features is obligatory in many species of Lycidae (net-winged beetles). They are studied here as an example of how developmental shifts and ecology interact to produce macroevolutionary impacts. We conducted a phylogenetic analysis of Lycidae based on DNA sequences from nuclear (18S and 28S rRNA) and mitochondrial (rrnL, cox1, cob and nad5) genes from a representative set of lineages (73 species), including 17 neotenic taxa. Major changes of basal relationships compared with those implied in the current classification generally supported three independent origins of neotenics in Lycidae. The southeast Asian Lyropaeinae and Ateliinae were in basal positions indicating evolutionary antiquity, also confirmed by molecular clock estimates, unlike the neotropical leptolycines nested within Calopterini and presumably much younger. neotenics exhibit typical K-selected traits including slow development, large body size, high investment in offspring and low dispersal. This correlated with low species richness and restricted ranges of neotenic lineages compared with their sisters. Yet, these factors did not impede the evolutionary persistence of affected lineages, even without reversals to fully metamorphosed forms, contradicting earlier suggestions of recent evolution from dispersive non-neotenics. PMID:18477542

The early stages of duplicate gene evolution

PubMed Central

Moore, Richard C.; Purugganan, Michael D.

2003-01-01

Gene duplications are one of the primary driving forces in the evolution of genomes and genetic systems. Gene duplicates account for 8–20% of the genes in eukaryotic genomes, and the rates of gene duplication are estimated at between 0.2% and 2% per gene per million years. Duplicate genes are believed to be a major mechanism for the establishment of new gene functions and the generation of evolutionary novelty, yet very little is known about the early stages of the evolution of duplicated gene pairs. It is unclear, for example, to what extent selection, rather than neutral genetic drift, drives the fixation and early evolution of duplicate loci. Analysis of recently duplicated genes in the Arabidopsis thaliana genome reveals significantly reduced species-wide levels of nucleotide polymorphisms in the progenitor and/or duplicate gene copies, suggesting that selective sweeps accompany the initial stages of the evolution of these duplicated gene pairs. Our results support recent theoretical work that indicates that fates of duplicate gene pairs may be determined in the initial phases of duplicate gene evolution and that positive selection plays a prominent role in the evolutionary dynamics of the very early histories of duplicate nuclear genes. PMID:14671323

Tangled trios? Characterizing a hybrid zone in Castilleja (Orobanchaceae)

Treesearch

Erika l. Hersch-Green; Richard Cronn

2009-01-01

Hybridization and polyploidization are exceedingly important processes because both influence the ecological envelope and evolutionary trajectory of land plants. These processes are frequently invoked for Castilleja (Indian paintbrushes) as contributors to morphological and genetic novelty and as complicating factors in species delimitations. Here...

Dimensions of integration in interdisciplinary explanations of the origin of evolutionary novelty.

PubMed

Love, Alan C; Lugar, Gary L

2013-12-01

Many philosophers of biology have embraced a version of pluralism in response to the failure of theory reduction but overlook how concepts, methods, and explanatory resources are in fact coordinated, such as in interdisciplinary research where the aim is to integrate different strands into an articulated whole. This is observable for the origin of evolutionary novelty-a complex problem that requires a synthesis of intellectual resources from different fields to arrive at robust answers to multiple allied questions. It is an apt locus for exploring new dimensions of explanatory integration because it necessitates coordination among historical and experimental disciplines (e.g., geology and molecular biology). These coordination issues are widespread for the origin of novel morphologies observed in the Cambrian Explosion. Despite an explicit commitment to an integrated, interdisciplinary explanation, some potential disciplinary contributors are excluded. Notable among these exclusions is the physics of ontogeny. We argue that two different dimensions of integration-data and standards-have been insufficiently distinguished. This distinction accounts for why physics-based explanatory contributions to the origin of novelty have been resisted: they do not integrate certain types of data and differ in how they conceptualize the standard of uniformitarianism in historical, causal explanations. Our analysis of these different dimensions of integration contributes to the development of more adequate and integrated explanatory frameworks. Copyright © 2013 Elsevier Ltd. All rights reserved.

Heterochrony, cannibalism, and the evolution of viviparity in Salamandra salamandra.

PubMed

Buckley, David; Alcobendas, Marina; García-París, Mario; Wake, Marvalee H

2007-01-01

The way in which novelties that lead to macroevolutionary events originate is a major question in evolutionary biology, and one that can be addressed using the fire salamander (Salamandra salamandra) as a model system. It is exceptional among amphibians in displaying intraspecific diversity of reproductive strategies. In S. salamandra, two distinct modes of reproduction co-occur: the common mode, ovoviviparity (females giving birth to many small larvae), and a phylogenetically derived reproductive strategy, viviparity (females producing only a few large, fully metamorphosed juveniles, which are nourished maternally). We examine the relationship between heterochronic modifications of the ontogeny and the evolution of the new reproductive mode in the fire salamander. The in vitro development of embryos of ovoviviparous and viviparous salamanders from fertilization to metamorphosis is compared, highlighting the key events that distinguish the two modes of reproduction. We identify the heterochronic events that, together with the intrauterine cannibalistic behavior, characterize the derived viviparous reproductive strategy. The ways in which evolutionary novelties can arise by modification of developmental programs can be studied in S. salamandra. Moreover, the variation in reproductive modes and the associated variation of sequences of development occur in neighboring, conspecific populations. Thus, S. salamandra is a unique biological system in which evolutionary developmental research questions can be addressed at the level of populations.

Evolutionary layering and the limits to cellular perfection

PubMed Central

Lynch, Michael

2012-01-01

Although observations from biochemistry and cell biology seemingly illustrate hundreds of examples of exquisite molecular adaptations, the fact that experimental manipulation can often result in improvements in cellular infrastructure raises the question as to what ultimately limits the level of molecular perfection achievable by natural selection. Here, it is argued that random genetic drift can impose a strong barrier to the advancement of molecular refinements by adaptive processes. Moreover, although substantial improvements in fitness may sometimes be accomplished via the emergence of novel cellular features that improve on previously established mechanisms, such advances are expected to often be transient, with overall fitness eventually returning to the level before incorporation of the genetic novelty. As a consequence of such changes, increased molecular/cellular complexity can arise by Darwinian processes, while yielding no long-term increase in adaptation and imposing increased energetic and mutational costs. PMID:23115338

On Dorsal Prothoracic Appendages in Treehoppers (Hemiptera: Membracidae) and the Nature of Morphological Evidence

PubMed Central

Mikó, István; Friedrich, Frank; Yoder, Matthew J.; Hines, Heather M.; Deitz, Lewis L.; Bertone, Matthew A.; Seltmann, Katja C.; Wallace, Matthew S.; Deans, Andrew R.

2012-01-01

A spectacular hypothesis was published recently, which suggested that the “helmet” (a dorsal thoracic sclerite that obscures most of the body) of treehoppers (Insecta: Hemiptera: Membracidae) is connected to the 1st thoracic segment (T1; prothorax) via a jointed articulation and therefore was a true appendage. Furthermore, the “helmet” was interpreted to share multiple characteristics with wings, which in extant pterygote insects are present only on the 2nd (T2) and 3rd (T3) thoracic segments. In this context, the “helmet” could be considered an evolutionary novelty. Although multiple lines of morphological evidence putatively supported the “helmet”-wing homology, the relationship of the “helmet” to other thoracic sclerites and muscles remained unclear. Our observations of exemplar thoraces of 10 hemipteran families reveal multiple misinterpretations relevant to the “helmet”-wing homology hypothesis as originally conceived: 1) the “helmet” actually represents T1 (excluding the fore legs); 2) the “T1 tergum” is actually the anterior dorsal area of T2; 3) the putative articulation between the “helmet” and T1 is actually the articulation between T1 and T2. We conclude that there is no dorsal, articulated appendage on the membracid T1. Although the posterior, flattened, cuticular evagination (PFE) of the membracid T1 does share structural and genetic attributes with wings, the PFE is actually widely distributed across Hemiptera. Hence, the presence of this structure in Membracidae is not an evolutionary novelty for this clade. We discuss this new interpretation of the membracid T1 and the challenges of interpreting and representing morphological data more broadly. We acknowledge that the lack of data standards for morphology is a contributing factor to misinterpreted results and offer an example for how one can reduce ambiguity in morphology by referencing anatomical concepts in published ontologies. PMID:22272287

Comparative analysis of pleurodiran and cryptodiran turtle embryos depicts the molecular ground pattern of the turtle carapacial ridge.

PubMed

Pascual-Anaya, Juan; Hirasawa, Tatsuya; Sato, Iori; Kuraku, Shigehiro; Kuratani, Shigeru

2014-01-01

The turtle shell is a wonderful example of a genuine morphological novelty, since it has no counterpart in any other extant vertebrate lineages. The evolutionary origin of the shell is a question that has fascinated evolutionary biologists for over two centuries and it still remains a mystery. One of the turtle innovations associated with the shell is the carapacial ridge (CR), a bulge that appears at both sides of the dorsal lateral trunk of the turtle embryo and that probably controls the formation of the carapace, the dorsal moiety of the shell. Although from the beginning of this century modern genetic techniques have been applied to resolve the evolutionary developmental origin of the CR, the use of different models with, in principle, dissimilar results has hampered the establishment of a common mechanism for the origin of the shell. Although modern turtles are divided into two major groups, Cryptodira (or hidden-necked turtles) and Pleurodira (or side-necked turtles), molecular developmental studies have been carried out mostly using cryptodiran models. In this study, we revisit the past data obtained from cryptodiran turtles in order to reconcile the different results. We also analyze the histological anatomy and the expression pattern of main CR factors in a pleurodiran turtle, the red-bellied short-necked turtle Emydura subglobosa. We suggest that the turtle shell probably originated concomitantly with the co-option of the canonical Wnt signaling pathway into the CR in the last common ancestor of the turtle.

False belief in infancy: a fresh look.

PubMed

Heyes, Cecilia

2014-09-01

Can infants appreciate that others have false beliefs? Do they have a theory of mind? In this article I provide a detailed review of more than 20 experiments that have addressed these questions, and offered an affirmative answer, using nonverbal 'violation of expectation' and 'anticipatory looking' procedures. Although many of these experiments are both elegant and ingenious, I argue that their results can be explained by the operation of domain-general processes and in terms of 'low-level novelty'. This hypothesis suggests that the infants' looking behaviour is a function of the degree to which the observed (perceptual novelty) and remembered or expected (imaginal novelty) low-level properties of the test stimuli - their colours, shapes and movements - are novel with respect to events encoded by the infants earlier in the experiment. If the low-level novelty hypothesis is correct, research on false belief in infancy currently falls short of demonstrating that infants have even an implicit theory of mind. However, I suggest that the use of two experimental strategies - inanimate control procedures, and self-informed belief induction - could be used in combination with existing methods to bring us much closer to understanding the evolutionary and developmental origins of theory of mind. © 2014 John Wiley & Sons Ltd.

The industrial melanism mutation in British peppered moths is a transposable element.

PubMed

Van't Hof, Arjen E; Campagne, Pascal; Rigden, Daniel J; Yung, Carl J; Lingley, Jessica; Quail, Michael A; Hall, Neil; Darby, Alistair C; Saccheri, Ilik J

2016-06-02

Discovering the mutational events that fuel adaptation to environmental change remains an important challenge for evolutionary biology. The classroom example of a visible evolutionary response is industrial melanism in the peppered moth (Biston betularia): the replacement, during the Industrial Revolution, of the common pale typica form by a previously unknown black (carbonaria) form, driven by the interaction between bird predation and coal pollution. The carbonaria locus has been coarsely localized to a 200-kilobase region, but the specific identity and nature of the sequence difference controlling the carbonaria-typica polymorphism, and the gene it influences, are unknown. Here we show that the mutation event giving rise to industrial melanism in Britain was the insertion of a large, tandemly repeated, transposable element into the first intron of the gene cortex. Statistical inference based on the distribution of recombined carbonaria haplotypes indicates that this transposition event occurred around 1819, consistent with the historical record. We have begun to dissect the mode of action of the carbonaria transposable element by showing that it increases the abundance of a cortex transcript, the protein product of which plays an important role in cell-cycle regulation, during early wing disc development. Our findings fill a substantial knowledge gap in the iconic example of microevolutionary change, adding a further layer of insight into the mechanism of adaptation in response to natural selection. The discovery that the mutation itself is a transposable element will stimulate further debate about the importance of 'jumping genes' as a source of major phenotypic novelty.

Marine invertebrates, model organisms, and the modern synthesis: epistemic values, evo-devo, and exclusion.

PubMed

Love, Alan C

2009-03-01

A central reason that undergirds the significance of evo-devo is the claim that development was left out of the Modern synthesis. This claim turns out to be quite complicated, both in terms of whether development was genuinely excluded and how to understand the different kinds of embryological research that might have contributed. The present paper reevaluates this central claim by focusing on the practice of model organism choice. Through a survey of examples utilized in the literature of the Modern synthesis, I identify a previously overlooked feature: exclusion of research on marine invertebrates. Understanding the import of this pattern requires interpreting it in terms of two epistemic values operating in biological research: theoretical generality and explanatory completeness. In tandem, these values clarify and enhance the significance of this exclusion. The absence of marine invertebrates implied both a lack of generality in the resulting theory and a lack of completeness with respect to particular evolutionary problems, such as evolvability and the origin of novelty. These problems were salient to embryological researchers aware of the variation and diversity of larval forms in marine invertebrates. In closing, I apply this analysis to model organism choice in evo-devo and discuss its relevance for an extended evolutionary synthesis.

Evolution of the vertebrate jaw: comparative embryology and molecular developmental biology reveal the factors behind evolutionary novelty

PubMed Central

Kuratani, Shigeru

2004-01-01

It is generally believed that the jaw arose through the simple transformation of an ancestral rostral gill arch. The gnathostome jaw differentiates from Hox-free crest cells in the mandibular arch, and this is also apparent in the lamprey. The basic Hox code, including the Hox-free default state in the mandibular arch, may have been present in the common ancestor, and jaw patterning appears to have been secondarily constructed in the gnathostomes. The distribution of the cephalic neural crest cells is similar in the early pharyngula of gnathostomes and lampreys, but different cell subsets form the oral apparatus in each group through epithelial–mesenchymal interactions: and this heterotopy is likely to have been an important evolutionary change that permitted jaw differentiation. This theory implies that the premandibular crest cells differentiate into the upper lip, or the dorsal subdivision of the oral apparatus in the lamprey, whereas the equivalent cell population forms the trabecula of the skull base in gnathostomes. Because the gnathostome oral apparatus is derived exclusively from the mandibular arch, the concepts ‘oral’ and ‘mandibular’ must be dissociated. The ‘lamprey trabecula’ develops from mandibular mesoderm, and is not homologous with the gnathostome trabecula, which develops from premandibular crest cells. Thus the jaw evolved as an evolutionary novelty through tissue rearrangements and topographical changes in tissue interactions. PMID:15575882

Evolutionary trends in directional hearing

PubMed Central

Carr, Catherine E.; Christensen-Dalsgaard, Jakob

2016-01-01

Tympanic hearing is a true evolutionary novelty that arose in parallel within early tetrapods. We propose that in these tetrapods, selection for sound localization in air acted upon pre-existing directionally sensitive brainstem circuits, similar to those in fishes. Auditory circuits in birds and lizards resemble this ancestral, directionally sensitive framework. Despite this anatomically similarity, coding of sound source location differs between birds and lizards. In birds, brainstem circuits compute sound location from interaural cues. Lizards, however, have coupled ears, and do not need to compute source location in the brain. Thus their neural processing of sound direction differs, although all show mechanisms for enhancing sound source directionality. Comparisons with mammals reveal similarly complex interactions between coding strategies and evolutionary history. PMID:27448850

Role of Partner Novelty in Sexual Functioning: A Review.

PubMed

Morton, Heather; Gorzalka, Boris B

2015-01-01

This review investigates whether sexual desire and arousal decline in response to partner familiarity, increase in response to partner novelty, and show differential responding in men and women. These questions were considered through the perspective of two leading evolutionary theories regarding human mating strategies: sexual strategies theory and attachment fertility theory. The hypotheses emerging from these theories were evaluated through a critical analysis of several areas of research including habituation of arousal to erotic stimuli, preferences regarding number of sexual partners, the effect of long-term monogamous relationships on sexual arousal and desire, and prevalence and risk factors associated with extradyadic behavior. The current literature best supports the predictions made by sexual strategies theory in that sexual functioning has evolved to promote short-term mating. Sexual arousal and desire appear to decrease in response to partner familiarity and increase in response to partner novelty in men and women. Evidence to date suggests this effect may be greater in men.

Temperature and Evolutionary Novelty as Forces behind the Evolution of General Intelligence

ERIC Educational Resources Information Center

Kanazawa, Satoshi

2008-01-01

How did human intelligence evolve to be so high? Lynn [Lynn, R. (1991). The evolution of race differences in intelligence. Mankind Quarterly, 32, 99-173] and Rushton [Rushton, J.P. (1995). Race, evolution, and behavior: A life history perspective. New Brunswick: Transaction] suggest that the main forces behind the evolution of human intelligence…

The evolutionary origin and diversification of feathers.

PubMed

Prum, Richard O; Brush, Alan H

2002-09-01

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

DNA Dispose, but Subjects Decide. Learning and the Extended Synthesis.

PubMed

Lindholm, Markus

Adaptation by means of natural selection depends on the ability of populations to maintain variation in heritable traits. According to the Modern Synthesis this variation is sustained by mutations and genetic drift. Epigenetics, evodevo, niche construction and cultural factors have more recently been shown to contribute to heritable variation, however, leading an increasing number of biologists to call for an extended view of speciation and evolution. An additional common feature across the animal kingdom is learning, defined as the ability to change behavior according to novel experiences or skills. Learning constitutes an additional source for phenotypic variation, and change in behavior may induce long lasting shifts in fitness, and hence favor evolutionary novelties. Based on published studies, I demonstrate how learning about food, mate choice and habitats has contributed substantially to speciation in the canonical story of Darwin's finches on the Galapagos Islands. Learning cannot be reduced to genetics, because it demands decisions, which requires a subject. Evolutionary novelties may hence emerge both from shifts in allelic frequencies and from shifts in learned, subject driven behavior. The existence of two principally different sources of variation also prevents the Modern Synthesis from self-referring explanations.

Developmental plasticity and the origin of species differences

PubMed Central

West-Eberhard, Mary Jane

2005-01-01

Speciation is the origin of reproductive isolation and divergence between populations, according to the “biological species concept” of Mayr. Studies of reproductive isolation have dominated research on speciation, leaving the origin of species differences relatively poorly understood. Here, I argue that the origin of species differences, and of novel phenotypes in general, involves the reorganization of ancestral phenotypes (developmental recombination) followed by the genetic accommodation of change. Because selection acts on phenotypes, not directly on genotypes or genes, novel traits can originate by environmental induction as well as mutation, then undergo selection and genetic accommodation fueled by standing genetic variation or by subsequent mutation and genetic recombination. Insofar as phenotypic novelties arise from adaptive developmental plasticity, they are not “random” variants, because their initial form reflects adaptive responses with an evolutionary history, even though they are initiated by mutations or novel environmental factors that are random with respect to (future) adaptation. Change in trait frequency involves genetic accommodation of the threshold or liability for expression of a novel trait, a process that follows rather than directs phenotypic change. Contrary to common belief, environmentally initiated novelties may have greater evolutionary potential than mutationally induced ones. Thus, genes are probably more often followers than leaders in evolutionary change. Species differences can originate before reproductive isolation and contribute to the process of speciation itself. Therefore, the genetics of speciation can profit from studies of changes in gene expression as well as changes in gene frequency and genetic isolation. PMID:15851679

The role of doublesex in the evolution of exaggerated horns in the Japanese rhinoceros beetle

PubMed Central

Ito, Yuta; Harigai, Ayane; Nakata, Moe; Hosoya, Tadatsugu; Araya, Kunio; Oba, Yuichi; Ito, Akinori; Ohde, Takahiro; Yaginuma, Toshinobu; Niimi, Teruyuki

2013-01-01

Male-specific exaggerated horns are an evolutionary novelty and have diverged rapidly via intrasexual selection. Here, we investigated the function of the conserved sex-determination gene doublesex (dsx) in the Japanese rhinoceros beetle (Trypoxylus dichotomus) using RNA interference (RNAi). Our results show that the sex-specific T. dichotomus dsx isoforms have an antagonistic function for head horn formation and only the male isoform has a role for thoracic horn formation. These results indicate that the novel sex-specific regulation of dsx during horn morphogenesis might have been the key evolutionary developmental event at the transition from sexually monomorphic to sexually dimorphic horns. PMID:23609854

The role of doublesex in the evolution of exaggerated horns in the Japanese rhinoceros beetle.

PubMed

Ito, Yuta; Harigai, Ayane; Nakata, Moe; Hosoya, Tadatsugu; Araya, Kunio; Oba, Yuichi; Ito, Akinori; Ohde, Takahiro; Yaginuma, Toshinobu; Niimi, Teruyuki

2013-06-01

Male-specific exaggerated horns are an evolutionary novelty and have diverged rapidly via intrasexual selection. Here, we investigated the function of the conserved sex-determination gene doublesex (dsx) in the Japanese rhinoceros beetle (Trypoxylus dichotomus) using RNA interference (RNAi). Our results show that the sex-specific T. dichotomus dsx isoforms have an antagonistic function for head horn formation and only the male isoform has a role for thoracic horn formation. These results indicate that the novel sex-specific regulation of dsx during horn morphogenesis might have been the key evolutionary developmental event at the transition from sexually monomorphic to sexually dimorphic horns.

Multiple aquatic invasions by an endemic, terrestrial Hawaiian moth radiation

PubMed Central

Rubinoff, Daniel; Schmitz, Patrick

2010-01-01

Insects are the most diverse form of life on the planet, dominating both terrestrial and freshwater ecosystems, yet no species has a life stage able to breath, feed, and develop either continually submerged or without access to water. Such truly amphibious insects are unrecorded. In mountain streams across the Hawaiian Islands, some caterpillars in the endemic moth genus Hyposmocoma are truly amphibious. These larvae can breathe and feed indefinitely both above and below the water's surface and can mature completely submerged or dry. Remarkably, a molecular phylogeny based on 2,243 bp from both nuclear (elongation factor 1α and carbomoylphosphate synthase) and mitochondrial (cytochrome oxidase I) genes representing 216 individuals and 89 species of Hyposmocoma reveals that this amphibious lifestyle is an example of parallel evolution and has arisen from strictly terrestrial clades at least three separate times in the genus starting more than 6 million years ago, before the current high islands existed. No other terrestrial genus of animals has sponsored so many independent aquatic invasions, and no other insects are able to remain active indefinitely above and below water. Why and how Hyposmocoma, an overwhelmingly terrestrial group, repeatedly evolved unprecedented aquatic species is unclear, although there are many other evolutionary anomalies across the Hawaiian archipelago. The uniqueness of the community assemblages of Hawaii's isolated biota is likely critical in generating such evolutionary novelty because this amphibious ecology is unknown anywhere else. PMID:20308549

Relaxed functional constraints on triplicate α-globin gene in the bank vole suggest a different evolutionary history from other rodents

PubMed Central

Marková, S; Searle, J B; Kotlík, P

2014-01-01

Gene duplication plays an important role in the origin of evolutionary novelties, but the mechanisms responsible for the retention and functional divergence of the duplicated copy are not fully understood. The α-globin genes provide an example of a gene family with different numbers of gene duplicates among rodents. Whereas Rattus and Peromyscus each have three adult α-globin genes (HBA-T1, HBA-T2 and HBA-T3), Mus has only two copies. High rates of amino acid evolution in the independently derived HBA-T3 genes of Peromyscus and Rattus have been attributed to positive selection. Using RACE PCR, reverse transcription-PCR (RT–PCR) and RNA-seq, we show that another rodent, the bank vole Clethrionomys glareolus, possesses three transcriptionally active α-globin genes. The bank vole HBA-T3 gene is distinguished from each HBA-T1 and HBA-T2 by 20 amino acids and is transcribed 23- and 4-fold lower than HBA-T1 and HBA-T2, respectively. Polypeptides corresponding to all three genes are detected by electrophoresis, demonstrating that the translated products of HBA-T3 are present in adult erythrocytes. Patterns of codon substitution and the presence of low-frequency null alleles suggest a postduplication relaxation of purifying selection on bank vole HBA-T3. PMID:24595364

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes

PubMed Central

Duchen, Pablo; Leuenberger, Christoph; Szilágyi, Sándor M.; Harmon, Luke; Eastman, Jonathan; Schweizer, Manuel

2017-01-01

Abstract Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson’s hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits. PMID:28204787

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

PubMed

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.

Planetary Bootstrap: A Prelude to Biosphere Phenomenology

NASA Astrophysics Data System (ADS)

Kazansky, Alexander B.

2004-08-01

This paper deals with systemic status as well as with some phenomenological and evolutionary aspects of biosphere. Biosphere is represented as multilevel autopoietic system in which different organizational levels are nested into each other. The conceptual model of punctuated epigenesis, biosphere evolutionary process is suggested, in which endogenous planetary organizational crises play role of evolutionary mechanism, creating novelty. The hypothesis is proposed, that the biosphere reaction on the humankind destructive activity reminds the distributed immune response of biological organism, described by F.Varela in his "cognitive immunology". The biosphere evolution is interpreted as the hermeneutical spiral of "Process Being" self-uncovering thus illustrating the historical process of transformation of biosphere as the type of Being in the periods of crises. Some arguments are adduced in favor of biosphere phenomenology development and application of the methods of second-order cybernetics to actual problems of planetary scale.

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes.

PubMed

Duchen, Pablo; Leuenberger, Christoph; Szilágyi, Sándor M; Harmon, Luke; Eastman, Jonathan; Schweizer, Manuel; Wegmann, Daniel

2017-11-01

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson's hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits. The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Evolutionary dynamics from a variational principle.

PubMed

Klimek, Peter; Thurner, Stefan; Hanel, Rudolf

2010-07-01

We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of some evolutionary systems. A key characteristic of evolutionary systems is the ongoing endogenous production of new species. These novel entities change the conditions for already existing species. Even Darwin's Demon, a hypothetical entity with exact knowledge of the abundance of all species and their fitness functions at a given time, could not prestate the impact of these novelties on established populations. We argue that fitness is always a posteriori knowledge--it measures but does not explain why a species has reproductive success or not. To overcome these conceptual limitations, a variational principle is proposed in a spin-model-like setup of evolutionary systems. We derive a functional which is minimized under the most general evolutionary formulation of a dynamical system, i.e., evolutionary trajectories causally emerge as a minimization of a functional. This functional allows the derivation of analytic solutions of the asymptotic diversity for stochastic evolutionary systems within a mean-field approximation. We test these approximations by numerical simulations of the corresponding model and find good agreement in the position of phase transitions in diversity curves. The model is further able to reproduce stylized facts of timeseries from several man-made and natural evolutionary systems. Light will be thrown on how species and their fitness landscapes dynamically coevolve.

Boosting-Based Optimization as a Generic Framework for Novelty and Fraud Detection in Complex Strategies

NASA Astrophysics Data System (ADS)

Gavrishchaka, Valeriy V.; Kovbasinskaya, Maria; Monina, Maria

2008-11-01

Novelty detection is a very desirable additional feature of any practical classification or forecasting system. Novelty and rare patterns detection is the main objective in such applications as fault/abnormality discovery in complex technical and biological systems, fraud detection and risk management in financial and insurance industry. Although many interdisciplinary approaches for rare event modeling and novelty detection have been proposed, significant data incompleteness due to the nature of the problem makes it difficult to find a universal solution. Even more challenging and much less formalized problem is novelty detection in complex strategies and models where practical performance criteria are usually multi-objective and the best state-of-the-art solution is often not known due to the complexity of the task and/or proprietary nature of the application area. For example, it is much more difficult to detect a series of small insider trading or other illegal transactions mixed with valid operations and distributed over long time period according to a well-designed strategy than a single, large fraudulent transaction. Recently proposed boosting-based optimization was shown to be an effective generic tool for the discovery of stable multi-component strategies/models from the existing parsimonious base strategies/models in financial and other applications. Here we outline how the same framework can be used for novelty and fraud detection in complex strategies and models.

Bistability of Evolutionary Stable Vaccination Strategies in the Reinfection SIRI Model.

PubMed

Martins, José; Pinto, Alberto

2017-04-01

We use the reinfection SIRI epidemiological model to analyze the impact of education programs and vaccine scares on individuals decisions to vaccinate or not. The presence of the reinfection provokes the novelty of the existence of three Nash equilibria for the same level of the morbidity relative risk instead of a single Nash equilibrium as occurs in the SIR model studied by Bauch and Earn (PNAS 101:13391-13394, 2004). The existence of three Nash equilibria, with two of them being evolutionary stable, introduces two scenarios with relevant and opposite features for the same level of the morbidity relative risk: the low-vaccination scenario corresponding to the evolutionary stable vaccination strategy, where individuals will vaccinate with a low probability; and the high-vaccination scenario corresponding to the evolutionary stable vaccination strategy, where individuals will vaccinate with a high probability. We introduce the evolutionary vaccination dynamics for the SIRI model and we prove that it is bistable. The bistability of the evolutionary dynamics indicates that the damage provoked by false scares on the vaccination perceived morbidity risks can be much higher and much more persistent than in the SIR model. Furthermore, the vaccination education programs to be efficient they need to implement a mechanism to suddenly increase the vaccination coverage level.

New genes contribute to genetic and phenotypic novelties in human evolution

PubMed Central

Zhang, Yong E.; Long, Manyuan

2014-01-01

New genes in human genomes have been found relevant in evolution and biology of humans. It was conservatively estimated that the human genome encodes more than 300 human-specific genes and 1,000 primate-specific genes. These new arrivals appear to be implicated in brain function and male reproduction. Surprisingly, increasing evidence indicates that they may also bring negative pleiotropic effects, while assuming various possible biological functions as sources of phenotypic novelties, suggesting a non-progressive route for functional evolution. Similar to these fixed new genes, polymorphic new genes were found to contribute to functional evolution within species, e.g. with respect to digestion or disease resistance, revealing that new genes can acquire new or diverged functions in its initial stage as prototypic genes. These progresses have provided new opportunity to explore the genetic basis of human biology and human evolutionary history in a new dimension. PMID:25218862

Cadherin genes and evolutionary novelties in the octopus.

PubMed

Wang, Z Yan; Ragsdale, Clifton W

2017-09-01

All animals with large brains must have molecular mechanisms to regulate neuronal process outgrowth and prevent neurite self-entanglement. In vertebrates, two major gene families implicated in these mechanisms are the clustered protocadherins and the atypical cadherins. However, the molecular mechanisms utilized in complex invertebrate brains, such as those of the cephalopods, remain largely unknown. Recently, we identified protocadherins and atypical cadherins in the octopus. The octopus protocadherin expansion shares features with the mammalian clustered protocadherins, including enrichment in neural tissues, clustered head-to-tail orientations in the genome, and a large first exon encoding all cadherin domains. Other octopus cadherins, including a newly-identified cadherin with 77 extracellular cadherin domains, are elevated in the suckers, a striking cephalopod novelty. Future study of these octopus genes may yield insights into the general functions of protocadherins in neural wiring and cadherin-related proteins in complex morphogenesis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolutionary developmental genetics of fruit morphological variation within the Solanaceae

PubMed Central

Wang, Li; Li, Jing; Zhao, Jing; He, Chaoying

2015-01-01

Morphological variations of fruits such as shape and size, and color are a result of adaptive evolution. The evolution of morphological novelties is particularly intriguing. An understanding of these evolutionary processes calls for the elucidation of the developmental and genetic mechanisms that result in particular fruit morphological characteristics, which determine seed dispersal. The genetic and developmental basis for fruit morphological variation was established at a microevolutionary time scale. Here, we summarize the progress on the evolutionary developmental genetics of fruit size, shape and color in the Solanaceae. Studies suggest that the recruitment of a pre-existing gene and subsequent modification of its interaction and regulatory networks are frequently involved in the evolution of morphological diversity. The basic mechanisms underlying changes in plant morphology are alterations in gene expression and/or gene function. We also deliberate on the future direction in evolutionary developmental genetics of fruit morphological variation such as fruit type. These studies will provide insights into plant developmental processes and will help to improve the productivity and fruit quality of crops. PMID:25918515

Tracing the evolutionary origin of vertebrate skeletal tissues: insights from cephalochordate amphioxus.

PubMed

Yong, Luok Wen; Yu, Jr-Kai

2016-08-01

Vertebrate mineralized skeletal tissues are widely considered as an evolutionary novelty. Despite the importance of these tissues to the adaptation and radiation of vertebrate animals, the evolutionary origin of vertebrate skeletal tissues remains largely unclear. Cephalochordates (Amphioxus) occupy a key phylogenetic position and can serve as a valuable model for studying the evolution of vertebrate skeletal tissues. Here we summarize recent advances in amphioxus developmental biology and comparative genomics that can help to elucidate the evolutionary origins of the vertebrate skeletal tissues and their underlying developmental gene regulatory networks (GRN). By making comparisons to the developmental studies in vertebrate models and recent discoveries in paleontology and genomics, it becomes evident that the collagen matrix-based connective tissues secreted by the somite-derived cells in amphioxus likely represent the rudimentary skeletal tissues in chordates. We propose that upon the foundation of this collagenous precursor, novel tissue mineralization genes that arose from gene duplications were incorporated into an ancestral mesodermal GRN that makes connective and supporting tissues, leading to the emergence of highly-mineralized skeletal tissues in early vertebrates. Copyright © 2016 Elsevier Ltd. All rights reserved.

Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera.

PubMed

Whittington, Emma; Forsythe, Desiree; Borziak, Kirill; Karr, Timothy L; Walters, James R; Dorus, Steve

2017-12-02

Rapid evolution is a hallmark of reproductive genetic systems and arises through the combined processes of sequence divergence, gene gain and loss, and changes in gene and protein expression. While studies aiming to disentangle the molecular ramifications of these processes are progressing, we still know little about the genetic basis of evolutionary transitions in reproductive systems. Here we conduct the first comparative analysis of sperm proteomes in Lepidoptera, a group that exhibits dichotomous spermatogenesis, in which males produce a functional fertilization-competent sperm (eupyrene) and an incompetent sperm morph lacking nuclear DNA (apyrene). Through the integrated application of evolutionary proteomics and genomics, we characterize the genomic patterns potentially associated with the origination and evolution of this unique spermatogenic process and assess the importance of genetic novelty in Lepidopteran sperm biology. Comparison of the newly characterized Monarch butterfly (Danaus plexippus) sperm proteome to those of the Carolina sphinx moth (Manduca sexta) and the fruit fly (Drosophila melanogaster) demonstrated conservation at the level of protein abundance and post-translational modification within Lepidoptera. In contrast, comparative genomic analyses across insects reveals significant divergence at two levels that differentiate the genetic architecture of sperm in Lepidoptera from other insects. First, a significant reduction in orthology among Monarch sperm genes relative to the remainder of the genome in non-Lepidopteran insect species was observed. Second, a substantial number of sperm proteins were found to be specific to Lepidoptera, in that they lack detectable homology to the genomes of more distantly related insects. Lastly, the functional importance of Lepidoptera specific sperm proteins is broadly supported by their increased abundance relative to proteins conserved across insects. Our results identify a burst of genetic novelty amongst sperm proteins that may be associated with the origin of heteromorphic spermatogenesis in ancestral Lepidoptera and/or the subsequent evolution of this system. This pattern of genomic diversification is distinct from the remainder of the genome and thus suggests that this transition has had a marked impact on lepidopteran genome evolution. The identification of abundant sperm proteins unique to Lepidoptera, including proteins distinct between specific lineages, will accelerate future functional studies aiming to understand the developmental origin of dichotomous spermatogenesis and the functional diversification of the fertilization incompetent apyrene sperm morph.

Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution

PubMed Central

Clarke, Thomas H.; Garb, Jessica E.; Hayashi, Cheryl Y.; Arensburger, Peter; Ayoub, Nadia A.

2015-01-01

The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae). PMID:26058392

Retracing Evolution of Red Fluorescence in GFP-Like Proteins from Faviina Corals

PubMed Central

Field, Steven F.; Matz, Mikhail V.

2010-01-01

Proteins of the green fluorescent protein family represent a convenient experimental model to study evolution of novelty at the molecular level. Here, we focus on the origin of Kaede-like red fluorescent proteins characteristic of the corals of the Faviina suborder. We demonstrate, using an original approach involving resurrection and analysis of the library of possible evolutionary intermediates, that it takes on the order of 12 mutations, some of which strongly interact epistatically, to fully recapitulate the evolution of a red fluorescent phenotype from the ancestral green. Five of the identified mutations would not have been found without the help of ancestral reconstruction, because the corresponding site states are shared between extant red and green proteins due to their recent descent from a dual-function common ancestor. Seven of the 12 mutations affect residues that are not in close contact with the chromophore and thus must exert their effect indirectly through adjustments of the overall protein fold; the relevance of these mutations could not have been anticipated from the purely theoretical analysis of the protein's structure. Our results introduce a powerful experimental approach for comparative analysis of functional specificity in protein families even in the cases of pronounced epistasis, provide foundation for the detailed studies of evolutionary trajectories leading to novelty and complexity, and will help rational modification of existing fluorescent labels. PMID:19793832

Endogenous Retroviruses in the Genomics Era.

PubMed

Johnson, Welkin E

2015-11-01

Endogenous retroviruses comprise millions of discrete genetic loci distributed within the genomes of extant vertebrates. These sequences, which are clearly related to exogenous retroviruses, represent retroviral infections of the deep past, and their abundance suggests that retroviruses were a near-constant presence throughout the evolutionary history of modern vertebrates. Endogenous retroviruses contribute in myriad ways to the evolution of host genomes, as mutagens and as sources of genetic novelty (both coding and regulatory) to be acted upon by the twin engines of random genetic drift and natural selection. Importantly, the richness and complexity of endogenous retrovirus data can be used to understand how viruses spread and adapt on evolutionary timescales by combining population genetics and evolutionary theory with a detailed understanding of retrovirus biology (gleaned from the study of extant retroviruses). In addition to revealing the impact of viruses on organismal evolution, such studies can help us better understand, by looking back in time, how life-history traits, as well as ecological and geological events, influence the movement of viruses within and between populations.

Feedbacks between geomorphology and biota controlling Earth surface processes and landforms: A review of foundation concepts and current understandings

NASA Astrophysics Data System (ADS)

Corenblit, Dov; Baas, Andreas C. W.; Bornette, Gudrun; Darrozes, José; Delmotte, Sébastien; Francis, Robert A.; Gurnell, Angela M.; Julien, Frédéric; Naiman, Robert J.; Steiger, Johannes

2011-06-01

This review article presents recent advances in the field of biogeomorphology related to the reciprocal coupling between Earth surface processes and landforms, and ecological and evolutionary processes. The aim is to present to the Earth Science community ecological and evolutionary concepts and associated recent conceptual developments for linking geomorphology and biota. The novelty of the proposed perspective is that (1) in the presence of geomorphologic-engineer species, which modify sediment and landform dynamics, natural selection operating at the scale of organisms may have consequences for the physical components of ecosystems, and particularly Earth surface processes and landforms; and (2) in return, these modifications of geomorphologic processes and landforms often feed back to the ecological characteristics of the ecosystem (structure and function) and thus to biological characteristics of engineer species and/or other species (adaptation and speciation). The main foundation concepts from ecology and evolutionary biology which have led only recently to an improved conception of landform dynamics in geomorphology are reviewed and discussed. The biogeomorphologic macroevolutionary insights proposed explicitly integrate geomorphologic niche-dimensions and processes within an ecosystem framework and reflect current theories of eco-evolutionary and ecological processes. Collectively, these lead to the definition of an integrated model describing the overall functioning of biogeomorphologic systems over ecological and evolutionary timescales.

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

PubMed

Borges, Renee M

2017-07-01

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

Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution.

PubMed

Clarke, Thomas H; Garb, Jessica E; Hayashi, Cheryl Y; Arensburger, Peter; Ayoub, Nadia A

2015-06-08

The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae). © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Cranial muscles in amphibians: development, novelties and the role of cranial neural crest cells

PubMed Central

Schmidt, Jennifer; Piekarski, Nadine; Olsson, Lennart

2013-01-01

Our research on the evolution of the vertebrate head focuses on understanding the developmental origins of morphological novelties. Using a broad comparative approach in amphibians, and comparisons with the well-studied quail-chicken system, we investigate how evolutionarily conserved or variable different aspects of head development are. Here we review research on the often overlooked development of cranial muscles, and on its dependence on cranial cartilage development. In general, cranial muscle cell migration and the spatiotemporal pattern of cranial muscle formation appears to be very conserved among the few species of vertebrates that have been studied. However, fate-mapping of somites in the Mexican axolotl revealed differences in the specific formation of hypobranchial muscles (tongue muscles) in comparison to the chicken. The proper development of cranial muscles has been shown to be strongly dependent on the mostly neural crest-derived cartilage elements in the larval head of amphibians. For example, a morpholino-based knock-down of the transcription factor FoxN3 in Xenopus laevis has drastic indirect effects on cranial muscle patterning, although the direct function of the gene is mostly connected to neural crest development. Furthermore, extirpation of single migratory streams of cranial neural crest cells in combination with fate-mapping in a frog shows that individual cranial muscles and their neural crest-derived connective tissue attachments originate from the same visceral arch, even when the muscles attach to skeletal components that are derived from a different arch. The same pattern has also been found in the chicken embryo, the only other species that has been thoroughly investigated, and thus might be a conserved pattern in vertebrates that reflects the fundamental nature of a mechanism that keeps the segmental order of the head in place despite drastic changes in adult anatomy. There is a need for detailed comparative fate-mapping of pre-otic paraxial mesoderm in amphibians, to determine developmental causes underlying the complicated changes in cranial muscle development and architecture within amphibians, and in particular how the novel mouth apparatus in frog tadpoles evolved. This will also form a foundation for further research into the molecular mechanisms that regulate rostral head morphogenesis. Our empirical studies are discussed within a theoretical framework concerned with the evolutionary origin and developmental basis of novel anatomical structures in general. We argue that a common developmental origin is not a fool-proof guide to homology, and that a view that sees only structures without homologs as novel is too restricted, because novelties must be produced by changes in the same framework of developmental processes. At the level of developmental processes and mechanisms, novel structures are therefore likely to have homologs, and we need to develop a hierarchical concept of novelty that takes this into account. PMID:22780231

Grand Views of Evolution.

PubMed

de Vladar, Harold P; Santos, Mauro; Szathmáry, Eörs

2017-05-01

Despite major advances in evolutionary theories, some aspects of evolution remain neglected: whether evolution: would come to a halt without abiotic change; is unbounded and open-ended; or is progressive and something beyond fitness is maximized. Here, we discuss some models of ecology and evolution and argue that ecological change, resulting in Red Queen dynamics, facilitates (but does not ensure) innovation. We distinguish three forms of open-endedness. In weak open-endedness, novel phenotypes can occur indefinitely. Strong open-endedness requires the continual appearance of evolutionary novelties and/or innovations. Ultimate open-endedness entails an indefinite increase in complexity, which requires unlimited heredity. Open-ended innovation needs exaptations that generate novel niches. This can result in new traits and new rules as the dynamics unfolds, suggesting that evolution is not fully algorithmic. Copyright © 2017 Elsevier Ltd. All rights reserved.

Male rats that differ in novelty exploration demonstrate distinct patterns of sexual behavior

PubMed Central

Cummings, Jennifer A.; Clinton, Sarah M.; Perry, Adam N.; Akil, Huda; Becker, Jill B.

2014-01-01

High versus low novelty exploration predicts a variety of behavioral differences. For example, rats selectively-bred for high novelty exploration (bred High Responders, bHR) exhibit exaggerated aggression, impulsivity, and proclivity to addictive behaviors compared to low novelty-reactive rats (bred Low Responders, bLRs), which are characterized by a high anxiety/depressive-like phenotype. Since bHR/bLR rats exhibit differences in dopaminergic circuitry and differential response to rewarding stimuli (i.e., psychostimulants, food), the present study examined whether they also differ in another key hedonic behavior – sex. Thus, adult bHR/bLR males were given five 30-min opportunities to engage in sexual activity with a receptive female. Sexual behavior and motivation were examined and compared between the groups. The bHR/bLR phenotype affected both sexual motivation and behavior, with bLR males demonstrating reduced motivation for sex compared with bHR males (i.e., fewer animals copulated, longer latency to engage in sex). The bHR males required more intromissions at a faster pace per ejaculation than did bLR males. Thus, neurobiological differences that affect motivation for drugs of abuse, aggression, and impulsivity in rats also affect sexual motivation and performance. PMID:23398441

Occurrence of neanderthal features in mandibles from the Atapuerca-SH site.

PubMed

Rosas, A

2001-01-01

Analysis of variation and distribution of evolutionary novelties is meaningful in understanding evolutionary processes. The mandible, as a morphological complex, comprises a large number of derived Neanderthal features. The present study investigates whether the features usually considered as European lineage apomorphies evolved independently; the occurrence of these features is studied in the mandibles from the Sima de los Huesos (SH) site (Atapuerca, Spain). For comparative purposes, a large sample of Neanderthal mandibles as well as older fossil Homo specimens have been used for the study. Chi-square tests were employed to test for independence. The SH mandibles present a set of features that clearly show the basic architecture of the Neanderthal mandible. A highly significant association is detected in the variation of the position of the mental foramen, the lateral prominence, and the anterior marginal tubercle, as well as in the development of retromolar space. However, a much weaker association is detected in the features of the internal aspect of the mandible, with a few exceptions. Features of the external aspect of the mandible occur chronologically earlier than those observed in the internal aspect. The hypothesis that two distinct and consecutive morphological processes have driven the emergence of the European lineage throughout the Middle Pleistocene is proposed. A first transformation affects the mandible by means of backwards displacement of the structures located at the external aspect, as well as the position of the condyle. A second process would modify the features of the internal aspect of the mandible, in which the relief of the masseteric and pterygoid fossae are affected, in association with a spatial rearrangement of the corpus and ramus. Analyzed individually, some of the considered features may be questioned as Neanderthal apomorphies (Trinkaus,1993; Franciscus and Trinkaus, 995); however, the joint occurrence of many of them suggests that the complex is an evolutionary novelty. Copyright 2001 Wiley-Liss, Inc.

Concentrated evolutionary novelties in the foot musculature of Odontophrynidae (Anura: Neobatrachia), with comments on adaptations for burrowing.

PubMed

Blotto, Boris L; Pereyra, Martin O; Faivovich, Julián; Dias, Pedro Henrique Dos Santos; Grant, Taran

2017-05-02

We studied the foot musculature of the fossorial family Odontophrynidae (composed of the genera Macrogenioglottus, Odontophrynus, and Proceratophrys) plus several outgroup taxa from Hyloidea and other burrowing taxa from across Anura. We found novel character-states supporting the monophyly of Odontophrynus, Proceratophrys, and Odontophrynus + Macrogenioglottus. The character-states observed in O. cultripes support conflicting phylogenetic positions within Odontophrynus. A comparison of some novel character-states with a diverse sample of burrowing taxa suggests that some modifications of the foot musculature might be involved in digging.

Learning and dynamics in social systems. Comment on "Collective learning modeling based on the kinetic theory of active particles" by D. Burini et al.

NASA Astrophysics Data System (ADS)

Dolfin, Marina

2016-03-01

The interesting novelty of the paper by Burini et al. [1] is that the authors present a survey and a new approach of collective learning based on suitable development of methods of the kinetic theory [2] and theoretical tools of evolutionary game theory [3]. Methods of statistical dynamics and kinetic theory lead naturally to stochastic and collective dynamics. Indeed, the authors propose the use of games where the state of the interacting entities is delivered by probability distributions.

Transcending Darwinism thinking laterally on the tree of life.

PubMed

Sapp, Jan

2009-01-01

The scope and significance of lateral gene transfer (LGT) has been discussed periodically since the early twentieth century. In sketching this history here we see that the pendulum of opinion has swung from one extreme that LGT is a rare phenomenon to the other that it is fundamental to evolution. That phages are sources of bacterial evolutionary innovation has been discussed since the 1920s in association with evidence that symbiosis is a major source of evolutionary innovation. Concepts of infectious heredity re-emerged with the rise of bacterial genetics after the Second World War, but LGT was generally discounted as a significant evolutionary force. LGT received increased attention in the 1960s and 1970s because of its role in antibiotic resistance outbreaks. Some speculated that the new molecular approaches to bacterial phylogenetics were ill-conceived because of LGT. With the rise of genomics in the 1990s, it became clear to phylogeneticists that LGT is the principal mode of generating evolutionary novelty in the prokaryotic world. All microbiologists agree today that the Darwinian concept of a bifurcating tree is an inadequate, if not misleading, representation of the evolutionary process in the microbial world. Phages are also reconceived not only as agents of bacterial gene exchange, but also as organisms in their own right, and fundamental in the evolution of new genes.

Whole-mount in situ hybridization in the rotifer Brachionus plicatilis representing a basal branch of lophotrochozoans.

PubMed

Boell, Louis A; Bucher, Gregor

2008-08-01

In order to broaden the comparative scope of evolutionary developmental biology and to refine our picture of animal macroevolution, it is necessary to establish new model organisms, especially from previously underrepresented groups, like the Lophotrochozoa. We have established the culture and protocols for molecular developmental biology in the rotifer species Brachionus plicatilis Müller (Rotifera, Monogononta). Rotifers are nonsegmented animals with enigmatic basal position within the lophotrochozoans and marked by several evolutionary novelties like the wheel organ (corona), the median eye, and the nonpaired posterior foot. The expression of Bp-Pax-6 is shown using whole-mount in situ hybridization. The inexpensive easy culture and experimental tractability of Brachionus as well as the range of interesting questions to which it holds the key make it a promising addition to the "zoo" of evo-devo model organisms.

Fossil evidence for the origin of Homo sapiens.

PubMed

Schwartz, Jeffrey H; Tattersall, Ian

2010-01-01

Our species Homo sapiens has never received a satisfactory morphological definition. Deriving partly from Linnaeus's exhortation simply to "know thyself," and partly from the insistence by advocates of the Evolutionary Synthesis in the mid-20th Century that species are constantly transforming ephemera that by definition cannot be pinned down by morphology, this unfortunate situation has led to huge uncertainty over which hominid fossils ought to be included in H. sapiens, and even over which of them should be qualified as "archaic" or as "anatomically modern," a debate that is an oddity in the broader context of paleontology. Here, we propose a suite of features that seems to characterize all H. sapiens alive today, and we review the fossil evidence in light of those features, paying particular attention to the bipartite brow and the "chin" as examples of how, given the continuum from developmentally regulated genes to adult morphology, we might consider features preserved in fossil specimens in a comparative analysis that includes extant taxa. We also suggest that this perspective on the origination of novelty, which has gained a substantial foothold in the general field of evolutionary developmental biology, has an intellectual place in paleoanthropology and hominid systematics, including in defining our species, H. sapiens. Beginning solely with the distinctive living species reveals a startling variety in morphologies among late middle and late Pleistocene hominids, none of which can be plausibly attributed to H. sapiens/H. neanderthalensis admixture. Allowing for a slightly greater envelope of variation than exists today, basic "modern" morphology seems to have appeared significantly earlier in time than the first stirrings of the modern symbolic cognitive system. Copyright © 2010 Wiley-Liss, Inc.

The Phylogenetic Origin of oskar Coincided with the Origin of Maternally Provisioned Germ Plasm and Pole Cells at the Base of the Holometabola

PubMed Central

Lynch, Jeremy A.; Özüak, Orhan; Khila, Abderrahman; Abouheif, Ehab; Desplan, Claude; Roth, Siegfried

2011-01-01

The establishment of the germline is a critical, yet surprisingly evolutionarily labile, event in the development of sexually reproducing animals. In the fly Drosophila, germ cells acquire their fate early during development through the inheritance of the germ plasm, a specialized maternal cytoplasm localized at the posterior pole of the oocyte. The gene oskar (osk) is both necessary and sufficient for assembling this substance. Both maternal germ plasm and oskar are evolutionary novelties within the insects, as the germline is specified by zygotic induction in basally branching insects, and osk has until now only been detected in dipterans. In order to understand the origin of these evolutionary novelties, we used comparative genomics, parental RNAi, and gene expression analyses in multiple insect species. We have found that the origin of osk and its role in specifying the germline coincided with the innovation of maternal germ plasm and pole cells at the base of the holometabolous insects and that losses of osk are correlated with changes in germline determination strategies within the Holometabola. Our results indicate that the invention of the novel gene osk was a key innovation that allowed the transition from the ancestral late zygotic mode of germline induction to a maternally controlled establishment of the germline found in many holometabolous insect species. We propose that the ancestral role of osk was to connect an upstream network ancestrally involved in mRNA localization and translational control to a downstream regulatory network ancestrally involved in executing the germ cell program. PMID:21552321

Metabolomics for secondary metabolite research.

PubMed

Breitling, Rainer; Ceniceros, Ana; Jankevics, Andris; Takano, Eriko

2013-11-11

Metabolomics, the global characterization of metabolite profiles, is becoming an increasingly powerful tool for research on secondary metabolite discovery and production. In this review we discuss examples of recent technological advances and biological applications of metabolomics in the search for chemical novelty and the engineered production of bioactive secondary metabolites.

The great billion-year war between ribosome- and capsid-encoding organisms (cells and viruses) as the major source of evolutionary novelties.

PubMed

Forterre, Patrick; Prangishvili, David

2009-10-01

Our conceptions on the origin, nature, and role of viruses have been shaken recently by several independent lines of research. There are many reasons to believe now that viruses are more ancient than modern cells and have always been more abundant and diverse than their cellular targets. Viruses can be defined as capsid-encoding organisms that transform their "host" cell into a viral factory. If capsid-encoding organisms (viruses) and ribosome-encoding organisms (cells) are the major types of living entities on our planet, it seems logical to conclude that their conflict has been a major engine of biological evolution (in the framework of natural selection). In particular, many novelties first selected in the viral world might have been transferred to cells as a consequence of the continuous flow of viral genes into cellular genomes. We discuss recent observations and hypotheses suggesting that viruses have played a major role at different stages of biological evolution, such as the RNA to DNA transition, the origin of the eukaryotic nucleus, or, alternatively, the origin of unique features in multicellular macrobes.

Sequence analyses of the distal-less homeobox gene family in East African cichlid fishes reveal signatures of positive selection.

PubMed

Diepeveen, Eveline T; Kim, Fabienne D; Salzburger, Walter

2013-07-17

Gen(om)e duplication events are hypothesized as key mechanisms underlying the origin of phenotypic diversity and evolutionary innovation. The diverse and species-rich lineage of teleost fishes is a renowned example of this scenario, because of the fish-specific genome duplication. Gene families, generated by this and other gene duplication events, have been previously found to play a role in the evolution and development of innovations in cichlid fishes - a prime model system to study the genetic basis of rapid speciation, adaptation and evolutionary innovation. The distal-less homeobox genes are particularly interesting candidate genes for evolutionary novelties, such as the pharyngeal jaw apparatus and the anal fin egg-spots. Here we study the dlx repertoire in 23 East African cichlid fishes to determine the rate of evolution and the signatures of selection pressure. Four intact dlx clusters were retrieved from cichlid draft genomes. Phylogenetic analyses of these eight dlx loci in ten teleost species, followed by an in-depth analysis of 23 East African cichlid species, show that there is disparity in the rates of evolution of the dlx paralogs. Dlx3a and dlx4b are the fastest evolving dlx genes, while dlx1a and dlx6a evolved more slowly. Subsequent analyses of the nonsynonymous-synonymous substitution rate ratios indicate that dlx3b, dlx4a and dlx5a evolved under purifying selection, while signs of positive selection were found for dlx1a, dlx2a, dlx3a and dlx4b. Our results indicate that the dlx repertoire of teleost fishes and cichlid fishes in particular, is shaped by differential selection pressures and rates of evolution after gene duplication. Although the divergence of the dlx paralogs are putative signs of new or altered functions, comparisons with available expression patterns indicate that the three dlx loci under strong purifying selection, dlx3b, dlx4a and dlx5a, are transcribed at high levels in the cichlids' pharyngeal jaw and anal fin. The dlx paralogs emerge as excellent candidate genes for the development of evolutionary innovations in cichlids, although further functional analyses are necessary to elucidate their respective contribution.

Applications of unmanned aerial vehicles in weed science

USDA-ARS?s Scientific Manuscript database

For most producers, unmanned aerial vehicles (UAV) are a novelty that has been little employed in their agricultural operations. An UAV will not fix every problem on the farm, but there are some practical applications for which UAVs have demonstrated value. Three examples of how UAVs have been used...

Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families.

PubMed

Lehti-Shiu, Melissa D; Panchy, Nicholas; Wang, Peipei; Uygun, Sahra; Shiu, Shin-Han

2017-01-01

Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental to plant development and environmental response. In addition, expansion of TF families has allowed functional divergence of duplicate copies, which has contributed to novel, and in some cases adaptive, traits in plants. Thus, TFs are central to the generation of the diverse plant species that we see today. Major plant agronomic traits, including those relevant to domestication, have also frequently arisen through changes in TF coding sequence or expression patterns. Here our goal is to provide an overview of plant TF evolution by first comparing the diversity of DNA-binding domains and the sizes of these domain families in plants and other eukaryotes. Because TFs are among the most highly expanded gene families in plants, the birth and death process of TFs as well as the mechanisms contributing to their retention are discussed. We also provide recent examples of how TFs have contributed to novel traits that are important in plant evolution and in agriculture.This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer. Copyright © 2016 Elsevier B.V. All rights reserved.

Neutron-captures in Low Mass Stars and the Early Solar System Record of Short-lived Radioactivities

NASA Astrophysics Data System (ADS)

Busso, Maurizio; Vescovi, Diego; Trippella, Oscar; Palmerini, Sara; Cristallo, Sergio; Piersanti, Luciano

2018-01-01

Noticeable improvements were recently introduced in the modelling of n-capture nucleosynthesis in the advanced evolutionary stages of giant stars (Asymptotic Giant Branch, or AGB, stars). Two such improvements are closely linked together and concern the introduction of non-parameterized, physical models for extended mixing processes and the adoption of accurate reaction rates for H- and He-burning reactions, including the one for the main neutron source 13C(α,n)16O. These improvements profited of a longstanding collaboration between stellar physicists and C. Spitaleri's team and of his seminal work both as a leader in the Nuclear Astrophysics scenario and as a talent-scout in the recruitment of young researchers in the field. We present an example of the innovative results that can be obtained thanks to the novelties introduced, by estimating the contributions from a nearby AGB star to the synthesis of short-lived (t1/2 ≤ 10 Myr) radioactive nuclei which were alive in early Solar System condensates. We find that the scenario indicating an AGB star as the source of such radioactivities, discussed for many years by researchers in this field, appears now to be no longer viable, when the mentioned improvements of AGB models and nuclear parameters are considered.

Phylogenetic investigation of human FGFR-bearing paralogons favors piecemeal duplication theory of vertebrate genome evolution.

PubMed

Ajmal, Wajya; Khan, Hiba; Abbasi, Amir Ali

2014-12-01

Understanding the genetic mechanisms underlying the organismal complexity and origin of novelties during vertebrate history is one of the central goals of evolutionary biology. Ohno (1970) was the first to postulate that whole genome duplications (WGD) have played a vital role in the evolution of new gene functions: permitting an increase in morphological, physiological and anatomical complexity during early vertebrate history. Here, we analyze the evolutionary history of human FGFR-bearing paralogon (human autosome 4/5/8/10) by the phylogenetic analysis of multigene families with triplicate and quadruplicate distribution on these chromosomes. Our results categorized the histories of 21 families into discrete co-duplicated groups. Genes of a particular co-duplicated group exhibit identical evolutionary history and have duplicated in concert with each other, whereas genes belonging to different groups have dissimilar histories and have not duplicated concurrently. Taken together with our previously published data, we submit that there is sufficient empirical evidence to disprove the 1R/2R hypothesis and to support the general prediction that vertebrate genome evolved by relatively small-scale, regional duplication events that spread across the history of life. Copyright © 2014 Elsevier Inc. All rights reserved.

Causal evidence between monsoon and evolution of rhizomyine rodents

PubMed Central

López-Antoñanzas, Raquel; Knoll, Fabien; Wan, Shiming; Flynn, Lawrence J.

2015-01-01

The modern Asian monsoonal systems are currently believed to have originated around the end of the Oligocene following a crucial step of uplift of the Tibetan-Himalayan highlands. Although monsoon possibly drove the evolution of many mammal lineages during the Neogene, no evidence thereof has been provided so far. We examined the evolutionary history of a clade of rodents, the Rhizomyinae, in conjunction with our current knowledge of monsoon fluctuations over time. The macroevolutionary dynamics of rhizomyines were analyzed within a well-constrained phylogenetic framework coupled with biogeographic and evolutionary rate studies. The evolutionary novelties developed by these rodents were surveyed in parallel with the fluctuations of the Indian monsoon so as to evaluate synchroneity and postulate causal relationships. We showed the existence of three drops in biodiversity during the evolution of rhizomyines, all of which reflected elevated extinction rates. Our results demonstrated linkage of monsoon variations with the evolution and biogeography of rhizomyines. Paradoxically, the evolution of rhizomyines was accelerated during the phases of weakening of the monsoons, not of strengthening, most probably because at those intervals forest habitats declined, which triggered extinction and progressive specialization toward a burrowing existence. PMID:25759260

Terrestrial reproduction as an adaptation to steep terrain in African toads

PubMed Central

Müller, Hendrik; Hafner, Julian; Penner, Johannes; Mazuch, Tomáš; Rödel, Mark-Oliver; Loader, Simon P.

2017-01-01

How evolutionary novelties evolve is a major question in evolutionary biology. It is widely accepted that changes in environmental conditions shift the position of selective optima, and advancements in phylogenetic comparative approaches allow the rigorous testing of such correlated transitions. A longstanding question in vertebrate biology has been the evolution of terrestrial life histories in amphibians and here, by investigating African bufonids, we test whether terrestrial modes of reproduction have evolved as adaptations to particular abiotic habitat parameters. We reconstruct and date the most complete species-level molecular phylogeny and estimate ancestral states for reproductive modes. By correlating continuous habitat measurements from remote sensing data and locality records with life-history transitions, we discover that terrestrial modes of reproduction, including viviparity evolved multiple times in this group, most often directly from fully aquatic modes. Terrestrial modes of reproduction are strongly correlated with steep terrain and low availability of accumulated water sources. Evolutionary transitions to terrestrial modes of reproduction occurred synchronously with or after transitions in habitat, and we, therefore, interpret terrestrial breeding as an adaptation to these abiotic conditions, rather than an exaptation that facilitated the colonization of montane habitats. PMID:28356450

Predicting evolutionary rescue via evolving plasticity in stochastic environments

PubMed Central

Baskett, Marissa L.

2016-01-01

Phenotypic plasticity and its evolution may help evolutionary rescue in a novel and stressful environment, especially if environmental novelty reveals cryptic genetic variation that enables the evolution of increased plasticity. However, the environmental stochasticity ubiquitous in natural systems may alter these predictions, because high plasticity may amplify phenotype–environment mismatches. Although previous studies have highlighted this potential detrimental effect of plasticity in stochastic environments, they have not investigated how it affects extinction risk in the context of evolutionary rescue and with evolving plasticity. We investigate this question here by integrating stochastic demography with quantitative genetic theory in a model with simultaneous change in the mean and predictability (temporal autocorrelation) of the environment. We develop an approximate prediction of long-term persistence under the new pattern of environmental fluctuations, and compare it with numerical simulations for short- and long-term extinction risk. We find that reduced predictability increases extinction risk and reduces persistence because it increases stochastic load during rescue. This understanding of how stochastic demography, phenotypic plasticity, and evolution interact when evolution acts on cryptic genetic variation revealed in a novel environment can inform expectations for invasions, extinctions, or the emergence of chemical resistance in pests. PMID:27655762

Causal evidence between monsoon and evolution of rhizomyine rodents.

PubMed

López-Antoñanzas, Raquel; Knoll, Fabien; Wan, Shiming; Flynn, Lawrence J

2015-03-11

The modern Asian monsoonal systems are currently believed to have originated around the end of the Oligocene following a crucial step of uplift of the Tibetan-Himalayan highlands. Although monsoon possibly drove the evolution of many mammal lineages during the Neogene, no evidence thereof has been provided so far. We examined the evolutionary history of a clade of rodents, the Rhizomyinae, in conjunction with our current knowledge of monsoon fluctuations over time. The macroevolutionary dynamics of rhizomyines were analyzed within a well-constrained phylogenetic framework coupled with biogeographic and evolutionary rate studies. The evolutionary novelties developed by these rodents were surveyed in parallel with the fluctuations of the Indian monsoon so as to evaluate synchroneity and postulate causal relationships. We showed the existence of three drops in biodiversity during the evolution of rhizomyines, all of which reflected elevated extinction rates. Our results demonstrated linkage of monsoon variations with the evolution and biogeography of rhizomyines. Paradoxically, the evolution of rhizomyines was accelerated during the phases of weakening of the monsoons, not of strengthening, most probably because at those intervals forest habitats declined, which triggered extinction and progressive specialization toward a burrowing existence.

Terrestrial reproduction as an adaptation to steep terrain in African toads.

PubMed

Liedtke, H Christoph; Müller, Hendrik; Hafner, Julian; Penner, Johannes; Gower, David J; Mazuch, Tomáš; Rödel, Mark-Oliver; Loader, Simon P

2017-03-29

How evolutionary novelties evolve is a major question in evolutionary biology. It is widely accepted that changes in environmental conditions shift the position of selective optima, and advancements in phylogenetic comparative approaches allow the rigorous testing of such correlated transitions. A longstanding question in vertebrate biology has been the evolution of terrestrial life histories in amphibians and here, by investigating African bufonids, we test whether terrestrial modes of reproduction have evolved as adaptations to particular abiotic habitat parameters. We reconstruct and date the most complete species-level molecular phylogeny and estimate ancestral states for reproductive modes. By correlating continuous habitat measurements from remote sensing data and locality records with life-history transitions, we discover that terrestrial modes of reproduction, including viviparity evolved multiple times in this group, most often directly from fully aquatic modes. Terrestrial modes of reproduction are strongly correlated with steep terrain and low availability of accumulated water sources. Evolutionary transitions to terrestrial modes of reproduction occurred synchronously with or after transitions in habitat, and we, therefore, interpret terrestrial breeding as an adaptation to these abiotic conditions, rather than an exaptation that facilitated the colonization of montane habitats. © 2017 The Author(s).

Evolutionary principles and their practical application

PubMed Central

Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

2011-01-01

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology. PMID:25567966

Evolutionary principles and their practical application.

PubMed

Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

2011-03-01

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology.

Novel azepino-perylenebisimides: synthesis, structure, and properties.

PubMed

Mishra, Ruchika; Panini, Piyush; Sankar, Jeyaraman

2014-08-01

The first example of an azepine ring formation by counterintuitive nucleophilic participation of DBU was observed at the sterically crowded bay area of electron-deficient perylenebisimide (PBI). This is also a rare example of the formation of a seven-membered ring via two consecutive C-N bond formations in a single step. Azepino-PBIs reveal panchromatic absorption covering the whole visible region. Further novelty of these PBIs lies within the fact that their photophysical characteristics can easily be modulated by suitable substituents.

Evidence for Evolution from the Vertebrate Fossil Record.

ERIC Educational Resources Information Center

Gingerich, Philip D.

1983-01-01

Discusses three examples of evolutionary transition in the vertebrate fossil record, considering evolutionary transitions at the species level. Uses archaic squirrel-like Paleocine primates, the earliest primates of modern aspect, as examples. Also reviews new evidence on the origin of whales and their transition from land to sea. (JN)

Increased genetic variation and evolutionary potential drive the success of an invasive grass.

PubMed

Lavergne, Sébastien; Molofsky, Jane

2007-03-06

Despite the increasing biological and economic impacts of invasive species, little is known about the evolutionary mechanisms that favor geographic range expansion and evolution of invasiveness in introduced species. Here, we focus on the invasive wetland grass Phalaris arundinacea L. and document the evolutionary consequences that resulted from multiple and uncontrolled introductions into North America of genetic material native to different European regions. Continental-scale genetic variation occurring in reed canarygrass' European range has been reshuffled and recombined within North American introduced populations, giving rise to a number of novel genotypes. This process alleviated genetic bottlenecks throughout reed canarygrass' introduced range, including in peripheral populations, where depletion of genetic diversity is expected and is observed in the native range. Moreover, reed canarygrass had higher genetic diversity and heritable phenotypic variation in its invasive range relative to its native range. The resulting high evolutionary potential of invasive populations allowed for rapid selection of genotypes with higher vegetative colonization ability and phenotypic plasticity. Our results show that repeated introductions of a single species may inadvertently create harmful invaders with high adaptive potential. Such invasive species may be able to evolve in response to changing climate, allowing them to have increasing impact on native communities and ecosystems in the future. More generally, multiple immigration events may thus trigger future adaptation and geographic spread of a species population by preventing genetic bottlenecks and generating genetic novelties through recombination.

Identifying Genetic Hotspots by Mapping Molecular Diversity of Widespread Trees: When Commonness Matters.

PubMed

Souto, Cintia P; Mathiasen, Paula; Acosta, María Cristina; Quiroga, María Paula; Vidal-Russell, Romina; Echeverría, Cristian; Premoli, Andrea C

2015-01-01

Conservation planning requires setting priorities at the same spatial scale at which decision-making processes are undertaken considering all levels of biodiversity, but current methods for identifying biodiversity hotspots ignore its genetic component. We developed a fine-scale approach based on the definition of genetic hotspots, which have high genetic diversity and unique variants that represent their evolutionary potential and evolutionary novelties. Our hypothesis is that wide-ranging taxa with similar ecological tolerances, yet of phylogenetically independent lineages, have been and currently are shaped by ecological and evolutionary forces that result in geographically concordant genetic patterns. We mapped previously published genetic diversity and unique variants of biparentally inherited markers and chloroplast sequences for 9 species from 188 and 275 populations, respectively, of the 4 woody dominant families of the austral temperate forest, an area considered a biodiversity hotspot. Spatial distribution patterns of genetic polymorphisms differed among taxa according to their ecological tolerances. Eight genetic hotspots were detected and we recommend conservation actions for some in the southern Coastal Range in Chile. Existing spatially explicit genetic data from multiple populations and species can help to identify biodiversity hotspots and guide conservation actions to establish science-based protected areas that will preserve the evolutionary potential of key habitats and species. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Past climate change on Sky Islands drives novelty in a core developmental gene network and its phenotype.

PubMed

Favé, Marie-Julie; Johnson, Robert A; Cover, Stefan; Handschuh, Stephan; Metscher, Brian D; Müller, Gerd B; Gopalan, Shyamalika; Abouheif, Ehab

2015-09-04

A fundamental and enduring problem in evolutionary biology is to understand how populations differentiate in the wild, yet little is known about what role organismal development plays in this process. Organismal development integrates environmental inputs with the action of gene regulatory networks to generate the phenotype. Core developmental gene networks have been highly conserved for millions of years across all animals, and therefore, organismal development may bias variation available for selection to work on. Biased variation may facilitate repeatable phenotypic responses when exposed to similar environmental inputs and ecological changes. To gain a more complete understanding of population differentiation in the wild, we integrated evolutionary developmental biology with population genetics, morphology, paleoecology and ecology. This integration was made possible by studying how populations of the ant species Monomorium emersoni respond to climatic and ecological changes across five 'Sky Islands' in Arizona, which are mountain ranges separated by vast 'seas' of desert. Sky Islands represent a replicated natural experiment allowing us to determine how repeatable is the response of M. emersoni populations to climate and ecological changes at the phenotypic, developmental, and gene network levels. We show that a core developmental gene network and its phenotype has kept pace with ecological and climate change on each Sky Island over the last ~90,000 years before present (BP). This response has produced two types of evolutionary change within an ant species: one type is unpredictable and contingent on the pattern of isolation of Sky lsland populations by climate warming, resulting in slight changes in gene expression, organ growth, and morphology. The other type is predictable and deterministic, resulting in the repeated evolution of a novel wingless queen phenotype and its underlying gene network in response to habitat changes induced by climate warming. Our findings reveal dynamics of developmental gene network evolution in wild populations. This holds important implications: (1) for understanding how phenotypic novelty is generated in the wild; (2) for providing a possible bridge between micro- and macroevolution; and (3) for understanding how development mediates the response of organisms to past, and potentially, future climate change.

The virtue of innovation: innovation through the lenses of biological evolution.

PubMed

Kell, Douglas B; Lurie-Luke, Elena

2015-02-06

We rehearse the processes of innovation and discovery in general terms, using as our main metaphor the biological concept of an evolutionary fitness landscape. Incremental and disruptive innovations are seen, respectively, as successful searches carried out locally or more widely. They may also be understood as reflecting evolution by mutation (incremental) versus recombination (disruptive). We also bring a platonic view, focusing on virtue and memory. We use 'virtue' as a measure of efforts, including the knowledge required to come up with disruptive and incremental innovations, and 'memory' as a measure of their lifespan, i.e. how long they are remembered. Fostering innovation, in the evolutionary metaphor, means providing the wherewithal to promote novelty, good objective functions that one is trying to optimize, and means to improve one's knowledge of, and ability to navigate, the landscape one is searching. Recombination necessarily implies multi- or inter-disciplinarity. These principles are generic to all kinds of creativity, novel ideas formation and the development of new products and technologies.

Whole-mount in situ hybridization in the Rotifer Brachionus plicatilis representing a basal branch of lophotrochozoans

PubMed Central

Boell, Louis A.

2008-01-01

In order to broaden the comparative scope of evolutionary developmental biology and to refine our picture of animal macroevolution, it is necessary to establish new model organisms, especially from previously underrepresented groups, like the Lophotrochozoa. We have established the culture and protocols for molecular developmental biology in the rotifer species Brachionus plicatilis Müller (Rotifera, Monogononta). Rotifers are nonsegmented animals with enigmatic basal position within the lophotrochozoans and marked by several evolutionary novelties like the wheel organ (corona), the median eye, and the nonpaired posterior foot. The expression of Bp-Pax-6 is shown using whole-mount in situ hybridization. The inexpensive easy culture and experimental tractability of Brachionus as well as the range of interesting questions to which it holds the key make it a promising addition to the “zoo” of evo-devo model organisms. Electronic supplementary material The online version of this article (doi:10.1007/s00427-008-0234-z) contains supplementary material, which is available to authorized users. PMID:18594859

The evolution of cichlid fish egg-spots is linked with a cis-regulatory change

PubMed Central

Santos, M. Emília; Braasch, Ingo; Boileau, Nicolas; Meyer, Britta S.; Sauteur, Loïc; Böhne, Astrid; Belting, Heinz-Georg; Affolter, Markus; Salzburger, Walter

2014-01-01

The origin of novel phenotypic characters is a key component in organismal diversification; yet, the mechanisms underlying the emergence of such evolutionary novelties are largely unknown. Here we examine the origin of egg-spots, an evolutionary innovation of the most species-rich group of cichlids, the haplochromines, where these conspicuous male fin colour markings are involved in mating. Applying a combination of RNAseq, comparative genomics and functional experiments, we identify two novel pigmentation genes, fhl2a and fhl2b, and show that especially the more rapidly evolving b-paralog is associated with egg-spot formation. We further find that egg-spot bearing haplochromines, but not other cichlids, feature a transposable element in the cis-regulatory region of fhl2b. Using transgenic zebrafish, we finally demonstrate that this region shows specific enhancer activities in iridophores, a type of pigment cells found in egg-spots, suggesting that a cis-regulatory change is causally linked to the gain of expression in egg-spot bearing haplochromines. PMID:25296686

Extending and expanding the Darwinian synthesis: the role of complex systems dynamics.

PubMed

Weber, Bruce H

2011-03-01

Darwinism is defined here as an evolving research tradition based upon the concepts of natural selection acting upon heritable variation articulated via background assumptions about systems dynamics. Darwin's theory of evolution was developed within a context of the background assumptions of Newtonian systems dynamics. The Modern Evolutionary Synthesis, or neo-Darwinism, successfully joined Darwinian selection and Mendelian genetics by developing population genetics informed by background assumptions of Boltzmannian systems dynamics. Currently the Darwinian Research Tradition is changing as it incorporates new information and ideas from molecular biology, paleontology, developmental biology, and systems ecology. This putative expanded and extended synthesis is most perspicuously deployed using background assumptions from complex systems dynamics. Such attempts seek to not only broaden the range of phenomena encompassed by the Darwinian Research Tradition, such as neutral molecular evolution, punctuated equilibrium, as well as developmental biology, and systems ecology more generally, but to also address issues of the emergence of evolutionary novelties as well as of life itself. Copyright © 2010 Elsevier Ltd. All rights reserved.

The virtue of innovation: innovation through the lenses of biological evolution

PubMed Central

Kell, Douglas B.; Lurie-Luke, Elena

2015-01-01

We rehearse the processes of innovation and discovery in general terms, using as our main metaphor the biological concept of an evolutionary fitness landscape. Incremental and disruptive innovations are seen, respectively, as successful searches carried out locally or more widely. They may also be understood as reflecting evolution by mutation (incremental) versus recombination (disruptive). We also bring a platonic view, focusing on virtue and memory. We use ‘virtue’ as a measure of efforts, including the knowledge required to come up with disruptive and incremental innovations, and ‘memory’ as a measure of their lifespan, i.e. how long they are remembered. Fostering innovation, in the evolutionary metaphor, means providing the wherewithal to promote novelty, good objective functions that one is trying to optimize, and means to improve one's knowledge of, and ability to navigate, the landscape one is searching. Recombination necessarily implies multi- or inter-disciplinarity. These principles are generic to all kinds of creativity, novel ideas formation and the development of new products and technologies. PMID:25505138

The major synthetic evolutionary transitions.

PubMed

Solé, Ricard

2016-08-19

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

The major synthetic evolutionary transitions

PubMed Central

Solé, Ricard

2016-01-01

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

Using protistan examples to dispel the myths of intelligent design.

PubMed

Farmer, Mark A; Habura, Andrea

2010-01-01

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

Heteronormativity in the University Classroom: Novelty Attachment and Content Substitution among Gay-Friendly Students

ERIC Educational Resources Information Center

Ripley, Matthew; Anderson, Eric; McCormack, Mark; Rockett, Ben

2012-01-01

This article explores the complex relationship between an openly gay instructor, homophobia, and heteronormativity in a university classroom. The authors first tabulated the frequency with which the instructor used the lives of heterosexuals and homosexuals as examples of content or as content itself, and then they interviewed 32 students about…

Glycopolymeric Materials for Advanced Applications

PubMed Central

Muñoz-Bonilla, Alexandra; Fernández-García, Marta

2015-01-01

In recent years, glycopolymers have particularly revolutionized the world of macromolecular chemistry and materials in general. Nevertheless, it has been in this century when scientists realize that these materials present great versatility in biosensing, biorecognition, and biomedicine among other areas. This article highlights most relevant glycopolymeric materials, considering that they are only a small example of the research done in this emerging field. The examples described here are selected on the base of novelty, innovation and implementation of glycopolymeric materials. In addition, the future perspectives of this topic will be commented on.

Evolutionary response when selection and genetic variation covary across environments.

PubMed

Wood, Corlett W; Brodie, Edmund D

2016-10-01

Although models of evolution usually assume that the strength of selection on a trait and the expression of genetic variation in that trait are independent, whenever the same ecological factor impacts both parameters, a correlation between the two may arise that accelerates trait evolution in some environments and slows it in others. Here, we address the evolutionary consequences and ecological causes of a correlation between selection and expressed genetic variation. Using a simple analytical model, we show that the correlation has a modest effect on the mean evolutionary response and a large effect on its variance, increasing among-population or among-generation variation in the response when positive, and diminishing variation when negative. We performed a literature review to identify the ecological factors that influence selection and expressed genetic variation across traits. We found that some factors - temperature and competition - are unlikely to generate the correlation because they affected one parameter more than the other, and identified others - most notably, environmental novelty - that merit further investigation because little is known about their impact on one of the two parameters. We argue that the correlation between selection and genetic variation deserves attention alongside other factors that promote or constrain evolution in heterogeneous landscapes. © 2016 John Wiley & Sons Ltd/CNRS.

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

PubMed Central

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

2016-01-01

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

Coevolution between invasive and native plants driven by chemical competition and soil biota.

PubMed

Lankau, Richard A

2012-07-10

Although reciprocal evolutionary responses between interacting species are a driving force behind the diversity of life, pairwise coevolution between plant competitors has received less attention than other species interactions and has been considered relatively less important in explaining ecological patterns. However, the success of species transported across biogeographic boundaries suggests a stronger role for evolutionary relationships in shaping plant interactions. Alliaria petiolata is a Eurasian species that has invaded North American forest understories, where it competes with native understory species in part by producing compounds that directly and indirectly slow the growth of competing species. Here I show that populations of A. petiolata from areas with a greater density of interspecific competitors invest more in a toxic allelochemical under common conditions. Furthermore, populations of a native competitor from areas with highly toxic invaders are more tolerant to competition from the invader, suggesting coevolutionary dynamics between the species. Field reciprocal transplants confirmed that native populations more tolerant to the invader had higher fitness when the invader was common, but these traits came at a cost when the invader was rare. Exotic species are often detrimentally dominant in their new range due to their evolutionary novelty; however, the development of new coevolutionary relationships may act to integrate exotic species into native communities.

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling.

PubMed

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

2016-01-01

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

Increased genetic variation and evolutionary potential drive the success of an invasive grass

PubMed Central

Lavergne, Sébastien; Molofsky, Jane

2007-01-01

Despite the increasing biological and economic impacts of invasive species, little is known about the evolutionary mechanisms that favor geographic range expansion and evolution of invasiveness in introduced species. Here, we focus on the invasive wetland grass Phalaris arundinacea L. and document the evolutionary consequences that resulted from multiple and uncontrolled introductions into North America of genetic material native to different European regions. Continental-scale genetic variation occurring in reed canarygrass' European range has been reshuffled and recombined within North American introduced populations, giving rise to a number of novel genotypes. This process alleviated genetic bottlenecks throughout reed canarygrass' introduced range, including in peripheral populations, where depletion of genetic diversity is expected and is observed in the native range. Moreover, reed canarygrass had higher genetic diversity and heritable phenotypic variation in its invasive range relative to its native range. The resulting high evolutionary potential of invasive populations allowed for rapid selection of genotypes with higher vegetative colonization ability and phenotypic plasticity. Our results show that repeated introductions of a single species may inadvertently create harmful invaders with high adaptive potential. Such invasive species may be able to evolve in response to changing climate, allowing them to have increasing impact on native communities and ecosystems in the future. More generally, multiple immigration events may thus trigger future adaptation and geographic spread of a species population by preventing genetic bottlenecks and generating genetic novelties through recombination. PMID:17360447

The significance of developmental robustness for species diversity.

PubMed

Melzer, Rainer; Theißen, Günter

2016-04-01

The origin of new species and of new forms is one of the fundamental characteristics of evolution. However, the mechanisms that govern the diversity and disparity of lineages remain poorly understood. Particularly unclear are the reasons why some taxa are vastly more species-rich than others and the manner in which species diversity and morphological disparity are interrelated. Evolutionary innovations and ecological opportunities are usually cited as among the major factors promoting the evolution of species diversity. In many cases it is likely that these factors are positively reinforcing, with evolutionary innovations creating ecological opportunities that in turn foster the origin of new innovations. However, we propose that a third factor, developmental robustness, is very often essential for this reinforcement to be effective. Evolutionary innovations need to be stably and robustly integrated into the developmental genetic programme of an organism to be a suitable substrate for selection to 'explore' ecological opportunities and morphological 'design' space (morphospace). In particular, we propose that developmental robustness of the bauplan is often a prerequisite for the exploration of morphospace and to enable the evolution of further novelties built upon this bauplan Thus, while robustness may reduce the morphological disparity at one level, it may be the basis for increased morphological disparity and for evolutionary innovations at another level, thus fostering species diversity. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach.

PubMed

Panahiazar, Maryam; Sheth, Amit P; Ranabahu, Ajith; Vos, Rutger A; Leebens-Mack, Jim

2013-01-01

Phylogenetic analyses can resolve historical relationships among genes, organisms or higher taxa. Understanding such relationships can elucidate a wide range of biological phenomena, including, for example, the importance of gene and genome duplications in the evolution of gene function, the role of adaptation as a driver of diversification, or the evolutionary consequences of biogeographic shifts. Phyloinformaticists are developing data standards, databases and communication protocols (e.g. Application Programming Interfaces, APIs) to extend the accessibility of gene trees, species trees, and the metadata necessary to interpret these trees, thus enabling researchers across the life sciences to reuse phylogenetic knowledge. Specifically, Semantic Web technologies are being developed to make phylogenetic knowledge interpretable by web agents, thereby enabling intelligently automated, high-throughput reuse of results generated by phylogenetic research. This manuscript describes an ontology-driven, semantic problem-solving environment for phylogenetic analyses and introduces artefacts that can promote phyloinformatic efforts to promote accessibility of trees and underlying metadata. PhylOnt is an extensible ontology with concepts describing tree types and tree building methodologies including estimation methods, models and programs. In addition we present the PhylAnt platform for annotating scientific articles and NeXML files with PhylOnt concepts. The novelty of this work is the annotation of NeXML files and phylogenetic related documents with PhylOnt Ontology. This approach advances data reuse in phyloinformatics.

The Tutor-Web: An Educational System for Classroom Presentation, Evaluation and Self-Study

ERIC Educational Resources Information Center

Stefansson, Gunnar

2004-01-01

A general Web-based system for use in education, the tutor-web, has been developed for storage and presentation of electronic slides for classroom use, along with reference material, examples and quizzes. The primary novelty of the system is the structured linkage between the various pieces of information, to maintain coherence and focus on the…

Digestive Organ in the Female Reproductive Tract Borrows Genes from Multiple Organ Systems to Adopt Critical Functions

PubMed Central

Meslin, Camille; Plakke, Melissa S.; Deutsch, Aaron B.; Small, Brandon S.; Morehouse, Nathan I.; Clark, Nathan L.

2015-01-01

Persistent adaptive challenges are often met with the evolution of novel physiological traits. Although there are specific examples of single genes providing new physiological functions, studies on the origin of complex organ functions are lacking. One such derived set of complex functions is found in the Lepidopteran bursa copulatrix, an organ within the female reproductive tract that digests nutrients from the male ejaculate or spermatophore. Here, we characterized bursa physiology and the evolutionary mechanisms by which it was equipped with digestive and absorptive functionality. By studying the transcriptome of the bursa and eight other tissues, we revealed a suite of highly expressed and secreted gene products providing the bursa with a combination of stomach-like traits for mechanical and enzymatic digestion of the male spermatophore. By subsequently placing these bursa genes in an evolutionary framework, we found that the vast majority of their novel digestive functions were co-opted by borrowing genes that continue to be expressed in nonreproductive tissues. However, a number of bursa-specific genes have also arisen, some of which represent unique gene families restricted to Lepidoptera and may provide novel bursa-specific functions. This pattern of promiscuous gene borrowing and relatively infrequent evolution of tissue-specific duplicates stands in contrast to studies of the evolution of novelty via single gene co-option. Our results suggest that the evolution of complex organ-level phenotypes may often be enabled (and subsequently constrained) by changes in tissue specificity that allow expression of existing genes in novel contexts, such as reproduction. The extent to which the selective pressures encountered in these novel roles require resolution via duplication and sub/neofunctionalization is likely to be determined by the need for specialized reproductive functionality. Thus, complex physiological phenotypes such as that found in the bursa offer important opportunities for understanding the relative role of pleiotropy and specialization in adaptive evolution. PMID:25725432

Development of the skull and pectoral girdle in Siberian sturgeon, Acipenser baerii, and Russian sturgeon, Acipenser gueldenstaedtii (Acipenseriformes: Acipenseridae).

PubMed

Warth, Peter; Hilton, Eric J; Naumann, Benjamin; Olsson, Lennart; Konstantinidis, Peter

2017-03-01

The head is considered the major novelty of the vertebrates and directly linked to their evolutionary success. Its form and development as well as its function, for example in feeding, is of major interest for evolutionary biologists. In this study, we describe the skeletal development of the cranium and pectoral girdle in Siberian (Acipenser baerii) and Russian sturgeon (A. gueldenstaedtii), two species that are commonly farmed in aquaculture and increasingly important in developmental studies. This study comprises the development of the neuro-, viscero- and dermatocranium and the dermal and chondral components of the pectoral girdle, from first condensation of chondrocytes in prehatchlings to the early juvenile stage and reveals a clear pattern in formation. The otic capsules, the parachordal cartilages, and the trabeculae cranii are the first centers of chondrification, at 8.4mm TL. These are followed by the mandibular, then the hyoid, and later the branchial arches. Teeth form early on the dentary, dermopalatine, and palatopterygoid, and then appear later in the buccal cavity as dorsal and ventral toothplates. With ongoing chondrification in the neurocranium a capsule around the brain and a strong rostrum are formed. Dermal ossifications start to form before closure of the dorsal neurocranial fenestrae. Perichondral ossification of cartilage bones occurs much later in ontogeny. Our results contribute data bearing on the homology of elements such as the lateral rostral canal bone that we regard homologous to the antorbital of other actinopterygians based on its sequence of formation, position and form. We further raise doubts on the homology of the posterior ceratobranchial among Actinopteri based on the formation of the hyoid arch elements. We also investigate the basibranchials and the closely associated unidentified gill-arch elements and show that they are not homologous. J. Morphol. 278:418-442, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Genome-scale transcriptional study of hybrid effects and regulatory divergence in an F1 hybrid Ruellia (Wild Petunias: Acanthaceae) and its parents.

PubMed

Zhuang, Yongbin; Tripp, Erin A

2017-01-17

New combinations of divergent genomes can give rise to novel genetic functions in resulting hybrid progeny. Such functions may yield opportunities for ecological divergence, contributing ultimately to reproductive isolation and evolutionary longevity of nascent hybrid lineages. In plants, the degree to which transgressive genotypes contribute to floral novelty remains a question of key interest. Here, we generated an F 1 hybrid plant between the red-flowered Ruellia elegans and yellow flowered R. speciosa. RNA-seq technology was used to explore differential gene expression between the hybrid and its two parents, with emphasis on genetic elements involved in the production of floral anthocyanin pigments. The hybrid was purple flowered and produced novel floral delphinidin pigments not manufactured by either parent. We found that nearly a fifth of all 86,475 unigenes expressed were unique to the hybrid. The majority of hybrid unigenes (80.97%) showed a pattern of complete dominance to one parent or the other although this ratio was uneven, suggesting asymmetrical influence of parental genomes on the progeny transcriptome. However, 8.87% of all transcripts within the hybrid were expressed at significantly higher or lower mean levels than observed for either parent. A total of 28 unigenes coding putatively for eight core enzymes in the anthocyanin pathway were recovered, along with three candidate MYBs involved in anthocyanin regulation. Our results suggest that models of gene evolution that explain phenotypic novelty and hybrid establishment in plants may need to include transgressive effects. Additionally, our results lend insight into the potential for floral novelty that derives from unions of divergent genomes. These findings serve as a starting point to further investigate molecular mechanisms involved in flower color transitions in Ruellia.

The genetic architecture of novel trophic specialists: larger effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation.

PubMed

Martin, Christopher H; Erickson, Priscilla A; Miller, Craig T

2017-01-01

The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here, we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining the origins of ecological novelty: a sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas, containing a large-jawed scale-eater and a short-jawed molluscivore with a skeletal nasal protrusion. These specialized niches and trophic traits are unique among over 2000 related species. Measurements of the fitness landscape on San Salvador demonstrate multiple fitness peaks and a larger fitness valley isolating the scale-eater from the putative ancestral intermediate phenotype of the generalist, suggesting that more large-effect QTL should contribute to its unique phenotype. We evaluated this prediction using an F2 intercross between these specialists. We present the first linkage map for pupfishes and detect significant QTL for sex and eight skeletal traits. Large-effect QTL contributed more to enlarged scale-eater jaws than the molluscivore nasal protrusion, consistent with predictions from the adaptive landscape. The microevolutionary genetic architecture of large-effect QTL for oral jaws parallels the exceptional diversification rates of oral jaws within the San Salvador radiation observed over macroevolutionary timescales and may have facilitated exceptional trophic novelty in this system. © 2016 John Wiley & Sons Ltd.

Context Matters: Multiple Novelty Tests Reveal Different Aspects of Shyness-Boldness in Farmed American Mink (Neovison vison).

PubMed

Noer, Christina Lehmkuhl; Needham, Esther Kjær; Wiese, Ann-Sophie; Balsby, Thorsten Johannes Skovbjerg; Dabelsteen, Torben

2015-01-01

Animal personality research is receiving increasing interest from related fields, such as evolutionary personality psychology. By merging the conceptual understanding of personality, the contributions to both fields of research may be enhanced. In this study, we investigate animal personality based on the definition of personality traits as underlying dispositional factors, which are not directly measurable, but which predispose individuals to react through different behavioural patterns. We investigated the shyness-boldness continuum reflected in the consistency of inter-individual variation in behavioural responses towards novelty in 47 farmed American mink (Neovison vison), which were raised in identical housing conditions. Different stages of approach behaviour towards novelty, and how these related within and across contexts, were explored. Our experimental design contained four tests: two novel object tests (non-social contexts) and two novel animated stimuli tests (social contexts). Our results showed consistency in shyness measures across multiple tests, indicating the existence of personality in farmed American mink. It was found that consistency in shyness measures differs across non-social and social contexts, as well as across the various stages in the approach towards novel objects, revealing that different aspects of shyness exist in the farmed American mink. To our knowledge this is the first study to reveal aspects of the shyness-boldness continuum in the American mink. Since the mink were raised in identical housing conditions, inherited factors may have been important in shaping the consistent inter-individual variation. Body weight and sex had no effect on the personality of the mink. Altogether, our results suggest that the shyness-boldness continuum cannot be explained by a simple underlying dispositional factor, but instead encompasses a broader term of hesitating behaviour that might comprise several different personality traits.

Uxoricide in pregnancy: ancient Greek domestic violence in evolutionary perspective.

PubMed

Deacy, Susan; McHardy, Fiona

2013-10-24

Previous studies of ancient Greek examples of uxoricide in pregnancy have concluded that the theme is used to suggest tyrannical abuse of power and that the violence is a product of the patriarchal nature of ancient society. This article uses evolutionary analyses of violence during pregnancy to argue that the themes of sexual jealousy and uncertainty over paternity are as crucial as the theme of power to an understanding of these examples and that the examples can be seen as typical instances of spousal abuse as it occurs in all types of society.

A novel mechanism for a survival advantage of vigilant individuals in groups.

PubMed

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

2013-11-01

In many animal species, vigilance is crucial for avoiding predation. In groups, however, nonvigilant individuals could benefit from the vigilance of others without any of the associated costs. In an evolutionary sense, such exploitation may be compensated if vigilant individuals have a survival advantage. The novelty in our model is that the probability to detect a predator is "distance dependent." We show that even if nonvigilant individuals benefit fully from information produced by vigilant individuals, vigilant individuals nevertheless enjoy a survival advantage. This happens because detection of predators is more likely when vigilant individuals happen to be targets of predation. We expect this distance-dependent mechanism to be compatible with previously reported mechanisms.

Regulatory Evolution and Theoretical Arguments in Evolutionary Biology

ERIC Educational Resources Information Center

Ioannidis, Stavros

2013-01-01

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

Disparity changes in 370 Ma Devonian fossils: the signature of ecological dynamics?

PubMed

Girard, Catherine; Renaud, Sabrina

2012-01-01

Early periods in Earth's history have seen a progressive increase in complexity of the ecosystems, but also dramatic crises decimating the biosphere. Such patterns are usually considered as large-scale changes among supra-specific groups, including morphological novelties, radiation, and extinctions. Nevertheless, in the same time, each species evolved by the way of micro-evolutionary processes, extended over millions of years into the evolution of lineages. How these two evolutionary scales interacted is a challenging issue because this requires bridging a gap between scales of observation and processes. The present study aims at transferring a typical macro-evolutionary approach, namely disparity analysis, to the study of fine-scale evolutionary variations in order to decipher what processes actually drove the dynamics of diversity at a micro-evolutionary level. The Late Frasnian to Late Famennian period was selected because it is punctuated by two major macro-evolutionary crises, as well as a progressive diversification of marine ecosystem. Disparity was estimated through this period on conodonts, tooth-like fossil remains of small eel-like predators that were part of the nektonic fauna. The study was focused on the emblematic genus of the period, Palmatolepis. Strikingly, both crises affected an already impoverished Palmatolepis disparity, increasing risks of random extinction. The major disparity signal rather emerged as a cycle of increase and decrease in disparity during the inter-crises period. The diversification shortly followed the first crisis and might correspond to an opportunistic occupation of empty ecological niche. The subsequent oriented shrinking in the morphospace occupation suggests that the ecological space available to Palmatolepis decreased through time, due to a combination of factors: deteriorating climate, expansion of competitors and predators. Disparity changes of Palmatolepis thus reflect changes in the structure of the ecological space itself, which was prone to evolve during this ancient period where modern ecosystems were progressively shaped.

Bringing Together Evolution on Serpentine and Polyploidy: Spatiotemporal History of the Diploid-Tetraploid Complex of Knautia arvensis (Dipsacaceae)

PubMed Central

Kolář, Filip; Fér, Tomáš; Štech, Milan; Trávníček, Pavel; Dušková, Eva; Schönswetter, Peter; Suda, Jan

2012-01-01

Polyploidization is one of the leading forces in the evolution of land plants, providing opportunities for instant speciation and rapid gain of evolutionary novelties. Highly selective conditions of serpentine environments act as an important evolutionary trigger that can be involved in various speciation processes. Whereas the significance of both edaphic speciation on serpentine and polyploidy is widely acknowledged in plant evolution, the links between polyploid evolution and serpentine differentiation have not yet been examined. To fill this gap, we investigated the evolutionary history of the perennial herb Knautia arvensis (Dipsacaceae), a diploid-tetraploid complex that exhibits an intriguing pattern of eco-geographic differentiation. Using plastid DNA sequencing and AFLP genotyping of 336 previously cytotyped individuals from 40 populations from central Europe, we unravelled the patterns of genetic variation among the cytotypes and the edaphic types. Diploids showed the highest levels of genetic differentiation, likely as a result of long term persistence of several lineages in ecologically distinct refugia and/or independent immigration. Recurrent polyploidization, recorded in one serpentine island, seems to have opened new possibilities for the local serpentine genotype. Unlike diploids, the serpentine tetraploids were able to escape from the serpentine refugium and spread further; this was also attributable to hybridization with the neighbouring non-serpentine tetraploid lineages. The spatiotemporal history of K. arvensis allows tracing the interplay of polyploid evolution and ecological divergence on serpentine, resulting in a complex evolutionary pattern. Isolated serpentine outcrops can act as evolutionary capacitors, preserving distinct karyological and genetic diversity. The serpentine lineages, however, may not represent evolutionary ‘dead-ends’ but rather dynamic systems with a potential to further influence the surrounding populations, e.g., via independent polyplodization and hybridization. The complex eco-geographical pattern together with the incidence of both primary and secondary diploid-tetraploid contact zones makes K. arvensis a unique system for addressing general questions of polyploid research. PMID:22792207

Disparity Changes in 370 Ma Devonian Fossils: The Signature of Ecological Dynamics?

PubMed Central

Girard, Catherine; Renaud, Sabrina

2012-01-01

Early periods in Earth's history have seen a progressive increase in complexity of the ecosystems, but also dramatic crises decimating the biosphere. Such patterns are usually considered as large-scale changes among supra-specific groups, including morphological novelties, radiation, and extinctions. Nevertheless, in the same time, each species evolved by the way of micro-evolutionary processes, extended over millions of years into the evolution of lineages. How these two evolutionary scales interacted is a challenging issue because this requires bridging a gap between scales of observation and processes. The present study aims at transferring a typical macro-evolutionary approach, namely disparity analysis, to the study of fine-scale evolutionary variations in order to decipher what processes actually drove the dynamics of diversity at a micro-evolutionary level. The Late Frasnian to Late Famennian period was selected because it is punctuated by two major macro-evolutionary crises, as well as a progressive diversification of marine ecosystem. Disparity was estimated through this period on conodonts, tooth-like fossil remains of small eel-like predators that were part of the nektonic fauna. The study was focused on the emblematic genus of the period, Palmatolepis. Strikingly, both crises affected an already impoverished Palmatolepis disparity, increasing risks of random extinction. The major disparity signal rather emerged as a cycle of increase and decrease in disparity during the inter-crises period. The diversification shortly followed the first crisis and might correspond to an opportunistic occupation of empty ecological niche. The subsequent oriented shrinking in the morphospace occupation suggests that the ecological space available to Palmatolepis decreased through time, due to a combination of factors: deteriorating climate, expansion of competitors and predators. Disparity changes of Palmatolepis thus reflect changes in the structure of the ecological space itself, which was prone to evolve during this ancient period where modern ecosystems were progressively shaped. PMID:22558396

A Powerful Toolkit for Synthetic Biology: Over 3.8 Billion Years of Evolution

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

2010-01-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested

A powerful toolkit for synthetic biology: Over 3.8 billion years of evolution.

PubMed

Rothschild, Lynn J

2010-04-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested.

Evolving a Behavioral Repertoire for a Walking Robot.

PubMed

Cully, A; Mouret, J-B

2016-01-01

Numerous algorithms have been proposed to allow legged robots to learn to walk. However, most of these algorithms are devised to learn walking in a straight line, which is not sufficient to accomplish any real-world mission. Here we introduce the Transferability-based Behavioral Repertoire Evolution algorithm (TBR-Evolution), a novel evolutionary algorithm that simultaneously discovers several hundreds of simple walking controllers, one for each possible direction. By taking advantage of solutions that are usually discarded by evolutionary processes, TBR-Evolution is substantially faster than independently evolving each controller. Our technique relies on two methods: (1) novelty search with local competition, which searches for both high-performing and diverse solutions, and (2) the transferability approach, which combines simulations and real tests to evolve controllers for a physical robot. We evaluate this new technique on a hexapod robot. Results show that with only a few dozen short experiments performed on the robot, the algorithm learns a repertoire of controllers that allows the robot to reach every point in its reachable space. Overall, TBR-Evolution introduced a new kind of learning algorithm that simultaneously optimizes all the achievable behaviors of a robot.

Human compulsivity: A perspective from evolutionary medicine.

PubMed

Stein, Dan J; Hermesh, Haggai; Eilam, David; Segalas, Cosi; Zohar, Joseph; Menchon, Jose; Nesse, Randolph M

2016-05-01

Biological explanations address not only proximal mechanisms (for example, the underlying neurobiology of obsessive-compulsive disorder), but also distal mechanisms (that is, a consideration of how particular neurobiological mechanisms evolved). Evolutionary medicine has emphasized a series of explanations for vulnerability to disease, including constraints, mismatch, and tradeoffs. The current paper will consider compulsive symptoms in obsessive-compulsive and related disorders and behavioral addictions from this evolutionary perspective. It will argue that while obsessive-compulsive disorder (OCD) is typically best conceptualized as a dysfunction, it is theoretically and clinically valuable to understand some symptoms of obsessive-compulsive and related disorders in terms of useful defenses. The symptoms of behavioral addictions can also be conceptualized in evolutionary terms (for example, mismatch), which in turn provides a sound foundation for approaching assessment and intervention. Copyright © 2016. Published by Elsevier B.V.

Computational Identification of Novel Genes: Current and Future Perspectives.

PubMed

Klasberg, Steffen; Bitard-Feildel, Tristan; Mallet, Ludovic

2016-01-01

While it has long been thought that all genomic novelties are derived from the existing material, many genes lacking homology to known genes were found in recent genome projects. Some of these novel genes were proposed to have evolved de novo, ie, out of noncoding sequences, whereas some have been shown to follow a duplication and divergence process. Their discovery called for an extension of the historical hypotheses about gene origination. Besides the theoretical breakthrough, increasing evidence accumulated that novel genes play important roles in evolutionary processes, including adaptation and speciation events. Different techniques are available to identify genes and classify them as novel. Their classification as novel is usually based on their similarity to known genes, or lack thereof, detected by comparative genomics or against databases. Computational approaches are further prime methods that can be based on existing models or leveraging biological evidences from experiments. Identification of novel genes remains however a challenging task. With the constant software and technologies updates, no gold standard, and no available benchmark, evaluation and characterization of genomic novelty is a vibrant field. In this review, the classical and state-of-the-art tools for gene prediction are introduced. The current methods for novel gene detection are presented; the methodological strategies and their limits are discussed along with perspective approaches for further studies.

Network Dynamics of Innovation Processes.

PubMed

Iacopini, Iacopo; Milojević, Staša; Latora, Vito

2018-01-26

We introduce a model for the emergence of innovations, in which cognitive processes are described as random walks on the network of links among ideas or concepts, and an innovation corresponds to the first visit of a node. The transition matrix of the random walk depends on the network weights, while in turn the weight of an edge is reinforced by the passage of a walker. The presence of the network naturally accounts for the mechanism of the "adjacent possible," and the model reproduces both the rate at which novelties emerge and the correlations among them observed empirically. We show this by using synthetic networks and by studying real data sets on the growth of knowledge in different scientific disciplines. Edge-reinforced random walks on complex topologies offer a new modeling framework for the dynamics of correlated novelties and are another example of coevolution of processes and networks.

Network Dynamics of Innovation Processes

NASA Astrophysics Data System (ADS)

Iacopini, Iacopo; Milojević, Staša; Latora, Vito

2018-01-01

We introduce a model for the emergence of innovations, in which cognitive processes are described as random walks on the network of links among ideas or concepts, and an innovation corresponds to the first visit of a node. The transition matrix of the random walk depends on the network weights, while in turn the weight of an edge is reinforced by the passage of a walker. The presence of the network naturally accounts for the mechanism of the "adjacent possible," and the model reproduces both the rate at which novelties emerge and the correlations among them observed empirically. We show this by using synthetic networks and by studying real data sets on the growth of knowledge in different scientific disciplines. Edge-reinforced random walks on complex topologies offer a new modeling framework for the dynamics of correlated novelties and are another example of coevolution of processes and networks.

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

PubMed

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

2017-03-28

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

Evolution in a fully constituted world: Charles Darwin's debts towards a static world in the Origin of Species (1859).

PubMed

Delisle, Richard G

2014-01-01

The Transformist Revolution was a long intellectual quest that has expanded from the 18th century to today. One area of inquiry after another has confronted the necessity of recasting its object of study under an evolutionary view: human history, geology, biology, astronomy, etc. No single scholar fully managed to make the transition from a static worldview to an evolutionary one during his or her own lifetime; Charles Darwin is no exception. Many versions of evolutionism were proposed during this revolution, versions offering all sorts of compromises between old and new views. Not sufficiently acknowledged in the historiography is the profoundness of Darwin's debts towards the old static view. As a dual child of the Scientific Revolution and natural theology, Darwin inherited key concepts such as stability, completeness, timelessness, unity, permanence, and uniformity. Darwin took these concepts into consideration while erecting his theory of biological evolution. Unsurprisingly, this theory was ill-equipped to embrace the directionality, historicity, and novelty that came along with a new evolutionary world. This paper analyses a fundamental idea at the heart of Darwin's Origins of Species (1859) inherited from a static, stable, and machine-like conception of the world: the notion of a fully constituted world. Although in principle antithetical to the very idea of evolution itself, Darwin found a way to 'loosen up' this notion so as to retain it in a way that allows for some kind of evolutionary change. Copyright © 2014 Elsevier Ltd. All rights reserved.

Reconstructing the Evolutionary History of Paralogous APETALA1/FRUITFULL-Like Genes in Grasses (Poaceae)

PubMed Central

Preston, Jill C.; Kellogg, Elizabeth A.

2006-01-01

Gene duplication is an important mechanism for the generation of evolutionary novelty. Paralogous genes that are not silenced may evolve new functions (neofunctionalization) that will alter the developmental outcome of preexisting genetic pathways, partition ancestral functions (subfunctionalization) into divergent developmental modules, or function redundantly. Functional divergence can occur by changes in the spatio-temporal patterns of gene expression and/or by changes in the activities of their protein products. We reconstructed the evolutionary history of two paralogous monocot MADS-box transcription factors, FUL1 and FUL2, and determined the evolution of sequence and gene expression in grass AP1/FUL-like genes. Monocot AP1/FUL-like genes duplicated at the base of Poaceae and codon substitutions occurred under relaxed selection mostly along the branch leading to FUL2. Following the duplication, FUL1 was apparently lost from early diverging taxa, a pattern consistent with major changes in grass floral morphology. Overlapping gene expression patterns in leaves and spikelets indicate that FUL1 and FUL2 probably share some redundant functions, but that FUL2 may have become temporally restricted under partial subfunctionalization to particular stages of floret development. These data have allowed us to reconstruct the history of AP1/FUL-like genes in Poaceae and to hypothesize a role for this gene duplication in the evolution of the grass spikelet. PMID:16816429

Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait.

PubMed

Olofsson, Jill K; Bianconi, Matheus; Besnard, Guillaume; Dunning, Luke T; Lundgren, Marjorie R; Holota, Helene; Vorontsova, Maria S; Hidalgo, Oriane; Leitch, Ilia J; Nosil, Patrik; Osborne, Colin P; Christin, Pascal-Antoine

2016-12-01

Physiological novelties are often studied at macro-evolutionary scales such that their micro-evolutionary origins remain poorly understood. Here, we test the hypothesis that key components of a complex trait can evolve in isolation and later be combined by gene flow. We use C 4 photosynthesis as a study system, a derived physiology that increases plant productivity in warm, dry conditions. The grass Alloteropsis semialata includes C 4 and non-C 4 genotypes, with some populations using laterally acquired C 4 -adaptive loci, providing an outstanding system to track the spread of novel adaptive mutations. Using genome data from C 4 and non-C 4 A. semialata individuals spanning the species' range, we infer and date past migrations of different parts of the genome. Our results show that photosynthetic types initially diverged in isolated populations, where key C 4 components were acquired. However, rare but recurrent subsequent gene flow allowed the spread of adaptive loci across genetic pools. Indeed, laterally acquired genes for key C 4 functions were rapidly passed between populations with otherwise distinct genomic backgrounds. Thus, our intraspecific study of C 4 -related genomic variation indicates that components of adaptive traits can evolve separately and later be combined through secondary gene flow, leading to the assembly and optimization of evolutionary innovations. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Affective Monitoring: A Generic Mechanism for Affect Elicitation

PubMed Central

Phaf, R. Hans; Rotteveel, Mark

2012-01-01

In this paper we sketch a new framework for affect elicitation, which is based on previous evolutionary and connectionist modeling and experimental work from our group. Affective monitoring is considered a local match–mismatch process within a module of the neural network. Negative affect is raised instantly by mismatches, incongruency, disfluency, novelty, incoherence, and dissonance, whereas positive affect follows from matches, congruency, fluency, familiarity, coherence, and resonance, at least when an initial mismatch can be solved quickly. Affective monitoring is considered an evolutionary-early conflict and change detection process operating at the same level as, for instance, attentional selection. It runs in parallel and imparts affective flavor to emotional behavior systems, which involve evolutionary-prepared stimuli and action tendencies related to for instance defensive, exploratory, attachment, or appetitive behavior. Positive affect is represented in the networks by high-frequency oscillations, presumably in the gamma band. Negative affect corresponds to more incoherent lower-frequency oscillations, presumably in the theta band. For affect to become conscious, large-scale synchronization of the oscillations over the network and the construction of emotional experiences are required. These constructions involve perceptions of bodily states and action tendencies, but also appraisals as well as efforts to regulate the emotion. Importantly, affective monitoring accompanies every kind of information processing, but conscious emotions, which result from the later integration of affect in a cognitive context, are much rarer events. PMID:22403557

Supervised novelty detection in brain tissue classification with an application to white matter hyperintensities

NASA Astrophysics Data System (ADS)

Kuijf, Hugo J.; Moeskops, Pim; de Vos, Bob D.; Bouvy, Willem H.; de Bresser, Jeroen; Biessels, Geert Jan; Viergever, Max A.; Vincken, Koen L.

2016-03-01

Novelty detection is concerned with identifying test data that differs from the training data of a classifier. In the case of brain MR images, pathology or imaging artefacts are examples of untrained data. In this proof-of-principle study, we measure the behaviour of a classifier during the classification of trained labels (i.e. normal brain tissue). Next, we devise a measure that distinguishes normal classifier behaviour from abnormal behavior that occurs in the case of a novelty. This will be evaluated by training a kNN classifier on normal brain tissue, applying it to images with an untrained pathology (white matter hyperintensities (WMH)), and determine if our measure is able to identify abnormal classifier behaviour at WMH locations. For our kNN classifier, behaviour is modelled as the mean, median, or q1 distance to the k nearest points. Healthy tissue was trained on 15 images; classifier behaviour was trained/tested on 5 images with leave-one-out cross-validation. For each trained class, we measure the distribution of mean/median/q1 distances to the k nearest point. Next, for each test voxel, we compute its Z-score with respect to the measured distribution of its predicted label. We consider a Z-score >=4 abnormal behaviour of the classifier, having a probability due to chance of 0.000032. Our measure identified >90% of WMH volume and also highlighted other non-trained findings. The latter being predominantly vessels, cerebral falx, brain mask errors, choroid plexus. This measure is generalizable to other classifiers and might help in detecting unexpected findings or novelties by measuring classifier behaviour.

A new heart for a new head in vertebrate cardiopharyngeal evolution.

PubMed

Diogo, Rui; Kelly, Robert G; Christiaen, Lionel; Levine, Michael; Ziermann, Janine M; Molnar, Julia L; Noden, Drew M; Tzahor, Eldad

2015-04-23

It has been more than 30 years since the publication of the new head hypothesis, which proposed that the vertebrate head is an evolutionary novelty resulting from the emergence of neural crest and cranial placodes. Neural crest generates the skull and associated connective tissues, whereas placodes produce sensory organs. However, neither crest nor placodes produce head muscles, which are a crucial component of the complex vertebrate head. We discuss emerging evidence for a surprising link between the evolution of head muscles and chambered hearts - both systems arise from a common pool of mesoderm progenitor cells within the cardiopharyngeal field of vertebrate embryos. We consider the origin of this field in non-vertebrate chordates and its evolution in vertebrates.

A new heart for a new head in vertebrate cardiopharyngeal evolution

PubMed Central

Diogo, Rui; Kelly, Robert G.; Christiaen, Lionel; Levine, Michael; Ziermann, Janine M.; Molnar, Julia L.; Noden, Drew M.; Tzahor, Eldad

2015-01-01

It has been more than 30 years since the publication of the new head hypothesis, which proposed that the vertebrate head is an evolutionary novelty resulting from the emergence of neural crest and cranial placodes. Neural crest generates the skull and associated connective tissues, whereas placodes produce sensory organs. However, neither crest nor placodes produce head muscles, which are a crucial component of the complex vertebrate head. We discuss emerging evidence for a surprising link between the evolution of head muscles and chambered hearts — both systems arise from a common pool of mesoderm progenitor cells within the cardiopharyngeal field of vertebrate embryos. We consider the origin of this field in non-vertebrate chordates and its evolution in vertebrates. PMID:25903628

Testing evolutionary hypotheses for phenotypic divergence using landscape genetics.

PubMed

Funk, W Chris; Murphy, Melanie A

2010-02-01

Understanding the evolutionary causes of phenotypic variation among populations has long been a central theme in evolutionary biology. Several factors can influence phenotypic divergence, including geographic isolation, genetic drift, divergent natural or sexual selection, and phenotypic plasticity. But the relative importance of these factors in generating phenotypic divergence in nature is still a tantalizing and unresolved problem in evolutionary biology. The origin and maintenance of phenotypic divergence is also at the root of many ongoing debates in evolutionary biology, such as the extent to which gene flow constrains adaptive divergence (Garant et al. 2007) and the relative importance of genetic drift, natural selection, and sexual selection in initiating reproductive isolation and speciation (Coyne & Orr 2004). In this issue, Wang & Summers (2010) test the causes of one of the most fantastic examples of phenotypic divergence in nature: colour pattern divergence among populations of the strawberry poison frog (Dendrobates pumilio) in Panama and Costa Rica (Fig. 1). This study provides a beautiful example of the use of the emerging field of landscape genetics to differentiate among hypotheses for phenotypic divergence. Using landscape genetic analyses, Wang & Summers were able to reject the hypotheses that colour pattern divergence is due to isolation-by-distance (IBD) or landscape resistance. Instead, the hypothesis left standing is that colour divergence is due to divergent selection, in turn driving reproductive isolation among populations with different colour morphs. More generally, this study provides a wonderful example of how the emerging field of landscape genetics, which has primarily been applied to questions in conservation and ecology, now plays an essential role in evolutionary research.

Field-Based Optimal Placement of Antennas for Body-Worn Wireless Sensors

PubMed Central

Januszkiewicz, Łukasz; Di Barba, Paolo; Hausman, Sławomir

2016-01-01

We investigate a case of automated energy-budget-aware optimization of the physical position of nodes (sensors) in a Wireless Body Area Network (WBAN). This problem has not been presented in the literature yet, as opposed to antenna and routing optimization, which are relatively well-addressed. In our research, which was inspired by a safety-critical application for firefighters, the sensor network consists of three nodes located on the human body. The nodes communicate over a radio link operating in the 2.4 GHz or 5.8 GHz ISM frequency band. Two sensors have a fixed location: one on the head (earlobe pulse oximetry) and one on the arm (with accelerometers, temperature and humidity sensors, and a GPS receiver), while the position of the third sensor can be adjusted within a predefined region on the wearer’s chest. The path loss between each node pair strongly depends on the location of the nodes and is difficult to predict without performing a full-wave electromagnetic simulation. Our optimization scheme employs evolutionary computing. The novelty of our approach lies not only in the formulation of the problem but also in linking a fully automated optimization procedure with an electromagnetic simulator and a simplified human body model. This combination turns out to be a computationally effective solution, which, depending on the initial placement, has a potential to improve performance of our example sensor network setup by up to about 20 dB with respect to the path loss between selected nodes. PMID:27196911

The rise of novelty in ecosystems.

PubMed

Radeloff, Volker C; Williams, John W; Bateman, Brooke L; Burke, Kevin D; Carter, Sarah K; Childress, Evan S; Cromwell, Kara J; Gratton, Claudio; Hasley, Andrew O; Kraemer, Benjamin M; Latzka, Alexander W; Marin-Spiotta, Erika; Meine, Curt D; Munoz, Samuel E; Neeson, Thomas M; Pidgeon, Anna M; Rissman, Adena R; Rivera, Ricardo J; Szymanski, Laura M; Usinowicz, Jacob

2015-12-01

Rapid and ongoing change creates novelty in ecosystems everywhere, both when comparing contemporary systems to their historical baselines, and predicted future systems to the present. However, the level of novelty varies greatly among places. Here we propose a formal and quantifiable definition of abiotic and biotic novelty in ecosystems, map abiotic novelty globally, and discuss the implications of novelty for the science of ecology and for biodiversity conservation. We define novelty as the degree of dissimilarity of a system, measured in one or more dimensions relative to a reference baseline, usually defined as either the present or a time window in the past. In this conceptualization, novelty varies in degree, it is multidimensional, can be measured, and requires a temporal and spatial reference. This definition moves beyond prior categorical definitions of novel ecosystems, and does not include human agency, self-perpetuation, or irreversibility as criteria. Our global assessment of novelty was based on abiotic factors (temperature, precipitation, and nitrogen deposition) plus human population, and shows that there are already large areas with high novelty today relative to the early 20th century, and that there will even be more such areas by 2050. Interestingly, the places that are most novel are often not the places where absolute changes are largest; highlighting that novelty is inherently different from change. For the ecological sciences, highly novel ecosystems present new opportunities to test ecological theories, but also challenge the predictive ability of ecological models and their validation. For biodiversity conservation, increasing novelty presents some opportunities, but largely challenges. Conservation action is necessary along the entire continuum of novelty, by redoubling efforts to protect areas where novelty is low, identifying conservation opportunities where novelty is high, developing flexible yet strong regulations and policies, and establishing long-term experiments to test management approaches. Meeting the challenge of novelty will require advances in the science of ecology, and new and creative. conservation approaches.

Current Issues in Evolutionary Paleontology.

ERIC Educational Resources Information Center

Scully, Erik Paul

1987-01-01

Describes some of the contributions made by the field of paleontology to theories in geology and biology. Suggests that the two best examples of modern evolutionary paleontology relate to the theory of punctuated equilibria, and the possibility that mass extinctions may be cyclic. (TW)

Biological causal links on physiological and evolutionary time scales.

PubMed

Karmon, Amit; Pilpel, Yitzhak

2016-04-26

Correlation does not imply causation. If two variables, say A and B, are correlated, it could be because A causes B, or that B causes A, or because a third factor affects them both. We suggest that in many cases in biology, the causal link might be bi-directional: A causes B through a fast-acting physiological process, while B causes A through a slowly accumulating evolutionary process. Furthermore, many trained biologists tend to consistently focus at first on the fast-acting direction, and overlook the slower process in the opposite direction. We analyse several examples from modern biology that demonstrate this bias (codon usage optimality and gene expression, gene duplication and genetic dispensability, stem cell division and cancer risk, and the microbiome and host metabolism) and also discuss an example from linguistics. These examples demonstrate mutual effects between the fast physiological processes and the slow evolutionary ones. We believe that building awareness of inference biases among biologists who tend to prefer one causal direction over another could improve scientific reasoning.

Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

PubMed Central

Longo, Mark S; Carone, Dawn M; Green, Eric D; O'Neill, Michael J; O'Neill, Rachel J

2009-01-01

Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB), are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN), euchromatic regions (EU), and an evolutionary breakpoint (EB) that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s) and endogenous retroviruses (ERVs) and a depletion of short interspersed nucleotide elements (SINEs) shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33), known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the divergence of marsupials and eutherians that may have predisposed these genomic regions to large-scale chromosomal instability. PMID:19630942

Use of game-theoretical methods in biochemistry and biophysics.

PubMed

Schuster, Stefan; Kreft, Jan-Ulrich; Schroeter, Anja; Pfeiffer, Thomas

2008-04-01

Evolutionary game theory can be considered as an extension of the theory of evolutionary optimisation in that two or more organisms (or more generally, units of replication) tend to optimise their properties in an interdependent way. Thus, the outcome of the strategy adopted by one species (e.g., as a result of mutation and selection) depends on the strategy adopted by the other species. In this review, the use of evolutionary game theory for analysing biochemical and biophysical systems is discussed. The presentation is illustrated by a number of instructive examples such as the competition between microorganisms using different metabolic pathways for adenosine triphosphate production, the secretion of extracellular enzymes, the growth of trees and photosynthesis. These examples show that, due to conflicts of interest, the global optimum (in the sense of being the best solution for the whole system) is not always obtained. For example, some yeast species use metabolic pathways that waste nutrients, and in a dense tree canopy, trees grow taller than would be optimal for biomass productivity. From the viewpoint of game theory, the examples considered can be described by the Prisoner's Dilemma, snowdrift game, Tragedy of the Commons and rock-scissors-paper game.

Co-option of the hormone-signalling module dafachronic acid-DAF-12 in nematode evolution.

PubMed

Bento, Gilberto; Ogawa, Akira; Sommer, Ralf J

2010-07-22

Morphological novelties are lineage-specific traits that serve new functions. Developmental polyphenisms have been proposed to be facilitators of phenotypic evolution, but little is known about the interplay between the associated genetic and environmental factors. Here, we study two alternative morphologies in the mouth of the nematode Pristionchus pacificus and the formation of teeth-like structures that are associated with bacteriovorous feeding and predatory behaviour on fungi and other worms. These teeth-like denticles represent an evolutionary novelty, which is restricted to some members of the nematode family Diplogastridae but is absent from Caenorhabditis elegans and related nematodes. We show that the mouth dimorphism is a polyphenism that is controlled by starvation and the co-option of an endocrine switch mechanism. Mutations in the nuclear hormone receptor DAF-12 and application of its ligand, the sterol hormone dafachronic acid, strongly influence this switch mechanism. The dafachronic acid-DAF-12 module has been shown to control the formation of arrested dauer larvae in both C. elegans and P. pacificus, as well as related life-history decisions in distantly related nematodes. The comparison of dauer formation and mouth morphology switch reveals that different thresholds of dafachronic acid signalling provide specificity. This study shows how hormonal signalling acts by coupling environmental change and genetic regulation and identifies dafachronic acid as a key hormone in nematode evolution.

Molecular classification of pesticides including persistent organic pollutants, phenylurea and sulphonylurea herbicides.

PubMed

Torrens, Francisco; Castellano, Gloria

2014-06-05

Pesticide residues in wine were analyzed by liquid chromatography-tandem mass spectrometry. Retentions are modelled by structure-property relationships. Bioplastic evolution is an evolutionary perspective conjugating effect of acquired characters and evolutionary indeterminacy-morphological determination-natural selection principles; its application to design co-ordination index barely improves correlations. Fractal dimensions and partition coefficient differentiate pesticides. Classification algorithms are based on information entropy and its production. Pesticides allow a structural classification by nonplanarity, and number of O, S, N and Cl atoms and cycles; different behaviours depend on number of cycles. The novelty of the approach is that the structural parameters are related to retentions. Classification algorithms are based on information entropy. When applying procedures to moderate-sized sets, excessive results appear compatible with data suffering a combinatorial explosion. However, equipartition conjecture selects criterion resulting from classification between hierarchical trees. Information entropy permits classifying compounds agreeing with principal component analyses. Periodic classification shows that pesticides in the same group present similar properties; those also in equal period, maximum resemblance. The advantage of the classification is to predict the retentions for molecules not included in the categorization. Classification extends to phenyl/sulphonylureas and the application will be to predict their retentions.

The evolution of parasitism in Nematoda.

PubMed

Blaxter, Mark; Koutsovoulos, Georgios

2015-02-01

Nematodes are abundant and diverse, and include many parasitic species. Molecular phylogenetic analyses have shown that parasitism of plants and animals has arisen at least 15 times independently. Extant nematode species also display lifestyles that are proposed to be on the evolutionary trajectory to parasitism. Recent advances have permitted the determination of the genomes and transcriptomes of many nematode species. These new data can be used to further resolve the phylogeny of Nematoda, and identify possible genetic patterns associated with parasitism. Plant-parasitic nematode genomes show evidence of horizontal gene transfer from other members of the rhizosphere, and these genes play important roles in the parasite-host interface. Similar horizontal transfer is not evident in animal parasitic groups. Many nematodes have bacterial symbionts that can be essential for survival. Horizontal transfer from symbionts to the nematode is also common, but its biological importance is unclear. Over 100 nematode species are currently targeted for sequencing, and these data will yield important insights into the biology and evolutionary history of parasitism. It is important that these new technologies are also applied to free-living taxa, so that the pre-parasitic ground state can be inferred, and the novelties associated with parasitism isolated.

Heterogeneous update mechanisms in evolutionary games: Mixing innovative and imitative dynamics

NASA Astrophysics Data System (ADS)

Amaral, Marco Antonio; Javarone, Marco Alberto

2018-04-01

Innovation and evolution are two processes of paramount relevance for social and biological systems. In general, the former allows the introduction of elements of novelty, while the latter is responsible for the motion of a system in its phase space. Often, these processes are strongly related, since an innovation can trigger the evolution, and the latter can provide the optimal conditions for the emergence of innovations. Both processes can be studied by using the framework of evolutionary game theory, where evolution constitutes an intrinsic mechanism. At the same time, the concept of innovation requires an opportune mathematical representation. Notably, innovation can be modeled as a strategy, or it can constitute the underlying mechanism that allows agents to change strategy. Here, we analyze the second case, investigating the behavior of a heterogeneous population, composed of imitative and innovative agents. Imitative agents change strategy only by imitating that of their neighbors, whereas innovative ones change strategy without the need for a copying source. The proposed model is analyzed by means of analytical calculations and numerical simulations in different topologies. Remarkably, results indicate that the mixing of mechanisms can be detrimental to cooperation near phase transitions. In those regions, the spatial reciprocity from imitative mechanisms is destroyed by innovative agents, leading to the downfall of cooperation. Our investigation sheds some light on the complex dynamics emerging from the heterogeneity of strategy revision methods, highlighting the role of innovation in evolutionary games.

The place of development in mathematical evolutionary theory.

PubMed

Rice, Sean H

2012-09-01

Development plays a critical role in structuring the joint offspring-parent phenotype distribution. It thus must be part of any truly general evolutionary theory. Historically, the offspring-parent distribution has often been treated in such a way as to bury the contribution of development, by distilling from it a single term, either heritability or additive genetic variance, and then working only with this term. I discuss two reasons why this approach is no longer satisfactory. First, the regression of expected offspring phenotype on parent phenotype can easily be nonlinear, and this nonlinearity can have a pronounced impact on the response to selection. Second, even when the offspring-parent regression is linear, it is nearly always a function of the environment, and the precise way that heritability covaries with the environment can have a substantial effect on adaptive evolution. Understanding these complexities of the offspring-parent distribution will require understanding of the developmental processes underlying the traits of interest. I briefly discuss how we can incorporate such complexity into formal evolutionary theory, and why it is likely to be important even for traits that are not traditionally the focus of evo-devo research. Finally, I briefly discuss a topic that is widely seen as being squarely in the domain of evo-devo: novelty. I argue that the same conceptual and mathematical framework that allows us to incorporate developmental complexity into simple models of trait evolution also yields insight into the evolution of novel traits. Copyright © 2011 Wiley Periodicals, Inc., A Wiley Company.

Heterogeneous update mechanisms in evolutionary games: Mixing innovative and imitative dynamics.

PubMed

Amaral, Marco Antonio; Javarone, Marco Alberto

2018-04-01

Innovation and evolution are two processes of paramount relevance for social and biological systems. In general, the former allows the introduction of elements of novelty, while the latter is responsible for the motion of a system in its phase space. Often, these processes are strongly related, since an innovation can trigger the evolution, and the latter can provide the optimal conditions for the emergence of innovations. Both processes can be studied by using the framework of evolutionary game theory, where evolution constitutes an intrinsic mechanism. At the same time, the concept of innovation requires an opportune mathematical representation. Notably, innovation can be modeled as a strategy, or it can constitute the underlying mechanism that allows agents to change strategy. Here, we analyze the second case, investigating the behavior of a heterogeneous population, composed of imitative and innovative agents. Imitative agents change strategy only by imitating that of their neighbors, whereas innovative ones change strategy without the need for a copying source. The proposed model is analyzed by means of analytical calculations and numerical simulations in different topologies. Remarkably, results indicate that the mixing of mechanisms can be detrimental to cooperation near phase transitions. In those regions, the spatial reciprocity from imitative mechanisms is destroyed by innovative agents, leading to the downfall of cooperation. Our investigation sheds some light on the complex dynamics emerging from the heterogeneity of strategy revision methods, highlighting the role of innovation in evolutionary games.

Evolutionary contributions to the study of human fertility.

PubMed

Sear, Rebecca

2015-01-01

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

Labels, cognomes, and cyclic computation: an ethological perspective.

PubMed

Murphy, Elliot

2015-01-01

For the past two decades, it has widely been assumed by linguists that there is a single computational operation, Merge, which is unique to language, distinguishing it from other cognitive domains. The intention of this paper is to progress the discussion of language evolution in two ways: (i) survey what the ethological record reveals about the uniqueness of the human computational system, and (ii) explore how syntactic theories account for what ethology may determine to be human-specific. It is shown that the operation Label, not Merge, constitutes the evolutionary novelty which distinguishes human language from non-human computational systems; a proposal lending weight to a Weak Continuity Hypothesis and leading to the formation of what is termed Computational Ethology. Some directions for future ethological research are suggested.

Photonic crystals cause active colour change in chameleons.

PubMed

Teyssier, Jérémie; Saenko, Suzanne V; van der Marel, Dirk; Milinkovitch, Michel C

2015-03-10

Many chameleons, and panther chameleons in particular, have the remarkable ability to exhibit complex and rapid colour changes during social interactions such as male contests or courtship. It is generally interpreted that these changes are due to dispersion/aggregation of pigment-containing organelles within dermal chromatophores. Here, combining microscopy, photometric videography and photonic band-gap modelling, we show that chameleons shift colour through active tuning of a lattice of guanine nanocrystals within a superficial thick layer of dermal iridophores. In addition, we show that a deeper population of iridophores with larger crystals reflects a substantial proportion of sunlight especially in the near-infrared range. The organization of iridophores into two superposed layers constitutes an evolutionary novelty for chameleons, which allows some species to combine efficient camouflage with spectacular display, while potentially providing passive thermal protection.

Photonic crystals cause active colour change in chameleons

NASA Astrophysics Data System (ADS)

Teyssier, Jérémie; Saenko, Suzanne V.; van der Marel, Dirk; Milinkovitch, Michel C.

2015-03-01

Many chameleons, and panther chameleons in particular, have the remarkable ability to exhibit complex and rapid colour changes during social interactions such as male contests or courtship. It is generally interpreted that these changes are due to dispersion/aggregation of pigment-containing organelles within dermal chromatophores. Here, combining microscopy, photometric videography and photonic band-gap modelling, we show that chameleons shift colour through active tuning of a lattice of guanine nanocrystals within a superficial thick layer of dermal iridophores. In addition, we show that a deeper population of iridophores with larger crystals reflects a substantial proportion of sunlight especially in the near-infrared range. The organization of iridophores into two superposed layers constitutes an evolutionary novelty for chameleons, which allows some species to combine efficient camouflage with spectacular display, while potentially providing passive thermal protection.

More than just orphans: are taxonomically-restricted genes important in evolution?

PubMed

Khalturin, Konstantin; Hemmrich, Georg; Fraune, Sebastian; Augustin, René; Bosch, Thomas C G

2009-09-01

Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. Here we focus on evidence from Hydra suggesting that taxonomically-restricted genes play a role in the creation of phylum-specific novelties such as cnidocytes, in the generation of morphological diversity, and in the innate defence system. We propose that taxon-specific genes drive morphological specification, enabling organisms to adapt to changing conditions.

Labels, cognomes, and cyclic computation: an ethological perspective

PubMed Central

Murphy, Elliot

2015-01-01

For the past two decades, it has widely been assumed by linguists that there is a single computational operation, Merge, which is unique to language, distinguishing it from other cognitive domains. The intention of this paper is to progress the discussion of language evolution in two ways: (i) survey what the ethological record reveals about the uniqueness of the human computational system, and (ii) explore how syntactic theories account for what ethology may determine to be human-specific. It is shown that the operation Label, not Merge, constitutes the evolutionary novelty which distinguishes human language from non-human computational systems; a proposal lending weight to a Weak Continuity Hypothesis and leading to the formation of what is termed Computational Ethology. Some directions for future ethological research are suggested. PMID:26089809

Optimal Management of Redundant Control Authority for Fault Tolerance

NASA Technical Reports Server (NTRS)

Wu, N. Eva; Ju, Jianhong

2000-01-01

This paper is intended to demonstrate the feasibility of a solution to a fault tolerant control problem. It explains, through a numerical example, the design and the operation of a novel scheme for fault tolerant control. The fundamental principle of the scheme was formalized in [5] based on the notion of normalized nonspecificity. The novelty lies with the use of a reliability criterion for redundancy management, and therefore leads to a high overall system reliability.

Why evolutionary biologists should get seriously involved in ecological monitoring and applied biodiversity assessment programs

PubMed Central

Brodersen, Jakob; Seehausen, Ole

2014-01-01

While ecological monitoring and biodiversity assessment programs are widely implemented and relatively well developed to survey and monitor the structure and dynamics of populations and communities in many ecosystems, quantitative assessment and monitoring of genetic and phenotypic diversity that is important to understand evolutionary dynamics is only rarely integrated. As a consequence, monitoring programs often fail to detect changes in these key components of biodiversity until after major loss of diversity has occurred. The extensive efforts in ecological monitoring have generated large data sets of unique value to macro-scale and long-term ecological research, but the insights gained from such data sets could be multiplied by the inclusion of evolutionary biological approaches. We argue that the lack of process-based evolutionary thinking in ecological monitoring means a significant loss of opportunity for research and conservation. Assessment of genetic and phenotypic variation within and between species needs to be fully integrated to safeguard biodiversity and the ecological and evolutionary dynamics in natural ecosystems. We illustrate our case with examples from fishes and conclude with examples of ongoing monitoring programs and provide suggestions on how to improve future quantitative diversity surveys. PMID:25553061

Response to novelty and cocaine stimulant effects: lack of stability across environments in female Swiss mice.

PubMed

Nyssen, Laura; Brabant, Christian; Didone, Vincent; Quertemont, Etienne

2016-02-01

In humans, novelty/sensation seeking is seen as a personality trait with a positive relationship with addiction vulnerability. In animal studies, one of the standard procedures to model novelty seeking is the "response to novelty," i.e., the levels of locomotor activity in a new environment. In rodents, a positive correlation was demonstrated between the response to novelty and several effects of drugs, especially the locomotor stimulant effects of cocaine. The present study was designed to test in mice whether the response to novelty is stable across environments and whether its relationship with the stimulant effects of cocaine is altered by environmental changes. Experiment 1 assessed the responses to novelty of the same mice in two different novel environments. Experiment 2 tested the correlation between response to novelty and acute stimulant effects of cocaine recorded in two distinct environments. The results show a weak correlation only during the first 5 min of the session between the responses to novelty measured in two distinct environments. Experiment 2 demonstrates that novelty responses and stimulant effects of cocaine are positively correlated only when both behavioral responses are measured in the same environment. In contrast, the relationship between response to novelty and acute stimulant effects of cocaine is completely lost when the behavioral responses are recorded in two different environments. The present results question the usual interpretation of the correlation between the response to novelty and the stimulant effects of cocaine as reflecting a relationship between two underlying individual stable characteristics.

Why don’t you use Evolutionary Algorithms in Big Data?

NASA Astrophysics Data System (ADS)

Stanovov, Vladimir; Brester, Christina; Kolehmainen, Mikko; Semenkina, Olga

2017-02-01

In this paper we raise the question of using evolutionary algorithms in the area of Big Data processing. We show that evolutionary algorithms provide evident advantages due to their high scalability and flexibility, their ability to solve global optimization problems and optimize several criteria at the same time for feature selection, instance selection and other data reduction problems. In particular, we consider the usage of evolutionary algorithms with all kinds of machine learning tools, such as neural networks and fuzzy systems. All our examples prove that Evolutionary Machine Learning is becoming more and more important in data analysis and we expect to see the further development of this field especially in respect to Big Data.

Midbrain dopamine receptor availability is inversely associated with novelty-seeking traits in humans.

PubMed

Zald, David H; Cowan, Ronald L; Riccardi, Patrizia; Baldwin, Ronald M; Ansari, M Sib; Li, Rui; Shelby, Evan S; Smith, Clarence E; McHugo, Maureen; Kessler, Robert M

2008-12-31

Novelty-seeking personality traits are a major risk factor for the development of drug abuse and other unsafe behaviors. Rodent models of temperament indicate that high novelty responding is associated with decreased inhibitory autoreceptor control of midbrain dopamine neurons. It has been speculated that individual differences in dopamine functioning also underlie the personality trait of novelty seeking in humans. However, differences in the dopamine system of rodents and humans, as well as the methods for assessing novelty responding/seeking across species leave unclear to what extent the animal models inform our understanding of human personality. In the present study we examined the correlation between novelty-seeking traits in humans and D(2)-like (D(2)/D(3)) receptor availability in the substantia nigra/ventral tegmental area. Based on the rodent literature we predicted that novelty seeking would be characterized by lowered levels of D(2)-like (auto)receptor availability in the midbrain. Thirty-four healthy adults (18 men, 16 women) completed the Tridimensional Personality Questionnaire-Novelty-Seeking Scale and PET scanning with the D(2)/D(3) ligand [(18)F]fallypride. Novelty-Seeking personality traits were inversely associated with D(2)-like receptor availability in the ventral midbrain, an effect that remained significant after controlling for age. We speculate that the lower midbrain (auto)receptor availability seen in high novelty seekers leads to accentuated dopaminergic responses to novelty and other conditions that induce dopamine release.

Midbrain dopamine receptor availability is inversely associated with novelty seeking traits in humans

PubMed Central

Zald, David H.; Cowan, Ronald L.; Riccardi, Patrizia; Baldwin, Ronald M.; Ansari, M. Sib; Li, Rui; Shelby, Evan S.; Smith, Clarence E.; McHugo, Maureen; Kessler, Robert M.

2009-01-01

Novelty seeking personality traits are a major risk factor for the development of drug abuse and other unsafe behaviors. Rodent models of temperament indicate that high novelty responding is associated with decreased inhibitory autoreceptor control of midbrain dopamine neurons. It has been speculated that individual differences in dopamine functioning also underlie the personality trait of novelty seeking in humans. However, differences in the dopamine system of rodents and humans, as well as the methods for assessing novelty responding/seeking across species leave unclear to what extent the animal models inform our understanding of human personality. In the present study we examined the correlation between novelty seeking traits in humans and D2-like (D2/D3) receptor availability in the substantia nigra/ventral tegmental area. Based on the rodent literature we predicted that novelty seeking would be characterized by lowered levels of D2-like (auto)receptor availability in the midbrain. 34 healthy adults (18 men, 16 women) completed the Tridimensional Personality Questionnaire-Novelty Seeking Scale and PET scanning with the D2/D3 ligand [18F]fallypride. Novelty seeking personality traits were inversely associated with D2-like receptor availability in the ventral midbrain, an effect that remained significant after controlling for age. We speculate that the lower midbrain (auto)receptor availability seen in high novelty seekers leads to accentuated dopaminergic responses to novelty and other conditions that induce DA release. PMID:19118170

Evolutionary rescue in vertebrates: evidence, applications and uncertainty

PubMed Central

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

2013-01-01

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

Development of X-TOOLSS: Preliminary Design of Space Systems Using Evolutionary Computation

NASA Technical Reports Server (NTRS)

Schnell, Andrew R.; Hull, Patrick V.; Turner, Mike L.; Dozier, Gerry; Alverson, Lauren; Garrett, Aaron; Reneau, Jarred

2008-01-01

Evolutionary computational (EC) techniques such as genetic algorithms (GA) have been identified as promising methods to explore the design space of mechanical and electrical systems at the earliest stages of design. In this paper the authors summarize their research in the use of evolutionary computation to develop preliminary designs for various space systems. An evolutionary computational solver developed over the course of the research, X-TOOLSS (Exploration Toolset for the Optimization of Launch and Space Systems) is discussed. With the success of early, low-fidelity example problems, an outline of work involving more computationally complex models is discussed.

Ghrelin influences novelty seeking behavior in rodents and men.

PubMed

Hansson, Caroline; Shirazi, Rozita H; Näslund, Jakob; Vogel, Heike; Neuber, Corinna; Holm, Göran; Anckarsäter, Henrik; Dickson, Suzanne L; Eriksson, Elias; Skibicka, Karolina P

2012-01-01

Recent discoveries indicate an important role for ghrelin in drug and alcohol reward and an ability of ghrelin to regulate mesolimbic dopamine activity. The role of dopamine in novelty seeking, and the association between this trait and drug and alcohol abuse, led us to hypothesize that ghrelin may influence novelty seeking behavior. To test this possibility we applied several complementary rodent models of novelty seeking behavior, i.e. inescapable novelty-induced locomotor activity (NILA), novelty-induced place preference and novel object exploration, in rats subjected to acute ghrelin receptor (growth hormone secretagogue receptor; GHSR) stimulation or blockade. Furthermore we assessed the possible association between polymorphisms in the genes encoding ghrelin and GHSR and novelty seeking behavior in humans. The rodent studies indicate an important role for ghrelin in a wide range of novelty seeking behaviors. Ghrelin-injected rats exhibited a higher preference for a novel environment and increased novel object exploration. Conversely, those with GHSR blockade drastically reduced their preference for a novel environment and displayed decreased NILA. Importantly, the mesolimbic ventral tegmental area selective GHSR blockade was sufficient to reduce the NILA response indicating that the mesolimbic GHSRs might play an important role in the observed novelty responses. Moreover, in untreated animals, a striking positive correlation between NILA and sucrose reward behavior was detected. Two GHSR single nucleotide polymorphisms (SNPs), rs2948694 and rs495225, were significantly associated with the personality trait novelty seeking, as assessed using the Temperament and Character Inventory (TCI), in human subjects. This study provides the first evidence for a role of ghrelin in novelty seeking behavior in animals and humans, and also points to an association between food reward and novelty seeking in rodents.

Ghrelin Influences Novelty Seeking Behavior in Rodents and Men

PubMed Central

Hansson, Caroline; Shirazi, Rozita H.; Näslund, Jakob; Vogel, Heike; Neuber, Corinna; Holm, Göran; Anckarsäter, Henrik; Dickson, Suzanne L.; Eriksson, Elias; Skibicka, Karolina P.

2012-01-01

Recent discoveries indicate an important role for ghrelin in drug and alcohol reward and an ability of ghrelin to regulate mesolimbic dopamine activity. The role of dopamine in novelty seeking, and the association between this trait and drug and alcohol abuse, led us to hypothesize that ghrelin may influence novelty seeking behavior. To test this possibility we applied several complementary rodent models of novelty seeking behavior, i.e. inescapable novelty-induced locomotor activity (NILA), novelty-induced place preference and novel object exploration, in rats subjected to acute ghrelin receptor (growth hormone secretagogue receptor; GHSR) stimulation or blockade. Furthermore we assessed the possible association between polymorphisms in the genes encoding ghrelin and GHSR and novelty seeking behavior in humans. The rodent studies indicate an important role for ghrelin in a wide range of novelty seeking behaviors. Ghrelin-injected rats exhibited a higher preference for a novel environment and increased novel object exploration. Conversely, those with GHSR blockade drastically reduced their preference for a novel environment and displayed decreased NILA. Importantly, the mesolimbic ventral tegmental area selective GHSR blockade was sufficient to reduce the NILA response indicating that the mesolimbic GHSRs might play an important role in the observed novelty responses. Moreover, in untreated animals, a striking positive correlation between NILA and sucrose reward behavior was detected. Two GHSR single nucleotide polymorphisms (SNPs), rs2948694 and rs495225, were significantly associated with the personality trait novelty seeking, as assessed using the Temperament and Character Inventory (TCI), in human subjects. This study provides the first evidence for a role of ghrelin in novelty seeking behavior in animals and humans, and also points to an association between food reward and novelty seeking in rodents. PMID:23227170

Unraveling Effects of Novelty on Creativity

ERIC Educational Resources Information Center

Gillebaart, Marleen; Förster, Jens; Rotteveel, Mark; Jehle, Astrid C. M.

2013-01-01

Novelty is inherent to creative processes. A positive effect of novelty on creative task performance was therefore predicted. However, creativity can benefit from divergent, as well as convergent thinking. Subsequently, novelty may benefit creative performance when divergent thinking is required, but it could inhibit creative performance when…

Novelty seeking, incentive salience and acquisition of cocaine self-administration in the rat

PubMed Central

Beckmann, Joshua S.; Marusich, Julie A.; Gipson, Cassandra D.; Bardo, Michael T.

2010-01-01

It has been suggested that incentive salience plays a major role in drug abuse and the development of addiction. Additionally, novelty seeking has been identified as a significant risk factor for drug abuse. However, how differences in the readiness to attribute incentive salience relate to novelty seeking and drug abuse vulnerability has not been explored. The present experiments examined how individual differences in incentive salience attribution relate to novelty seeking and acquisition of cocaine self-administration in a preclinical model. Rats were first assessed in an inescapable novelty task and a novelty place preference task (measures of novelty seeking), followed by a Pavlovian conditioned approach task for food (a measure of incentive salience attribution). Rats then were trained to self-administer cocaine (0.3 or 1.0 mg/kg/infusion) using an autoshaping procedure. The results demonstrate that animals that attributed incentive salience to a food-associated cue were higher novelty seekers and acquired cocaine self-administration more quickly at the lower dose. The results suggest that novelty-seeking behavior may be a mediator of incentive salience attribution and that incentive salience magnitude may be an indicator of drug reward. PMID:20655954

Effect of fractionated extracts and isolated pure compounds of Spondias mombin (L. Anacardiaceae) leaves on novelty-induced rearing and grooming behaviours in mice.

PubMed

Ayoka, Abiodun O; Owolabi, Rotimi A; Bamitale, Samuel K; Akomolafe, Rufus O; Aladesanmi, Joseph A; Ukponmwan, Eghe O

2013-01-01

This study attempted to elucidate the neurotransmitter systems involved in the neurophysiological properties of ethanolic extract, fractions and pure isolates of Spondias mombin leaves in mice (n = 6) after intraperitoneal (i.p.) route of administration.The crude ethanolic extract of Spondian mombin leaves was fractionated using the partitioning method to obtain the ethylacetate, butanolic and aqueous fractions. Open column chromatographic fractionation of the ethylacetate fraction yielded seven sub-fractions, out of which the pure coumaroyl, quercetin and gallic acid derivatives were obtained after purification on Sephadex LH 20. The ethanolic extract, butanolic fraction, ethylacetate subfractions and pure isolates of the Spondian mombin leaves were tested on novelty-induced rearing and grooming behaviours in mice with standard pharmacological tools using the open field method. The extract and its fractions decreased novelty-induced rearing in a dose-dependent manner. While the Coumaroyl derivative had no effect on novelty-induced rearing, it significantly reversed the inhibitory effect of yohimbine, propranolol and haloperidol on novelty-induced rearing. Quercetin significantly potentiated the inhibitory effect of yohimbine on novelty-induced rearing. Naloxone significantly potentiated the quercetin-induced suppression of novelty-induced rearing. Gallic acid derivative significantly potentiated the inhibitory effect of yohimbine on novelty-induced rearing. Naloxone, atropine and haloperidol pretreatments significantly potentiated gallic acid derivative-induced suppression of novelty-induced rearing.The extract and its fractions had biphasic effect on novelty-induced grooming in mice. Coumaroyl derivative significantly increased novelty-induced grooming, while quercetin and gallic acid derivative decreased novelty-induced grooming significantly. The three pure isolates significantly reversed the effects of yohimbine and atropine on the novelty-induced grooming in mice. Propranolol-induced increase in novelty-induced grooming was significantly reversed by coumaroyl and gallic acid derivatives. Pre-treatment with naloxone significantly increased the gallic acid derivative-induced suppression of novelty-induced grooming. Pre-treatment with haloperidol reversed the effect of coumaroyl derivative and potentiated the inhibitory effect of quercetin derivative and gallic acid derivative significantly. This study suggested that adrenergic and dopaminergic neuro-transmissions are strongly involved in the neural mechanisms of the effect of the three pure isolates derivative, while opioid neuro-transmission is strongly linked with the neural mechanism of behavioural effect of coumaroyl derivative.

Coevolution in the Galapagos: An Example for the Biology Classroom.

ERIC Educational Resources Information Center

Biggs, Alton L.

1990-01-01

Several examples of coevolution which can be used in biology classes are presented. Discussed are evolutionary processes in general, giant cacti, and reptile and cacti association. The effects of human interference are briefly described. (CW)

Is it new? Personal and contextual influences on perceptions of novelty and creativity.

PubMed

Zhou, Jing; Wang, Xiaoye May; Song, Lynda Jiwen; Wu, Junfeng

2017-02-01

Novelty recognition is the crucial starting point for extracting value from the ideas generated by others. In this paper we develop an associative evaluation account for how personal and contextual factors motivate individuals to perceive novelty and creativity. We report 4 studies that systematically tested hypotheses developed from this perspective. Study 1 (a laboratory experiment) showed that perceivers' regulatory focus, as an experimentally induced state, affected novelty perception. Study 2 (a field study) found that perceivers' promotion focus and prevention focus, measured as chronic traits, each interacted with normative level of novelty and creativity: perceivers who scored higher on promotion focus perceived more novelty (or creativity) in novel (or creative) targets than those who scored lower, whereas perceivers who scored higher on prevention focus perceived less novelty (or creativity) in novel (or creative) targets than those who scored lower. Study 3 (a field study) showed that organizational culture affected the perception of novelty and creativity. Study 4 (a laboratory experiment) found perceiver-by-idea-by-context 3-way interaction effects: for perceivers with prevention focus, the positive relation between normative level of novelty and novelty ratings was weakened in the loss-framing condition versus the gain-framing condition. We discuss implications of the findings for future research and management practice. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Possible role of acetylcholine in regulating spatial novelty effects on theta rhythm and grid cells

PubMed Central

Barry, Caswell; Heys, James G.; Hasselmo, Michael E.

2012-01-01

Existing pharmacological and lesion data indicate that acetylcholine plays an important role in memory formation. For example, increased levels of acetylcholine in the hippocampal formation are known to be associated with successful encoding while disruption of the cholinergic system leads to impairments on a range of mnemonic tasks. However, cholinergic signaling from the medial septum also plays a central role in generating and pacing theta-band oscillations throughout the hippocampal formation. Recent experimental results suggest a potential link between these distinct phenomena. Environmental novelty, a condition associated with strong cholinergic drive, has been shown to induce an expansion in the firing pattern of entorhinal grid cells and a reduction in the frequency of theta measured from the LFP. Computational modeling suggests the spatial activity of grid cells is produced by interference between neuronal oscillators; scale being determined by theta-band oscillations impinging on entorhinal stellate cells, the frequency of which is modulated by acetylcholine. Here we propose that increased cholinergic signaling in response to environmental novelty triggers grid expansion by reducing the frequency of the oscillations. Furthermore, we argue that cholinergic induced grid expansion may enhance, or even induce, encoding by producing a mismatch between expanded grid cells and other spatial inputs to the hippocampus, such as boundary vector cells. Indeed, a further source of mismatch is likely to occur between grid cells of different native scales which may expand by different relative amounts. PMID:22363266

Cigarette pack design and adolescent smoking susceptibility: a cross-sectional survey

PubMed Central

Ford, Allison; MacKintosh, Anne Marie; Moodie, Crawford; Richardson, Sol; Hastings, Gerard

2013-01-01

Objectives To compare adolescents’ responses to three different styles of cigarette packaging: novelty (branded packs designed with a distinctive shape, opening style or bright colour), regular (branded pack with no special design features) and plain (brown pack with a standard shape and opening and all branding removed, aside from brand name). Design Cross-sectional in-home survey. Setting UK. Participants Random location quota sample of 1025 never smokers aged 11–16 years. Main outcome measures Susceptibility to smoking and composite measures of pack appraisal and pack receptivity derived from 11 survey items. Results Mean responses to the three pack types were negative for all survey items. However, ‘novelty’ packs were rated significantly less negatively than the ‘regular’ pack on most items, and the novelty and regular packs were rated less negatively than the ‘plain’ pack. For the novelty packs, logistic regressions, controlling for factors known to influence youth smoking, showed that susceptibility was associated with positive appraisal and also receptivity. For example, those receptive to the innovative Silk Cut Superslims pack were more than four times as likely to be susceptible to smoking than those not receptive to this pack (AOR=4.42, 95% CI 2.50 to 7.81, p<0.001). For the regular pack, an association was found between positive appraisal and susceptibility but not with receptivity and susceptibility. There was no association with pack appraisal or receptivity for the plain pack. Conclusions Pack structure (shape and opening style) and colour are independently associated, not just with appreciation of and receptivity to the pack, but also with susceptibility to smoke. In other words, those who think most highly of novelty cigarette packaging are also the ones who indicate that they are most likely to go on to smoke. Plain packaging, in contrast, was found to directly reduce the appeal of smoking to adolescents. PMID:24056481

The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes

PubMed Central

Janoušek, Václav; Laukaitis, Christina M.; Yanchukov, Alexey

2016-01-01

Abstract Retrotransposons comprise a large portion of mammalian genomes. They contribute to structural changes and more importantly to gene regulation. The expansion and diversification of gene families have been implicated as sources of evolutionary novelties. Given the roles retrotransposons play in genomes, their contribution to the evolution of gene families warrants further exploration. In this study, we found a significant association between two major retrotransposon classes, LINEs and LTRs, and lineage-specific gene family expansions in both the human and mouse genomes. The distribution and diversity differ between LINEs and LTRs, suggesting that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role promoting gene duplication. Our findings also suggest that gene family expansions, especially in the mouse genome, undergo two phases. The first phase is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Altogether we provide evidence of the contribution of retrotransposons to the expansion and evolution of gene families. Our findings emphasize the putative importance of these elements in diversification and adaptation in the human and mouse lineages. PMID:27503295

Investigating Undergraduate Students' Use of Intuitive Reasoning and Evolutionary Knowledge in Explanations of Antibiotic Resistance

ERIC Educational Resources Information Center

Richard, Melissa; Coley, John D.; Tanner, Kimberly D.

2017-01-01

Natural selection is a central concept throughout biology; however, it is a process frequently misunderstood. Bacterial resistance to antibiotic medications provides a contextual example of the relevance of evolutionary theory and is also commonly misunderstood. While research has shed light on student misconceptions of natural selection, minimal…

Evolutionary Biology: Its Value to Society

ERIC Educational Resources Information Center

Carson, Hampton L.

1972-01-01

Cites examples of the contribution of basic research in evolutionary biology to the solution of problems facing society (1) by dispelling myths about human origins, the nature of the individual, and the nature of race (2) by providing basic data concerning the effects of overpopulation, the production of improved sources of food, resistance of…

The Evolution of Altruistic Preferences: Mothers versus Fathers.

PubMed

Alger, Ingela; Cox, Donald

2013-09-01

What can evolutionary biology tell us about male-female differences in preferences concerning family matters? Might mothers be more solicitous toward offspring than fathers, for example? The economics literature has documented gender differences-children benefit more from money put in the hands of mothers rather than fathers, for example-and these differences are thought to be partly due to preferences. Yet for good reason family economics is mostly concerned with how prices and incomes affect behavior against a backdrop of exogenous preferences. Evolutionary biology complements this approach by treating preferences as the outcome of natural selection. We mine the well-developed biological literature to make a prima facie case for evolutionary roots of parental preferences. We consider the most rudimentary of traits-sex differences in gamete size and internal fertilization-and explain how they have been thought to generate male-female differences in altruism toward children and other preferences related to family behavior. The evolutionary approach to the family illuminates connections between issues typically thought distinct in family economics, such as parental care and marriage markets.

Humanism and multiculturalism: an evolutionary alliance.

PubMed

Comas-Diaz, Lillian

2012-12-01

Humanism and multiculturalism are partners in an evolutionary alliance. Humanistic and multicultural psychotherapies have historically influenced each other. Humanism represents the third force in psychotherapy, while multiculturalism embodies the fourth developmental stage. Multiculturalism embraces humanistic values grounded in collective and social justice contexts. Examples of multicultural humanistic constructs include contextualism, holism, and liberation. Certainly, the multicultural-humanistic connection is a necessary shift in the evolution of psychotherapy. Humanism and multiculturalism participate in the development of an inclusive and evolutionary psychotherapy. (c) 2012 APA, all rights reserved.

Quantitative analysis of the evolution of novelty in cinema through crowdsourced keywords.

PubMed

Sreenivasan, Sameet

2013-09-26

The generation of novelty is central to any creative endeavor. Novelty generation and the relationship between novelty and individual hedonic value have long been subjects of study in social psychology. However, few studies have utilized large-scale datasets to quantitatively investigate these issues. Here we consider the domain of American cinema and explore these questions using a database of films spanning a 70 year period. We use crowdsourced keywords from the Internet Movie Database as a window into the contents of films, and prescribe novelty scores for each film based on occurrence probabilities of individual keywords and keyword-pairs. These scores provide revealing insights into the dynamics of novelty in cinema. We investigate how novelty influences the revenue generated by a film, and find a relationship that resembles the Wundt-Berlyne curve. We also study the statistics of keyword occurrence and the aggregate distribution of keywords over a 100 year period.

Quantitative analysis of the evolution of novelty in cinema through crowdsourced keywords

PubMed Central

Sreenivasan, Sameet

2013-01-01

The generation of novelty is central to any creative endeavor. Novelty generation and the relationship between novelty and individual hedonic value have long been subjects of study in social psychology. However, few studies have utilized large-scale datasets to quantitatively investigate these issues. Here we consider the domain of American cinema and explore these questions using a database of films spanning a 70 year period. We use crowdsourced keywords from the Internet Movie Database as a window into the contents of films, and prescribe novelty scores for each film based on occurrence probabilities of individual keywords and keyword-pairs. These scores provide revealing insights into the dynamics of novelty in cinema. We investigate how novelty influences the revenue generated by a film, and find a relationship that resembles the Wundt-Berlyne curve. We also study the statistics of keyword occurrence and the aggregate distribution of keywords over a 100 year period. PMID:24067890

Ecology and evolution of plant–pollinator interactions

PubMed Central

Mitchell, Randall J.; Irwin, Rebecca E.; Flanagan, Rebecca J.; Karron, Jeffrey D.

2009-01-01

Background Some of the most exciting advances in pollination biology have resulted from interdisciplinary research combining ecological and evolutionary perspectives. For example, these two approaches have been essential for understanding the functional ecology of floral traits, the dynamics of pollen transport, competition for pollinator services, and patterns of specialization and generalization in plant–pollinator interactions. However, as research in these and other areas has progressed, many pollination biologists have become more specialized in their research interests, focusing their attention on either evolutionary or ecological questions. We believe that the continuing vigour of a synthetic and interdisciplinary field like pollination biology depends on renewed connections between ecological and evolutionary approaches. Scope In this Viewpoint paper we highlight the application of ecological and evolutionary approaches to two themes in pollination biology: (1) links between pollinator behaviour and plant mating systems, and (2) generalization and specialization in pollination systems. We also describe how mathematical models and synthetic analyses have broadened our understanding of pollination biology, especially in human-modified landscapes. We conclude with several suggestions that we hope will stimulate future research. This Viewpoint also serves as the introduction to this Special Issue on the Ecology and Evolution of Plant–Pollinator Interactions. These papers provide inspiring examples of the synergy between evolutionary and ecological approaches, and offer glimpses of great accomplishments yet to come. PMID:19482881

Ecology and evolution of plant-pollinator interactions.

PubMed

Mitchell, Randall J; Irwin, Rebecca E; Flanagan, Rebecca J; Karron, Jeffrey D

2009-06-01

Some of the most exciting advances in pollination biology have resulted from interdisciplinary research combining ecological and evolutionary perspectives. For example, these two approaches have been essential for understanding the functional ecology of floral traits, the dynamics of pollen transport, competition for pollinator services, and patterns of specialization and generalization in plant-pollinator interactions. However, as research in these and other areas has progressed, many pollination biologists have become more specialized in their research interests, focusing their attention on either evolutionary or ecological questions. We believe that the continuing vigour of a synthetic and interdisciplinary field like pollination biology depends on renewed connections between ecological and evolutionary approaches. In this Viewpoint paper we highlight the application of ecological and evolutionary approaches to two themes in pollination biology: (1) links between pollinator behaviour and plant mating systems, and (2) generalization and specialization in pollination systems. We also describe how mathematical models and synthetic analyses have broadened our understanding of pollination biology, especially in human-modified landscapes. We conclude with several suggestions that we hope will stimulate future research. This Viewpoint also serves as the introduction to this Special Issue on the Ecology and Evolution of Plant-Pollinator Interactions. These papers provide inspiring examples of the synergy between evolutionary and ecological approaches, and offer glimpses of great accomplishments yet to come.

Individual heterogeneity in life histories and eco-evolutionary dynamics

PubMed Central

Vindenes, Yngvild; Langangen, Øystein

2015-01-01

Individual heterogeneity in life history shapes eco-evolutionary processes, and unobserved heterogeneity can affect demographic outputs characterising life history and population dynamical properties. Demographic frameworks like matrix models or integral projection models represent powerful approaches to disentangle mechanisms linking individual life histories and population-level processes. Recent developments have provided important steps towards their application to study eco-evolutionary dynamics, but so far individual heterogeneity has largely been ignored. Here, we present a general demographic framework that incorporates individual heterogeneity in a flexible way, by separating static and dynamic traits (discrete or continuous). First, we apply the framework to derive the consequences of ignoring heterogeneity for a range of widely used demographic outputs. A general conclusion is that besides the long-term growth rate lambda, all parameters can be affected. Second, we discuss how the framework can help advance current demographic models of eco-evolutionary dynamics, by incorporating individual heterogeneity. For both applications numerical examples are provided, including an empirical example for pike. For instance, we demonstrate that predicted demographic responses to climate warming can be reversed by increased heritability. We discuss how applications of this demographic framework incorporating individual heterogeneity can help answer key biological questions that require a detailed understanding of eco-evolutionary dynamics. PMID:25807980

Differential housing and novelty response: Protection and risk from locomotor sensitization

PubMed Central

Garcia, Erik J.; Haddon, Tara N.; Saucier, Donald A.; Cain, Mary E.

2017-01-01

High novelty seeking increases the risk for drug experimentation and locomotor sensitization. Locomotor sensitization to psychostimulants is thought to reflect neurological adaptations that promote the transition to compulsive drug taking. Rats reared in enrichment (EC) show less locomotor sensitization when compared to rats reared in isolation (IC) or standard conditions (SC). The current research study was designed to test if novelty response contributed locomotor sensitization and more importantly, if the different housing environments could change the novelty response to protect against the development of locomotor sensitization in both adolescence and adulthood. Experiment 1: rats were tested for their response to novelty using the inescapable novelty test (IEN) and pseudorandomly assigned to enriched (EC), isolated (IC), or standard (SC) housing conditions for 30 days. After housing, they were tested with IEN. Rats were then administered amphetamine (0.5 mg/kg) or saline and locomotor activity was measured followed by a sensitization test 14 days later. Experiment 2: rats were tested in the IEN test early adulthood and given five administrations of amphetamine (0.3 mg/kg) or saline and then either stayed in or switched housing environments for 30 days. Rats were then re-tested in the IEN test in late adulthood and administered five more injections of their respective treatments and tested for locomotor sensitization. Results indicate that IC and SC increased the response to novelty. EC housing decreased locomotor response to amphetamine and saline, and SC housing increased the locomotor response to amphetamine. Mediation results indicated that the late adult novelty response fully mediates the locomotor response to amphetamine and saline, while the early adulthood novelty response did not. Conclusions Differential housing changes novelty and amphetamine locomotor response. Novelty response is altered into adulthood and provides evidence that enrichment can be used to reduce drug vulnerability. PMID:28108176

Capacity of novelty-induced locomotor activity and the hole-board test to predict sensitivity to the conditioned rewarding effects of cocaine.

PubMed

Arenas, M Carmen; Daza-Losada, Manuel; Vidal-Infer, Antonio; Aguilar, Maria A; Miñarro, José; Rodríguez-Arias, Marta

2014-06-22

Novelty-seeking in rodents, defined as enhanced specific exploration of novel situations, is considered to predict the response of animals to drugs of abuse and, thus, allow "drug-vulnerable" individuals to be identified. The main objective of this study was to assess the predictive ability of two well-known paradigms of the novelty-seeking trait - novelty-induced locomotor activity (which distinguishes High- and Low-Responder mice, depending on their motor activity) and the hole-board test (which determines High- and Low-Novelty Seeker mice depending on the number of head dips they perform) - to identify subjects that would subsequently be more sensitive to the conditioned rewarding effects of cocaine in a population of young adult (PND 56) and adolescent (PND 35) OF1 mice of both sexes. Conditioned place preference (CPP), a useful tool for evaluating the sensitivity of individuals to the incentive properties of addictive drugs, was induced with a sub-threshold dose of cocaine (1 mg/kg, i.p.). Our results showed that novelty-induced motor activity had a greater predictive capacity to identify "vulnerable-drug" individuals among young-adult mice (PND 56), while the hole-board test was more effective in adolescents (PND 35). High-NR young-adults, which presented higher motor activity in the first ten minutes of the test (novelty-reactivity), were 3.9 times more likely to develop cocaine-induced CPP than Low-NR young-adults. When total activity (1h) was evaluated (novelty-habituation), only High-R (novelty-non-habituating) young-adult male and Low-R (novelty-habituating) female mice produced a high conditioning score. However, only High-Novelty Seeker male and female adolescents and Low-Novelty Seeker female young-adult animals (according to the hole-board test), acquired cocaine-induced CPP. These findings should contribute to the development of screening methods for identifying at-risk human drug users and prevention strategies for those with specific vulnerabilities. Copyright © 2014 Elsevier Inc. All rights reserved.

Literary study and evolutionary theory : A review essay.

PubMed

Carroll, J

1998-09-01

Several recent books have claimed to integrate literary study with evolutionary biology. All of the books here considered, except Robert Storey's, adopt conceptions of evolutionary theory that are in some way marginal to the Darwinian adaptationist program. All the works attempt to connect evolutionary study with various other disciplines or methodologies: for example, with cultural anthropology, cognitive psychology, the psychology of emotion, neurobiology, chaos theory, or structuralist linguistics. No empirical paradigm has yet been established for this field, but important steps have been taken, especially by Storey, in formulating basic principles, identifying appropriate disciplinary connections, and marking out lines of inquiry. Reciprocal efforts are needed from biologists and social scientists.

Photonic crystals cause active colour change in chameleons

PubMed Central

Teyssier, Jérémie; Saenko, Suzanne V.; van der Marel, Dirk; Milinkovitch, Michel C.

2015-01-01

Many chameleons, and panther chameleons in particular, have the remarkable ability to exhibit complex and rapid colour changes during social interactions such as male contests or courtship. It is generally interpreted that these changes are due to dispersion/aggregation of pigment-containing organelles within dermal chromatophores. Here, combining microscopy, photometric videography and photonic band-gap modelling, we show that chameleons shift colour through active tuning of a lattice of guanine nanocrystals within a superficial thick layer of dermal iridophores. In addition, we show that a deeper population of iridophores with larger crystals reflects a substantial proportion of sunlight especially in the near-infrared range. The organization of iridophores into two superposed layers constitutes an evolutionary novelty for chameleons, which allows some species to combine efficient camouflage with spectacular display, while potentially providing passive thermal protection. PMID:25757068

Something Old, Something New: A Developmental Transition from Familiarity to Novelty Preferences with Hidden Objects

ERIC Educational Resources Information Center

Shinskey, Jeanne L.; Munakata, Yuko

2010-01-01

Novelty seeking is viewed as adaptive, and novelty preferences in infancy predict cognitive performance into adulthood. Yet 7-month-olds prefer familiar stimuli to novel ones when searching for hidden objects, in contrast to their strong novelty preferences with visible objects (Shinskey & Munakata, 2005). According to a graded representations…

How should novelty be valued in science?

PubMed

Cohen, Barak A

2017-07-25

Scientists are under increasing pressure to do "novel" research. Here I explore whether there are risks to overemphasizing novelty when deciding what constitutes good science. I review studies from the philosophy of science to help understand how important an explicit emphasis on novelty might be for scientific progress. I also review studies from the sociology of science to anticipate how emphasizing novelty might impact the structure and function of the scientific community. I conclude that placing too much value on novelty could have counterproductive effects on both the rate of progress in science and the organization of the scientific community. I finish by recommending that our current emphasis on novelty be replaced by a renewed emphasis on predictive power as a characteristic of good science.

Male sexual behavior does not require elevated testosterone in a lizard (Coleonyx elegans, Eublepharidae).

PubMed

Golinski, Alison; John-Alder, Henry; Kratochvíl, Lukáš

2011-01-01

Male sexual behavior depends on gonadal androgens in species of all major vertebrate lineages, including reptiles. However, male sexual behavior includes distinct appetitive and consummatory phases, typically denoted as courtship and mounting, with potentially different hormonal control. Different proximate controls of courtship versus mounting could enable disconnected evolutionary losses and gains of various aspects of male sexual behavior. Male courtship display, which is activated by testosterone (T) in many species, is an ancestral trait in the lizard family Eublepharidae. However, Coleonyx elegans (Yucatan Banded Gecko) lost the courtship display, while retaining a highly simplified male sexual behavior that involves only mounting for copulation. We performed surgical manipulations (castration with and without T replacement in adult males; implantation of adult females with exogenous T) to investigate hormonal mechanisms involved in this evolutionary novelty. Our results indicate that the expression of simplified sexual behavior in C. elegans does not require elevated circulating levels of T, a finding that is previously unreported in lizards. In females, however, exogenous T induced male-like mounting. Thus, the mounting phase of sexual behavior is not activated by T in the traditional sense of this term but probably requires post-natal, maturational organization (if not periodic reorganization) by androgens. We conclude that the simplification of male sexual behavior and its independence from elevated levels of circulating androgens in C. elegans evolved via 1) evolutionary loss of the androgen-activated courtship display and 2) retention of the mounting phase, which has a longer "functional memory" for the effects of androgenic steroids. Copyright © 2010 Elsevier Inc. All rights reserved.

Developmental studies of the lamprey and hierarchical evolutionary steps towards the acquisition of the jaw

PubMed Central

Kuratani, Shigeru

2005-01-01

The evolution of animal morphology can be understood as a series of changes in developmental programs. Among vertebrates, some developmental stages are conserved across species, representing particular developmental constraints. One of the most conserved stages is the vertebrate pharyngula, in which similar embryonic morphology is observed and the Hox code is clearly expressed. The oral developmental program also appears to be constrained to some extent, as both its morphology and the the Hox-code-default state of the oropharyngeal region are well conserved between the lamprey and gnathostome embryos. These features do not by themselves explain the evolution of jaws, but should be regarded as a prerequisite for evolutionary diversification of the mandibular arch. By comparing the pharyngula morphology of the lamprey and gnathostomes, it has become clear that the oral pattern is not entirely identical; in particular, the positional differentiation of the rostral ectomesenchyme is shifted between these animals. Therefore, the jaw seems to have arisen as an evolutionary novelty by overriding ancestral constraints, a process in which morphological homologies are partially lost. This change involves the heterotopic shift of tissue interaction, which appears to have been preceded by the transition from monorhiny to diplorhiny, as well as separation of the hypophysis. When gene expression patterns are compared between the lamprey and gnathostomes, cell-autonomously functioning genes tend to be associated with identical cell types or equivalent anatomical domains, whereas growth-factor-encoding genes have changed their expression domains during evolution. Thus, the heterotopic evolution may be based on changes in the regulation of signalling-molecule-encoding genes. PMID:16313390

Conservation of chromosomes syntenic with avian autosomes in squamate reptiles revealed by comparative chromosome painting.

PubMed

Pokorná, Martina; Giovannotti, Massimo; Kratochvíl, Lukáš; Caputo, Vincenzo; Olmo, Ettore; Ferguson-Smith, Malcolm A; Rens, Willem

2012-08-01

In contrast to mammals, birds exhibit a slow rate of chromosomal evolution. It is not clear whether high chromosome conservation is an evolutionary novelty of birds or was inherited from an earlier avian ancestor. The evolutionary conservatism of macrochromosomes between birds and turtles supports the latter possibility; however, the rate of chromosomal evolution is largely unknown in other sauropsids. In squamates, we previously reported strong conservatism of the chromosomes syntenic with the avian Z, which could reflect a peculiarity of this part of the genome. The chromosome 1 of iguanians and snakes is largely syntenic with chromosomes 3, 5 and 7 of the avian ancestral karyotype. In this project, we used comparative chromosome painting to determine how widely this synteny is conserved across nine families covering most of the main lineages of Squamata. The results suggest that the association of the avian ancestral chromosomes 3, 5 and 7 can be dated back to at least the early Jurassic and could be an ancestral characteristic for Unidentata (Serpentes, Iguania, Anguimorpha, Laterata and Scinciformata). In Squamata chromosome conservatism therefore also holds for the parts of the genome which are homologous to bird autosomes, and following on from this, a slow rate of chromosomal evolution could be a common characteristic of all sauropsids. The large evolutionary stasis in chromosome organization in birds therefore seems to be inherited from their ancestors, and it is particularly striking in comparison with mammals, probably the only major tetrapod lineage with an increased rate of chromosomal rearrangements as a whole.

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

PubMed

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

2017-11-15

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

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2016-06-01

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

Remote Sensing and Information Technology for Large Farms

NASA Technical Reports Server (NTRS)

Williams, John E.; Ramsay, Jimmie A.

2003-01-01

A method of applying remote sensing (RS) and information-management technology to help large farms produce at maximum efficiency is undergoing development. The novelty of the method does not lie in the concept of precision agriculture, which involves variation of seeding, of application of chemicals, and of irrigation according to the spatially and temporally local variations in the growth stages and health of crops and in the chemical and physical conditions of soils. The novelty also does not lie in the use of RS data registered with other data in a geographic information system (GIS) to guide the use of precise agricultural techniques. Instead, the novelty lies in a systematic approach to overcoming obstacles that, heretofore, have impeded the timely distribution of reliable, relevant, and sufficient GIS data to support day-to-day, acre-to-acre decisions concerning the application of precise agricultural techniques to increase production and decrease cost. The development and promotion of the method are inspired in part by a vision of equipping farm machinery to accept GIS (including RS) data and using the data for automated or semi-automated implementation of precise agricultural techniques. Primary examples of relevant GIS data include information on plant stress, soil moisture, and effects of applied chemicals, all derived by automated computational analysis of measurements taken by one or more airborne spectroradiometers. Proper management and timeliness of the large amount of GIS information are of paramount concern in agriculture. Information on stresses and changes in crops is especially perishable and important to farmers. The need for timeliness and management of information is satisfied by use of computing hardware and software capable of (1) rapid geo-rectification and other processing of RS data, (2) packaging the output data in the form of GIS plots, and (3) making the data available to farmers and other subscribers by Internet password access. It is a goal of this development program to make RS data available no later than the data after an aerial survey. In addition, data from prior surveys are kept in the data base. Farmers can, for example, use current and prior data to analyze changes.

Remote Sensing and Information Technology for Large Farms

NASA Technical Reports Server (NTRS)

Williams, John E.; Ramsay, Jimmie A.

2002-01-01

A method of applying of remote sensing (RS) and information management technology to help large farms produce at maximum efficiency is undergoing development. The novelty of the method does not lie in the concept of "precision agriculture," which involves variation of seeding, of application of chemicals, and of irrigation according to the spatially and temporally local variations in the growth stages and health of crops and in the chemical and physical conditions of soils. The novelty also does not lie in the use of RS data registered with other data in a geographic information system (GIS) to guide the use of precise agricultural techniques. Instead, the novelty lies in a systematic approach to overcoming obstacles that, heretofore, have impeded the timely distribution of reliable, relevant, and sufficient GIS data to support day-to-day, acre-to-acre decisions concerning the application of precise agricultural techniques to increase production and decrease cost. The development and promotion of the method are inspired in part by a vision of equipping farm machinery to accept GIS (including RS) data and using the data for automated or semiautomated implementation of precise agricultural techniques. Primary examples of relevant GIS data include information on plant stress, soil moisture, and effects of applied chemicals, all derived by automated computational analysis of measurements taken by one or more airborne spectroradiometers. Proper management and timeliness of the large amount of GIS information are of paramount concern in agriculture. Information on stresses and changes in crops is especially perishable and important to farmers. The need for timeliness and management of information is satisfied by use of computing hardware and software capable of (1) rapid georectification and other processing of RS data, (2) packaging the output data in the form of GIS plots, and (3) making the data available to farmers and other subscribers by Internet password access. It is a goal of this development program to make RS data available no later than the data after an aerial survey. In addition, data from prior surveys are kept in the data base. Farmers can, for example, use current and prior data to analyze changes.

D4 dopamine-receptor (DRD4) alleles and novelty seeking in substance-dependent, personality-disorder, and control subjects.

PubMed Central

Gelernter, J; Kranzler, H; Coccaro, E; Siever, L; New, A; Mulgrew, C L

1997-01-01

Two reports have been published suggesting an association between the personality trait of novelty seeking and the DRD4*7R allele at the D4 dopamine-receptor locus (with heterozygotes or homozygotes for DRD4*7R having higher novelty seeking). We studied novelty seeking and four coding-sequence polymorphisms affecting protein structure in the D4 dopamine-receptor gene (DRD4) in a sample of 341 American subjects, of whom 224 are of primarily European ancestry and 117 are of primarily African ancestry. These subjects had diagnoses of substance dependence or personality disorder (PD) or were screened to exclude major psychiatric diagnosis. We found that, although the substance-dependent subjects had significantly higher novelty seeking than the control and PD subjects, they did not differ in DRD4*7R allele frequency. There was no association between any DRD4 polymorphism and novelty seeking in any population or diagnostic group, except for a significant association between the DRD4*7R allele and lower novelty seeking among European American females and African American substance abusers. The novelty seeking of subjects heterozygous for a null mutation did not differ from that of subjects with two functional alleles. We conclude that the most likely explanation of these results is that the DRD4 VNTR does not influence directly the trait of novelty seeking, in these samples. PMID:9345090

Constructive neutral evolution: exploring evolutionary theory's curious disconnect.

PubMed

Stoltzfus, Arlin

2012-10-13

Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing view of the causes of evolution suggests. In particular, a mutationist conception of evolution as a 2-step origin-fixation process has been a source of theoretical innovation for 40 years, appearing not only in the Neutral Theory, but also in recent breakthroughs in modeling adaptation (the "mutational landscape" model), and in practical software for sequence analysis. In this conception, mutation is not a source of raw materials, but an agent that introduces novelty, while selection is not an agent that shapes features, but a stochastic sieve. This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution. Alex Kondrashov, Eugene Koonin and Johann Peter Gogarten reviewed this article.

A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes.

PubMed

Mishra, Bud; Daruwala, Raoul-Sam; Zhou, Yi; Ugel, Nadia; Policriti, Alberto; Antoniotti, Marco; Paxia, Salvatore; Rejali, Marc; Rudra, Archisman; Cherepinsky, Vera; Silver, Naomi; Casey, William; Piazza, Carla; Simeoni, Marta; Barbano, Paolo; Spivak, Marina; Feng, Jiawu; Gill, Ofer; Venkatesh, Mysore; Cheng, Fang; Sun, Bing; Ioniata, Iuliana; Anantharaman, Thomas; Hubbard, E Jane Albert; Pnueli, Amir; Harel, David; Chandru, Vijay; Hariharan, Ramesh; Wigler, Michael; Park, Frank; Lin, Shih-Chieh; Lazebnik, Yuri; Winkler, Franz; Cantor, Charles R; Carbone, Alessandra; Gromov, Mikhael

2003-01-01

We collaborate in a research program aimed at creating a rigorous framework, experimental infrastructure, and computational environment for understanding, experimenting with, manipulating, and modifying a diverse set of fundamental biological processes at multiple scales and spatio-temporal modes. The novelty of our research is based on an approach that (i) requires coevolution of experimental science and theoretical techniques and (ii) exploits a certain universality in biology guided by a parsimonious model of evolutionary mechanisms operating at the genomic level and manifesting at the proteomic, transcriptomic, phylogenic, and other higher levels. Our current program in "systems biology" endeavors to marry large-scale biological experiments with the tools to ponder and reason about large, complex, and subtle natural systems. To achieve this ambitious goal, ideas and concepts are combined from many different fields: biological experimentation, applied mathematical modeling, computational reasoning schemes, and large-scale numerical and symbolic simulations. From a biological viewpoint, the basic issues are many: (i) understanding common and shared structural motifs among biological processes; (ii) modeling biological noise due to interactions among a small number of key molecules or loss of synchrony; (iii) explaining the robustness of these systems in spite of such noise; and (iv) cataloging multistatic behavior and adaptation exhibited by many biological processes.

Constructive neutral evolution: exploring evolutionary theory’s curious disconnect

PubMed Central

2012-01-01

Abstract Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing view of the causes of evolution suggests. In particular, a mutationist conception of evolution as a 2-step origin-fixation process has been a source of theoretical innovation for 40 years, appearing not only in the Neutral Theory, but also in recent breakthroughs in modeling adaptation (the “mutational landscape” model), and in practical software for sequence analysis. In this conception, mutation is not a source of raw materials, but an agent that introduces novelty, while selection is not an agent that shapes features, but a stochastic sieve. This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution. Reviewers Alex Kondrashov, Eugene Koonin and Johann Peter Gogarten reviewed this article. PMID:23062217

Deep-sea whale fall fauna from the Atlantic resembles that of the Pacific Ocean.

PubMed

Sumida, Paulo Y G; Alfaro-Lucas, Joan M; Shimabukuro, Mauricio; Kitazato, Hiroshi; Perez, Jose A A; Soares-Gomes, Abilio; Toyofuku, Takashi; Lima, Andre O S; Ara, Koichi; Fujiwara, Yoshihiro

2016-02-24

Whale carcasses create remarkable habitats in the deep-sea by producing concentrated sources of organic matter for a food-deprived biota as well as places of evolutionary novelty and biodiversity. Although many of the faunal patterns on whale falls have already been described, the biogeography of these communities is still poorly known especially from basins other than the NE Pacific Ocean. The present work describes the community composition of the deepest natural whale carcass described to date found at 4204 m depth on Southwest Atlantic Ocean with manned submersible Shinkai 6500. This is the first record of a natural whale fall in the deep Atlantic Ocean. The skeleton belonged to an Antarctic Minke whale composed of only nine caudal vertebrae, whose degradation state suggests it was on the bottom for 5-10 years. The fauna consisted mainly of galatheid crabs, a new species of the snail Rubyspira and polychaete worms, including a new Osedax species. Most of the 41 species found in the carcass are new to science, with several genera shared with NE Pacific whale falls and vent and seep ecosystems. This similarity suggests the whale-fall fauna is widespread and has dispersed in a stepping stone fashion, deeply influencing its evolutionary history.

Elevated Extinction Rates as a Trigger for Diversification Rate Shifts: Early Amniotes as a Case Study

PubMed Central

Brocklehurst, Neil; Ruta, Marcello; Müller, Johannes; Fröbisch, Jörg

2015-01-01

Tree shape analyses are frequently used to infer the location of shifts in diversification rate within the Tree of Life. Many studies have supported a causal relationship between shifts and temporally coincident events such as the evolution of “key innovations”. However, the evidence for such relationships is circumstantial. We investigated patterns of diversification during the early evolution of Amniota from the Carboniferous to the Triassic, subjecting a new supertree to analyses of tree balance in order to infer the timing and location of diversification shifts. We investigated how uneven origination and extinction rates drive diversification shifts, and use two case studies (herbivory and an aquatic lifestyle) to examine whether shifts tend to be contemporaneous with evolutionary novelties. Shifts within amniotes tend to occur during periods of elevated extinction, with mass extinctions coinciding with numerous and larger shifts. Diversification shifts occurring in clades that possess evolutionary innovations do not coincide temporally with the appearance of those innovations, but are instead deferred to periods of high extinction rate. We suggest such innovations did not cause increases in the rate of cladogenesis, but allowed clades to survive extinction events. We highlight the importance of examining general patterns of diversification before interpreting specific shifts. PMID:26592209

Environmental effects on the structure of the G-matrix.

PubMed

Wood, Corlett W; Brodie, Edmund D

2015-11-01

Genetic correlations between traits determine the multivariate response to selection in the short term, and thereby play a causal role in evolutionary change. Although individual studies have documented environmentally induced changes in genetic correlations, the nature and extent of environmental effects on multivariate genetic architecture across species and environments remain largely uncharacterized. We reviewed the literature for estimates of the genetic variance-covariance (G) matrix in multiple environments, and compared differences in G between environments to the divergence in G between conspecific populations (measured in a common garden). We found that the predicted evolutionary trajectory differed as strongly between environments as it did between populations. Between-environment differences in the underlying structure of G (total genetic variance and the relative magnitude and orientation of genetic correlations) were equal to or greater than between-population differences. Neither environmental novelty, nor the difference in mean phenotype predicted these differences in G. Our results suggest that environmental effects on multivariate genetic architecture may be comparable to the divergence that accumulates over dozens or hundreds of generations between populations. We outline avenues of future research to address the limitations of existing data and characterize the extent to which lability in genetic correlations shapes evolution in changing environments. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Deep-sea whale fall fauna from the Atlantic resembles that of the Pacific Ocean

NASA Astrophysics Data System (ADS)

Sumida, Paulo Y. G.; Alfaro-Lucas, Joan M.; Shimabukuro, Mauricio; Kitazato, Hiroshi; Perez, Jose A. A.; Soares-Gomes, Abilio; Toyofuku, Takashi; Lima, Andre O. S.; Ara, Koichi; Fujiwara, Yoshihiro

2016-02-01

Whale carcasses create remarkable habitats in the deep-sea by producing concentrated sources of organic matter for a food-deprived biota as well as places of evolutionary novelty and biodiversity. Although many of the faunal patterns on whale falls have already been described, the biogeography of these communities is still poorly known especially from basins other than the NE Pacific Ocean. The present work describes the community composition of the deepest natural whale carcass described to date found at 4204 m depth on Southwest Atlantic Ocean with manned submersible Shinkai 6500. This is the first record of a natural whale fall in the deep Atlantic Ocean. The skeleton belonged to an Antarctic Minke whale composed of only nine caudal vertebrae, whose degradation state suggests it was on the bottom for 5-10 years. The fauna consisted mainly of galatheid crabs, a new species of the snail Rubyspira and polychaete worms, including a new Osedax species. Most of the 41 species found in the carcass are new to science, with several genera shared with NE Pacific whale falls and vent and seep ecosystems. This similarity suggests the whale-fall fauna is widespread and has dispersed in a stepping stone fashion, deeply influencing its evolutionary history.

The dynamics of correlated novelties.

PubMed

Tria, F; Loreto, V; Servedio, V D P; Strogatz, S H

2014-07-31

Novelties are a familiar part of daily life. They are also fundamental to the evolution of biological systems, human society, and technology. By opening new possibilities, one novelty can pave the way for others in a process that Kauffman has called "expanding the adjacent possible". The dynamics of correlated novelties, however, have yet to be quantified empirically or modeled mathematically. Here we propose a simple mathematical model that mimics the process of exploring a physical, biological, or conceptual space that enlarges whenever a novelty occurs. The model, a generalization of Polya's urn, predicts statistical laws for the rate at which novelties happen (Heaps' law) and for the probability distribution on the space explored (Zipf's law), as well as signatures of the process by which one novelty sets the stage for another. We test these predictions on four data sets of human activity: the edit events of Wikipedia pages, the emergence of tags in annotation systems, the sequence of words in texts, and listening to new songs in online music catalogues. By quantifying the dynamics of correlated novelties, our results provide a starting point for a deeper understanding of the adjacent possible and its role in biological, cultural, and technological evolution.

The dynamics of correlated novelties

NASA Astrophysics Data System (ADS)

Tria, F.; Loreto, V.; Servedio, V. D. P.; Strogatz, S. H.

2014-07-01

Novelties are a familiar part of daily life. They are also fundamental to the evolution of biological systems, human society, and technology. By opening new possibilities, one novelty can pave the way for others in a process that Kauffman has called ``expanding the adjacent possible''. The dynamics of correlated novelties, however, have yet to be quantified empirically or modeled mathematically. Here we propose a simple mathematical model that mimics the process of exploring a physical, biological, or conceptual space that enlarges whenever a novelty occurs. The model, a generalization of Polya's urn, predicts statistical laws for the rate at which novelties happen (Heaps' law) and for the probability distribution on the space explored (Zipf's law), as well as signatures of the process by which one novelty sets the stage for another. We test these predictions on four data sets of human activity: the edit events of Wikipedia pages, the emergence of tags in annotation systems, the sequence of words in texts, and listening to new songs in online music catalogues. By quantifying the dynamics of correlated novelties, our results provide a starting point for a deeper understanding of the adjacent possible and its role in biological, cultural, and technological evolution.

The dynamics of correlated novelties

PubMed Central

Tria, F.; Loreto, V.; Servedio, V. D. P.; Strogatz, S. H.

2014-01-01

Novelties are a familiar part of daily life. They are also fundamental to the evolution of biological systems, human society, and technology. By opening new possibilities, one novelty can pave the way for others in a process that Kauffman has called “expanding the adjacent possible”. The dynamics of correlated novelties, however, have yet to be quantified empirically or modeled mathematically. Here we propose a simple mathematical model that mimics the process of exploring a physical, biological, or conceptual space that enlarges whenever a novelty occurs. The model, a generalization of Polya's urn, predicts statistical laws for the rate at which novelties happen (Heaps' law) and for the probability distribution on the space explored (Zipf's law), as well as signatures of the process by which one novelty sets the stage for another. We test these predictions on four data sets of human activity: the edit events of Wikipedia pages, the emergence of tags in annotation systems, the sequence of words in texts, and listening to new songs in online music catalogues. By quantifying the dynamics of correlated novelties, our results provide a starting point for a deeper understanding of the adjacent possible and its role in biological, cultural, and technological evolution. PMID:25080941

Novelty's effect on memory encoding.

PubMed

Rangel-Gomez, Mauricio; Janenaite, Sigita; Meeter, Martijn

2015-07-01

It is often thought that novelty benefits memory formation. However, support for this idea mostly comes from paradigms that are open to alternative explanations. In the present study we manipulated novelty in a word-learning task through task-irrelevant background images. These background images were either standard (presented repeatedly), or novel (presented only once). Two types of background images were used: Landscape pictures and fractals. EEG was also recorded during encoding. Contrary to the idea that novelty aids memory formation, memory performance was not affected by the novelty of the background. In the evoked response potentials, we found evidence of distracting effects of novelty: both the N1 and P3b components were smaller to words studied with novel backgrounds, and the amplitude of the N2b component correlated negatively with subsequent retrieval. We conclude that although evidence from other studies does suggest benefits on a longer time scale, novelty has no instantaneous benefits for learning. Copyright © 2015 Elsevier B.V. All rights reserved.

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

PubMed

Bouzat, Juan L; Hoostal, Matthew J

2013-05-01

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

Differential housing and novelty response: Protection and risk from locomotor sensitization.

PubMed

Garcia, Erik J; Haddon, Tara N; Saucier, Donald A; Cain, Mary E

2017-03-01

High novelty seeking increases the risk for drug experimentation and locomotor sensitization. Locomotor sensitization to psychostimulants is thought to reflect neurological adaptations that promote the transition to compulsive drug taking. Rats reared in enrichment (EC) show less locomotor sensitization when compared to rats reared in isolation (IC) or standard conditions (SC). The current research study was designed to test if novelty response contributed locomotor sensitization and more importantly, if the different housing environments could change the novelty response to protect against the development of locomotor sensitization in both adolescence and adulthood. Experiment 1: rats were tested for their response to novelty using the inescapable novelty test (IEN) and pseudorandomly assigned to enriched (EC), isolated (IC), or standard (SC) housing conditions for 30days. After housing, they were tested with IEN. Rats were then administered amphetamine (0.5mg/kg) or saline and locomotor activity was measured followed by a sensitization test 14days later. Experiment 2: rats were tested in the IEN test early adulthood and given five administrations of amphetamine (0.3mg/kg) or saline and then either stayed in or switched housing environments for 30days. Rats were then re-tested in the IEN test in late adulthood and administered five more injections of their respective treatments and tested for locomotor sensitization. Results indicate that IC and SC increased the response to novelty. EC housing decreased locomotor response to amphetamine and saline, and SC housing increased the locomotor response to amphetamine. Mediation results indicated that the late adult novelty response fully mediates the locomotor response to amphetamine and saline, while the early adulthood novelty response did not. Differential housing changes novelty and amphetamine locomotor response. Novelty response is altered into adulthood and provides evidence that enrichment can be used to reduce drug vulnerability. Copyright © 2017 Elsevier Inc. All rights reserved.

A Bright Future for Evolutionary Methods in Drug Design.

PubMed

Le, Tu C; Winkler, David A

2015-08-01

Most medicinal chemists understand that chemical space is extremely large, essentially infinite. Although high-throughput experimental methods allow exploration of drug-like space more rapidly, they are still insufficient to fully exploit the opportunities that such large chemical space offers. Evolutionary methods can synergistically blend automated synthesis and characterization methods with computational design to identify promising regions of chemical space more efficiently. We describe how evolutionary methods are implemented, and provide examples of published drug development research in which these methods have generated molecules with increased efficacy. We anticipate that evolutionary methods will play an important role in future drug discovery. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

How will climate novelty influence ecological forecasts? Using the Quaternary to assess future reliability.

PubMed

Fitzpatrick, Matthew C; Blois, Jessica L; Williams, John W; Nieto-Lugilde, Diego; Maguire, Kaitlin C; Lorenz, David J

2018-03-23

Future climates are projected to be highly novel relative to recent climates. Climate novelty challenges models that correlate ecological patterns to climate variables and then use these relationships to forecast ecological responses to future climate change. Here, we quantify the magnitude and ecological significance of future climate novelty by comparing it to novel climates over the past 21,000 years in North America. We then use relationships between model performance and climate novelty derived from the fossil pollen record from eastern North America to estimate the expected decrease in predictive skill of ecological forecasting models as future climate novelty increases. We show that, in the high emissions scenario (RCP 8.5) and by late 21st century, future climate novelty is similar to or higher than peak levels of climate novelty over the last 21,000 years. The accuracy of ecological forecasting models is projected to decline steadily over the coming decades in response to increasing climate novelty, although models that incorporate co-occurrences among species may retain somewhat higher predictive skill. In addition to quantifying future climate novelty in the context of late Quaternary climate change, this work underscores the challenges of making reliable forecasts to an increasingly novel future, while highlighting the need to assess potential avenues for improvement, such as increased reliance on geological analogs for future novel climates and improving existing models by pooling data through time and incorporating assemblage-level information. © 2018 John Wiley & Sons Ltd.

Comparison of some evolutionary algorithms for optimization of the path synthesis problem

NASA Astrophysics Data System (ADS)

Grabski, Jakub Krzysztof; Walczak, Tomasz; Buśkiewicz, Jacek; Michałowska, Martyna

2018-01-01

The paper presents comparison of the results obtained in a mechanism synthesis by means of some selected evolutionary algorithms. The optimization problem considered in the paper as an example is the dimensional synthesis of the path generating four-bar mechanism. In order to solve this problem, three different artificial intelligence algorithms are employed in this study.

High locomotor reactivity to novelty is associated with an increased propensity to choose saccharin over cocaine: new insights into the vulnerability to addiction.

PubMed

Vanhille, Nathalie; Belin-Rauscent, Aude; Mar, Adam C; Ducret, Eric; Belin, David

2015-02-01

Drug addiction is associated with a relative devaluation of natural or socially-valued reinforcers that are unable to divert addicts from seeking and consuming the drug. Before protracted drug exposure, most rats prefer natural rewards, such as saccharin, over cocaine. However, a subpopulation of animals prefer cocaine over natural rewards and are thought to be vulnerable to addiction. Specific behavioral traits have been associated with different dimensions of drug addiction. For example, anxiety predicts loss of control over drug intake whereas sensation seeking and sign-tracking are markers of a greater sensitivity to the rewarding properties of the drug. However, how these behavioral traits predict the disinterest for natural reinforcers remains unknown. In a population of rats, we identified sensation seekers (HR) on the basis of elevated novelty-induced locomotor reactivity, high anxious rats (HA) based on the propensity to avoid open arms in an elevated-plus maze and sign-trackers (ST) that are prone to approach, and interaction with, reward-associated stimuli. Rats were then tested on their preference for saccharin over cocaine in a discrete-trial choice procedure. We show that HR rats display a greater preference for saccharin over cocaine compared with ST and HA whereas the motivation for the drug was comparable between the three groups. The present data suggest that high locomotor reactivity to novelty, or sensation seeking, by predisposing to an increased choice toward non-drug rewards at early stages of drug use history, may prevent the establishment of chronic cocaine use.

Familiarity-Based Stimulus Generalization of Conditioned Suppression

PubMed Central

2017-01-01

We report that stimulus novelty/familiarity is able to modulate stimulus generalization and discuss the theoretical implications of novelty/familiarity coding. Rats in Skinner boxes received clicker → shock pairings before generalization testing to a tone. Before clicker training, different groups of rats received preexposure treatments designed to systematically modulate the clicker and the tone’s novelty and familiarity. Rats whose preexposure matched novelty/familiarity (i.e., either both or neither clicker and tone were preexposed) showed enhanced suppression to the tone relative to rats whose preexposure mixed novelty/familiarity (i.e., only clicker or tone was preexposed). This was not the result of sensory preconditioning to clicker and tone. PMID:28383938

Mechanisms of hippocampal long-term depression are required for memory enhancement by novelty exploration.

PubMed

Dong, Zhifang; Gong, Bo; Li, Hongjie; Bai, Yanrui; Wu, Xiaoyan; Huang, Yan; He, Wenting; Li, Tingyu; Wang, Yu Tian

2012-08-29

It is well known that novel environments can enhance learning and memory. However, the underlying mechanisms remain poorly understood. Here, we report that, in freely moving rats, novelty exploration facilitates the production of hippocampal CA1 long-term depression (LTD), a well characterized form of synaptic plasticity believed to be a cellular substrate of spatial learning, and thereby converts short-term memory (STM) into long-term memory (LTM) in an inhibitory avoidance learning procedure. Blocking the induction or the expression of CA1 LTD with two mechanistically and structurally distinct inhibitors prevents not only novelty acquisition but also the novelty exploration-promoted conversion of STM into LTM. Moreover, production of LTD with a strong electrical stimulation induction protocol or facilitation of hippocampal LTD by pharmacological inhibition of glutamate transporter activity mimics the behavioral effects of novelty exploration, sufficiently promoting the conversion of STM into LTM. Together, our findings suggest that induction of LTD may play an essential role not only in novelty acquisition but also in novelty-mediated memory enhancement.

The von Restorff effect in amnesia: the contribution of the hippocampal system to novelty-related memory enhancements.

PubMed

Kishiyama, M M; Yonelinas, A P; Lazzara, M M

2004-01-01

The ability to detect novelty is a characteristic of all mammalian nervous systems (Sokolov, 1963), and it plays a critical role in memory in the sense that items that are novel, or distinctive, are remembered better than those that are less distinct (von Restorff, 1933). Although several brain areas are sensitive to stimulus novelty, it is not yet known which regions play a role in producing novelty-related effects on memory. In the current study, we investigated novelty effects on recognition memory in amnesic patients and healthy control subjects. The control subjects demonstrated better recognition for items that were novel (i.e., presented in an infrequent color), and this effect was found for both recollection and familiarity-based responses. However, the novelty advantage was effectively eliminated in patients with extensive medial temporal lobe damage, mild hypoxic patients expected to have relatively selective hippocampal damage, and in a patient with thalamic lesions. The results indicate that the human medial temporal lobes play a critical role in producing normal novelty effects in memory.

Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues

PubMed Central

Hall, Brian K; Gillis, J Andrew

2013-01-01

Urochordates (ascidians) have recently supplanted cephalochordates (amphioxus) as the extant sister taxon of vertebrates. Given that urochordates possess migratory cells that have been classified as ‘neural crest-like’– and that cephalochordates lack such cells – this phylogenetic hypothesis may have significant implications with respect to the origin of the neural crest and neural crest-derived skeletal tissues in vertebrates. We present an overview of the genes and gene regulatory network associated with specification of the neural crest in vertebrates. We then use these molecular data – alongside cell behaviour, cell fate and embryonic context – to assess putative antecedents (latent homologues) of the neural crest or neural crest cells in ascidians and cephalochordates. Ascidian migratory mesenchymal cells – non-pigment-forming trunk lateral line cells and pigment-forming ‘neural crest-like cells’ (NCLC) – are unlikely latent neural crest cell homologues. Rather, Snail-expressing cells at the neural plate of border of urochordates and cephalochordates likely represent the extent of neural crest elaboration in non-vertebrate chordates. We also review evidence for the evolutionary origin of two neural crest-derived skeletal tissues – cartilage and dentine. Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest. Cartilage, on the other hand, likely has a much deeper origin within the Metazoa. The mesodermally derived cellular cartilages of some protostome invertebrates are much more similar to vertebrate cartilage than is the acellular ‘cartilage-like’ tissue in cephalochordate pharyngeal arches. Cartilage, therefore, is not a vertebrate novelty, and a well-developed chondrogenic program was most likely co-opted from mesoderm to the neural crest along the vertebrate stem. We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion – first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates. PMID:22414251

Research traditions and evolutionary explanations in medicine.

PubMed

Méthot, Pierre-Olivier

2011-02-01

In this article, I argue that distinguishing 'evolutionary' from 'Darwinian' medicine will help us assess the variety of roles that evolutionary explanations can play in a number of medical contexts. Because the boundaries of evolutionary and Darwinian medicine overlap to some extent, however, they are best described as distinct 'research traditions' rather than as competing paradigms. But while evolutionary medicine does not stand out as a new scientific field of its own, Darwinian medicine is united by a number of distinctive theoretical and methodological claims. For example, evolutionary medicine and Darwinian medicine can be distinguished with respect to the styles of evolutionary explanations they employ. While the former primarily involves 'forward looking' explanations, the latter depends mostly on 'backward looking' explanations. A forward looking explanation tries to predict the effects of ongoing evolutionary processes on human health and disease in contemporary environments (e.g., hospitals). In contrast, a backward looking explanation typically applies evolutionary principles from the vantage point of humans' distant biological past in order to assess present states of health and disease. Both approaches, however, are concerned with the prevention and control of human diseases. In conclusion, I raise some concerns about the claim that 'nothing in medicine makes sense except in the light of evolution'.

Links between Evolution, Development, Human Anatomy, Pathology, and Medicine, with A Proposition of A Re-defined Anatomical Position and Notes on Constraints and Morphological "Imperfections".

PubMed

Diogo, Rui; Molnar, Julia

2016-06-01

Surprisingly the oldest formal discipline in medicine (anatomy) has not yet felt the full impact of evolutionary developmental biology. In medical anatomy courses and textbooks, the human body is still too often described as though it is a "perfect machine." In fact, the study of human anatomy predates evolutionary theory; therefore, many of its conventions continue to be outdated, making it difficult to study, understand, and treat the human body, and to compare it with that of other, nonbipedal animals, including other primates. Moreover, such an erroneous view of our anatomy as "perfect" can be used to fuel nonevolutionary ideologies such as intelligent design. In the section An Evolutionary and Developmental Approach to Human Anatomical Position of this paper, we propose the redefinition of the "human standard anatomical position" used in textbooks to be consistent with human evolutionary and developmental history. This redefined position also simplifies, for students and practitioners of the health professions, the study and learning of embryonic muscle groups (each group including muscles derived from the same/ontogenetically closely related primordium/primordia) and joint movements and highlights the topological correspondence between the upper and lower limbs. Section Evolutionary and Developmental Constraints, "Imperfections" and Sports Pathologies continues the theme by describing examples of apparently "illogical" characteristics of the human body that only make sense when one understands the developmental and evolutionary constraints that have accumulated over millions of years. We focus, in particular, on musculoskeletal functional problems and sports pathologies to emphasize the links with pathology and medicine. These examples demonstrate how incorporating evolutionary theory into anatomy education can be helpful for medical students, teachers, researchers, and physicians, as well as for anatomists, functional morphologists, and evolutionary and developmental biologists. © 2016 Wiley Periodicals, Inc.

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

NASA Astrophysics Data System (ADS)

Fu, Shihua; Li, Haitao; Zhao, Guodong

2018-05-01

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

Clever sillies: why high IQ people tend to be deficient in common sense.

PubMed

Charlton, Bruce G

2009-12-01

In previous editorials I have written about the absent-minded and socially-inept 'nutty professor' stereotype in science, and the phenomenon of 'psychological neoteny' whereby intelligent modern people (including scientists) decline to grow-up and instead remain in a state of perpetual novelty-seeking adolescence. These can be seen as specific examples of the general phenomenon of 'clever sillies' whereby intelligent people with high levels of technical ability are seen (by the majority of the rest of the population) as having foolish ideas and behaviours outside the realm of their professional expertise. In short, it has often been observed that high IQ types are lacking in 'common sense'--and especially when it comes to dealing with other human beings. General intelligence is not just a cognitive ability; it is also a cognitive disposition. So, the greater cognitive abilities of higher IQ tend also to be accompanied by a distinctive high IQ personality type including the trait of 'Openness to experience', 'enlightened' or progressive left-wing political values, and atheism. Drawing on the ideas of Kanazawa, my suggested explanation for this association between intelligence and personality is that an increasing relative level of IQ brings with it a tendency differentially to over-use general intelligence in problem-solving, and to over-ride those instinctive and spontaneous forms of evolved behaviour which could be termed common sense. Preferential use of abstract analysis is often useful when dealing with the many evolutionary novelties to be found in modernizing societies; but is not usually useful for dealing with social and psychological problems for which humans have evolved 'domain-specific' adaptive behaviours. And since evolved common sense usually produces the right answers in the social domain; this implies that, when it comes to solving social problems, the most intelligent people are more likely than those of average intelligence to have novel but silly ideas, and therefore to believe and behave maladaptively. I further suggest that this random silliness of the most intelligent people may be amplified to generate systematic wrongness when intellectuals are in addition 'advertising' their own high intelligence in the evolutionarily novel context of a modern IQ meritocracy. The cognitively-stratified context of communicating almost-exclusively with others of similar intelligence, generates opinions and behaviours among the highest IQ people which are not just lacking in common sense but perversely wrong. Hence the phenomenon of 'political correctness' (PC); whereby false and foolish ideas have come to dominate, and moralistically be enforced upon, the ruling elites of whole nations.

Evidence for viable, non-clonal but fatherless Boa constrictors.

PubMed

Booth, Warren; Johnson, Daniel H; Moore, Sharon; Schal, Coby; Vargo, Edward L

2011-04-23

Parthenogenesis in vertebrates is considered an evolutionary novelty. In snakes, all of which exhibit genetic sex determination with ZZ : ZW sex chromosomes, this rare form of asexual reproduction has failed to yield viable female WW offspring. Only through complex experimental manipulations have WW females been produced, and only in fish and amphibians. Through microsatellite DNA fingerprinting, we provide the first evidence of facultative parthenogenesis in a Boa constrictor, identifying multiple, viable, non-experimentally induced females for the first time in any vertebrate lineage. Although the elevated homozygosity of the offspring in relation to the mother suggests that the mechanism responsible may be terminal fusion automixis, no males were produced, potentially indicating maternal sex chromosome hemizygosity (WO). These findings provide the first evidence of parthenogenesis in the family Boidae (Boas), and suggest that WW females may be more common within basal reptilian lineages than previously assumed.

Alternative cytoskeletal landscapes: cytoskeletal novelty and evolution in basal excavate protists

PubMed Central

Dawson, Scott C.; Paredez, Alexander R.

2016-01-01

Microbial eukaryotes encompass the majority of eukaryotic evolutionary and cytoskeletal diversity. The cytoskeletal complexity observed in multicellular organisms appears to be an expansion of components present in genomes of diverse microbial eukaryotes such as the basal lineage of flagellates, the Excavata. Excavate protists have complex and diverse cytoskeletal architectures and life cycles – essentially alternative cytoskeletal “landscapes” – yet still possess conserved microtubule- and actin-associated proteins. Comparative genomic analyses have revealed that a subset of excavates, however, lack many canonical actin-binding proteins central to actin cytoskeleton function in other eukaryotes. Overall, excavates possess numerous uncharacterized and “hypothetical” genes, and may represent an undiscovered reservoir of novel cytoskeletal genes and cytoskeletal mechanisms. The continued development of molecular genetic tools in these complex microbial eukaryotes will undoubtedly contribute to our overall understanding of cytoskeletal diversity and evolution. PMID:23312067

Sociological and Communication-Theoretical Perspectives on the Commercialization of the Sciences

NASA Astrophysics Data System (ADS)

Leydesdorff, Loet

2013-10-01

Both self-organization and organization are important for the further development of the sciences: the two dynamics condition and enable each other. Commercial and public considerations can interact and "interpenetrate" in historical organization; different codes of communication are then "recombined". However, self-organization in the symbolically generalized codes of communication can be expected to operate at the global level. The Triple Helix model allows for both a neo-institutional appreciation in terms of historical networks of university-industry-government relations and a neo-evolutionary interpretation in terms of three functions: (1) novelty production, (2) wealth generation, and (3) political control. Using this model, one can appreciate both subdynamics. The mutual information in three dimensions enables us to measure the trade-off between organization and self-organization as a possible synergy. The question of optimization between commercial and public interests in the different sciences can thus be made empirical.

Evidence for viable, non-clonal but fatherless Boa constrictors

PubMed Central

Booth, Warren; Johnson, Daniel H.; Moore, Sharon; Schal, Coby; Vargo, Edward L.

2011-01-01

Parthenogenesis in vertebrates is considered an evolutionary novelty. In snakes, all of which exhibit genetic sex determination with ZZ : ZW sex chromosomes, this rare form of asexual reproduction has failed to yield viable female WW offspring. Only through complex experimental manipulations have WW females been produced, and only in fish and amphibians. Through microsatellite DNA fingerprinting, we provide the first evidence of facultative parthenogenesis in a Boa constrictor, identifying multiple, viable, non-experimentally induced females for the first time in any vertebrate lineage. Although the elevated homozygosity of the offspring in relation to the mother suggests that the mechanism responsible may be terminal fusion automixis, no males were produced, potentially indicating maternal sex chromosome hemizygosity (WO). These findings provide the first evidence of parthenogenesis in the family Boidae (Boas), and suggest that WW females may be more common within basal reptilian lineages than previously assumed. PMID:21047849

Morphological phylogeny of Tradescantia L. (Commelinaceae) sheds light on a new infrageneric classification for the genus and novelties on the systematics of subtribe Tradescantiinae

PubMed Central

Pellegrini, Marco O. O.

2017-01-01

Abstract Throughout the years, three infrageneric classifications were proposed for Tradescantia along with several informal groups and species complexes. The current infrageneric classification accepts 12 sections – with T. sect. Tradescantia being further divided into four series – and assimilates many concepts adopted by previous authors. Recent molecular-based phylogenetic studies indicate that the currently accepted sections might not represent monophyletic groups within Tradescantia. Based on newly gathered morphological data on the group, complemented with available micromorphological, cytological and phytochemical data, I present the first morphology-based evolutionary hypothesis for Tradescantia. Furthermore, I reduce subtribe Thyrsantheminae to a synonym of subtribe Tradescantiinae, and propose a new infrageneric classification for Tradescantia, based on the total evidence of the present morphological phylogeny, in accordance to the previously published molecular data. PMID:29118649

Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity.

PubMed

Fan, Pengxiang; Miller, Abigail M; Liu, Xiaoxiao; Jones, A Daniel; Last, Robert L

2017-12-12

Plants produce hundreds of thousands of structurally diverse specialized metabolites via multistep biosynthetic networks, including compounds of ecological and therapeutic importance. These pathways are restricted to specific plant groups, and are excellent systems for understanding metabolic evolution. Tomato and other plants in the nightshade family synthesize protective acylated sugars in the tip cells of glandular trichomes on stems and leaves. We describe a metabolic innovation in wild tomato species that contributes to acylsucrose structural diversity. A small number of amino acid changes in two acylsucrose acyltransferases alter their acyl acceptor preferences, resulting in reversal of their order of reaction and increased product diversity. This study demonstrates how small numbers of amino acid changes in multiple pathway enzymes can lead to diversification of specialized metabolites in plants. It also highlights the power of a combined genetic, genomic and in vitro biochemical approach to identify the evolutionary mechanisms leading to metabolic novelty.

Dinosaur evolution. Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds.

PubMed

Lee, Michael S Y; Cau, Andrea; Naish, Darren; Dyke, Gareth J

2014-08-01

Recent discoveries have highlighted the dramatic evolutionary transformation of massive, ground-dwelling theropod dinosaurs into light, volant birds. Here, we apply Bayesian approaches (originally developed for inferring geographic spread and rates of molecular evolution in viruses) in a different context: to infer size changes and rates of anatomical innovation (across up to 1549 skeletal characters) in fossils. These approaches identify two drivers underlying the dinosaur-bird transition. The theropod lineage directly ancestral to birds undergoes sustained miniaturization across 50 million years and at least 12 consecutive branches (internodes) and evolves skeletal adaptations four times faster than other dinosaurs. The distinct, prolonged phase of miniaturization along the bird stem would have facilitated the evolution of many novelties associated with small body size, such as reorientation of body mass, increased aerial ability, and paedomorphic skulls with reduced snouts but enlarged eyes and brains. Copyright © 2014, American Association for the Advancement of Science.

Pf16 and phiPMW: Expanding the realm of Pseudomonas putida bacteriophages

PubMed Central

Krylov, Victor N.; Shaburova, Olga V.; McGrath, John W.; Allen, Christopher C. R.; Quinn, John P.; Kulakov, Leonid A.

2017-01-01

We present the analysis of two novel Pseudomonas putida phages, pf16 and phiPMW. Pf16 represents a peripherally related T4-like phage, and is the first of its kind infecting a Pseudomonad, with evidence suggesting cyanophage origins. Extensive divergence has resulted in pf16 occupying a newly defined clade designated as the pf16-related phages, lying at the interface of the Schizo T-Evens and Exo T-Evens. Recombination with an ancestor of the P. putida phage AF is likely responsible for the tropism of this phage. phiPMW represents a completely novel Pseudomonas phage with a genome containing substantial genetic novelty through its many hypothetical proteins. Evidence suggests that this phage has been extensively shaped through gene transfer events and vertical evolution. Phylogenetics shows that this phage has an evolutionary history involving FelixO1-related viruses but is in itself highly distinct from this group. PMID:28877269

Geologic map of the Agnesi quadrangle (V-45), Venus

USGS Publications Warehouse

Hansen, Vicki L.; Tharalson, Erik R.

2014-01-01

Two general classes of hypotheses have emerged to address the near random spatial distribution of ~970 apparently pristine impact craters across the surface of Venus: (1) catastrophic/episodic resurfacing and (2) equilibrium/evolutionary resurfacing. Catastrophic/episodic hypotheses propose that a global-scale, temporally punctuated event or events dominated Venus’ evolution and that the generally uniform impact crater distribution (Schaber and others, 1992; Phillips and others, 1992; Herrick and others, 1997) reflects craters that accumulated during relative global quiescence since that event (for example, Strom and others, 1994; Herrick, 1994; Turcotte and others, 1999). Equilibrium/evolutionary hypotheses suggest instead that the near random crater distribution results from relatively continuous, but spatially localized, resurfacing in which volcanic and (or) tectonic processes occur across the planet through time, although the style of operative processes may have varied temporally and spatially (for example, Phillips and others, 1992; Guest and Stofan, 1999; Hansen and Young, 2007). Geologic relations within the map area allow us to test the catastrophic/episodic versus equilibrium/evolutionary resurfacing hypotheses.

Self-extinction through optimizing selection.

PubMed

Parvinen, Kalle; Dieckmann, Ulf

2013-09-21

Evolutionary suicide is a process in which selection drives a viable population to extinction. So far, such selection-driven self-extinction has been demonstrated in models with frequency-dependent selection. This is not surprising, since frequency-dependent selection can disconnect individual-level and population-level interests through environmental feedback. Hence it can lead to situations akin to the tragedy of the commons, with adaptations that serve the selfish interests of individuals ultimately ruining a population. For frequency-dependent selection to play such a role, it must not be optimizing. Together, all published studies of evolutionary suicide have created the impression that evolutionary suicide is not possible with optimizing selection. Here we disprove this misconception by presenting and analyzing an example in which optimizing selection causes self-extinction. We then take this line of argument one step further by showing, in a further example, that selection-driven self-extinction can occur even under frequency-independent selection. Copyright © 2013 Elsevier Ltd. All rights reserved.

Comparison of outliers and novelty detection to identify ionospheric TEC irregularities during geomagnetic storm and substorm

NASA Astrophysics Data System (ADS)

Pattisahusiwa, Asis; Houw Liong, The; Purqon, Acep

2016-08-01

In this study, we compare two learning mechanisms: outliers and novelty detection in order to detect ionospheric TEC disturbance by November 2004 geomagnetic storm and January 2005 substorm. The mechanisms are applied by using v-SVR learning algorithm which is a regression version of SVM. Our results show that both mechanisms are quiet accurate in learning TEC data. However, novelty detection is more accurate than outliers detection in extracting anomalies related to geomagnetic events. The detected anomalies by outliers detection are mostly related to trend of data, while novelty detection are associated to geomagnetic events. Novelty detection also shows evidence of LSTID during geomagnetic events.

A Psychophysiological Study of Processing HIV/AIDS Public Service Announcements: The Effects of Novelty Appeals, Sexual Appeals, Narrative Versus Statistical Evidence, and Viewer's Sex.

PubMed

Zhang, Jueman Mandy; Chen, Gina Masullo; Chock, T Makana; Wang, Yi; Ni, Liqiang; Schweisberger, Valarie

2016-07-01

This study used self-reports and physiological measures-heart rate (HR) and skin conductance level (SCL)-to examine the effects of novelty appeals, sexual appeals, narrative versus statistical evidence, and viewer's sex on cognitive and emotional processing of HIV/AIDS public service announcements (PSAs) among heterosexually active single college students. Novelty or sexual appeals differently affected self-reported attention and cognitive effort as measured by HR. High- rather than low-novelty HIV/AIDS PSAs, perceived as more attention-eliciting, did not lead to more cognitive effort. High- rather than low-sex HIV/AIDS PSAs, not perceived as more attention-eliciting, led to more cognitive effort as reflected by greater HR deceleration. Novelty or sexual appeals also affected self-reported emotional arousal and SCL differently. HIV/AIDS PSAs with high rather than low levels of novelty or sexual appeals led to greater self-reported arousal, but not greater SCL. Message evidence interacted with message appeals to affect cognitive effort. Participants exerted greater cognitive effort during high- rather than low-novelty narrative HIV/AIDS PSAs, and during low- rather than high-novelty statistical ones. The advantage of high over low sexual appeals was more obvious in statistical than in narrative HIV/AIDS PSAs. Males reported greater emotional arousal than females during high- rather than low-sex HIV/AIDS PSAs.

Evolutionary Models of Irregular Warfare

DTIC Science & Technology

2013-03-01

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

From philosophy to science (to natural philosophy): evolutionary developmental perspectives.

PubMed

Love, Alan C

2008-03-01

This paper focuses on abstraction as a mode of reasoning that facilitates a productive relationship between philosophy and science. Using examples from evolutionary developmental biology, I argue that there are two areas where abstraction can be relevant to science: reasoning explication and problem clarification. The value of abstraction is characterized in terms of methodology (modeling or data gathering) and epistemology (explanatory evaluation or data interpretation).

Meta-analysis of magnitudes, differences and variation in evolutionary parameters.

PubMed

Morrissey, M B

2016-10-01

Meta-analysis is increasingly used to synthesize major patterns in the large literatures within ecology and evolution. Meta-analytic methods that do not account for the process of observing data, which we may refer to as 'informal meta-analyses', may have undesirable properties. In some cases, informal meta-analyses may produce results that are unbiased, but do not necessarily make the best possible use of available data. In other cases, unbiased statistical noise in individual reports in the literature can potentially be converted into severe systematic biases in informal meta-analyses. I first present a general description of how failure to account for noise in individual inferences should be expected to lead to biases in some kinds of meta-analysis. In particular, informal meta-analyses of quantities that reflect the dispersion of parameters in nature, for example, the mean absolute value of a quantity, are likely to be generally highly misleading. I then re-analyse three previously published informal meta-analyses, where key inferences were of aspects of the dispersion of values in nature, for example, the mean absolute value of selection gradients. Major biological conclusions in each original informal meta-analysis closely match those that could arise as artefacts due to statistical noise. I present alternative mixed-model-based analyses that are specifically tailored to each situation, but where all analyses may be implemented with widely available open-source software. In each example meta-re-analysis, major conclusions change substantially. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Evolving the future: Toward a science of intentional change

PubMed Central

Wilson, David Sloan; Hayes, Steven C.; Biglan, Anthony; Embry, Dennis D.

2015-01-01

Humans possess great capacity for behavioral and cultural change, but our ability to manage change is still limited. This article has two major objectives: first, to sketch a basic science of intentional change centered on evolution; second, to provide examples of intentional behavioral and cultural change from the applied behavioral sciences, which are largely unknown to the basic sciences community. All species have evolved mechanisms of phenotypic plasticity that enable them to respond adaptively to their environments. Some mechanisms of phenotypic plasticity count as evolutionary processes in their own right. The human capacity for symbolic thought provides an inheritance system having the same kind of combinatorial diversity as does genetic recombination and antibody formation. Taking these propositions seriously allows an integration of major traditions within the basic behavioral sciences, such as behaviorism, social constructivism, social psychology, cognitive psychology, and evolutionary psychology, which are often isolated and even conceptualized as opposed to one another. The applied behavioral sciences include well-validated examples of successfully managing behavioral and cultural change at scales ranging from individuals to small groups to large populations. However, these examples are largely unknown beyond their disciplinary boundaries, for lack of a unifying theoretical framework. Viewed from an evolutionary perspective, they are examples of managing evolved mechanisms of phenotypic plasticity, including open-ended processes of variation and selection. Once the many branches of the basic and applied behavioral sciences become conceptually unified, we are closer to a science of intentional change than one might think. PMID:24826907

The availability of novelty sweets within high school localities.

PubMed

Aljawad, A; Morgan, M Z; Rees, J S; Fairchild, R

2016-06-10

Background Reducing sugar consumption is a primary focus of current global public health policy. Achieving 5% of total energy from free sugars will be difficult acknowledging the concentration of free sugars in sugar sweetened beverages, confectionery and as hidden sugars in many savoury items. The expansion of the novelty sweet market in the UK has significant implications for children and young adults as they contribute to dental caries, dental erosion and obesity.Objective To identify the most available types of novelty sweets within the high school fringe in Cardiff, UK and to assess their price range and where and how they were displayed in shops.Subjects and methods Shops within a ten minute walking distance around five purposively selected high schools in the Cardiff aea representing different levels of deprivation were visited. Shops in Cardiff city centre and three supermarkets were also visited to identify the most commonly available novelty sweets.Results The ten most popular novelty sweets identified in these scoping visits were (in descending order): Brain Licker, Push Pop, Juicy Drop, Lickedy Lips, Big Baby Pop, Vimto candy spray, Toxic Waste, Tango candy spray, Brain Blasterz Bitz and Mega Mouth candy spray. Novelty sweets were located on low shelves which were accessible to all age-groups in 73% (14 out of 19) of the shops. Novelty sweets were displayed in the checkout area in 37% (seven out of 19) shops. The price of the top ten novelty sweets ranged from 39p to £1.Conclusion A wide range of acidic and sugary novelty sweets were easily accessible and priced within pocket money range. Those personnel involved in delivering dental and wider health education or health promotion need to be aware of recent developments in children's confectionery. The potential effects of these novelty sweets on both general and dental health require further investigation.

Evolutionary transitions in controls reconcile adaptation with continuity of evolution.

PubMed

Badyaev, Alexander V

2018-05-19

Evolution proceeds by accumulating functional solutions, necessarily forming an uninterrupted lineage from past solutions of ancestors to the current design of extant forms. At the population level, this process requires an organismal architecture in which the maintenance of local adaptation does not preclude the ability to innovate in the same traits and their continuous evolution. Representing complex traits as networks enables us to visualize a fundamental principle that resolves tension between adaptation and continuous evolution: phenotypic states encompassing adaptations traverse the continuous multi-layered landscape of past physical, developmental and functional associations among traits. The key concept that captures such traversing is network controllability - the ability to move a network from one state into another while maintaining its functionality (reflecting evolvability) and to efficiently propagate information or products through the network within a phenotypic state (maintaining its robustness). Here I suggest that transitions in network controllability - specifically in the topology of controls - help to explain how robustness and evolvability are balanced during evolution. I will focus on evolutionary transitions in degeneracy of metabolic networks - a ubiquitous property of phenotypic robustness where distinct pathways achieve the same end product - to suggest that associated changes in network controls is a common rule underlying phenomena as distinct as phenotypic plasticity, organismal accommodation of novelties, genetic assimilation, and macroevolutionary diversification. Capitalizing on well understood principles by which network structure translates into function of control nodes, I show that accumulating redundancy in one type of network controls inevitably leads to the emergence of another type of controls, forming evolutionary cycles of network controllability that, ultimately, reconcile local adaptation with continuity of evolution. Copyright © 2018 Elsevier Ltd. All rights reserved.

An evolutionary cosmology for scientists--and the modern world in general.

PubMed

Charlton, Bruce G

2007-01-01

I believe that people will not feel comfortable and positive about the contemporary world until we can endorse and believe an evolutionary cosmology which is appropriate to modern conditions. A cosmology is a mythical account of the universe as it presents itself to the human mind; it needs to be poetic, symbolic, inspiring of a sense of awe and mystery. Furthermore, a complete cosmology should include the three levels of macro-, meso- and micro-cosm, in order to understand the nature of the universe, human society, and the individual's relation to them. Traditional cosmologies described an eternal underlying structure to ultimate reality--a static ideal state towards which the world ought to gravitate. However, modern life is characterized by rapid growth, novelty, destruction and fluidity of all kinds of structures, a feature which traditional static cosmologies interpret negatively and pessimistically. A modern cosmology therefore needs to be focused on underlying dynamic process instead of structure and stasis. Biologists are better placed than many to appreciate a cosmology based on evolutionary change; because this is the mainstream understanding of adaptation and diversity in the natural world. The same dynamic, neophiliac and open-ended process of 'creative destruction' can be seen at work in science, economics, and modern spirituality. But a modern cosmology will only be experienced as both deep and spontaneous when it takes the form of a mythic account that is first encountered and assimilated during childhood. Since myths arise as a consequence of human creativity; there is a vital future mythogenic role for artists in the realm of ideas, images and stories: people such as mystics, poets and philosophers--including, I hope and expect, creatively inspired scientists.

Novelty and the 1919 Eclipse Experiments

NASA Astrophysics Data System (ADS)

Hudson, Robert G.

In her 1996 book, Error and the Growth of Experimental Knowledge, Deborah Mayo argues that use- (or heuristic) novelty is not a criterion we need to consider in assessing the evidential value of observations. Using the notion of a "severe" test, Mayo claims that such novelty is valuable only when it leads to severity, and never otherwise. To illustrate her view, she examines the historical case involving the famous 1919 British eclipse expeditions that generated observations supporting Einstein's theory of gravitation over Newton's. My plan here is to defend use-novelty as a valuable methodological principle. I begin by exposing a weakness in Mayo's criticism of use-novelty. Remedying this weakness re-establishes the worth of use-novelty under specific conditions; in particular, heuristically novel data are to be preferred, as I will say, "prima facie". Armed with this revised version of use-novelty, I re-examine the history of the eclipse experiments and offer an interpretation of this episode that to an extent-and contrary to Mayo-restores the mildly heretical, Earman/Glymour evaluation of this episode offered in their (1980). I conclude by responding to criticism of my assessment of Mayo's work.

Novelty, coherence, and Mendeleev's periodic table.

PubMed

Schindler, Samuel

2014-03-01

Predictivism is the view that successful predictions of "novel" evidence carry more confirmational weight than accommodations of already known evidence. Novelty, in this context, has traditionally been conceived of as temporal novelty. However temporal predictivism has been criticized for lacking a rationale: why should the time order of theory and evidence matter? Instead, it has been proposed, novelty should be construed in terms of use-novelty, according to which evidence is novel if it was not used in the construction of a theory. Only if evidence is use-novel can it fully support the theory entailing it. As I point out in this paper, the writings of the most influential proponent of use-novelty contain a weaker and a stronger version of use-novelty. However both versions, I argue, are problematic. With regard to the appraisal of Mendeleev' periodic table, the most contentious historical case in the predictivism debate, I argue that temporal predictivism is indeed supported, although in ways not previously appreciated. On the basis of this case, I argue for a form of so-called symptomatic predictivism according to which temporally novel predictions carry more confirmational weight only insofar as they reveal the theory's presumed coherence of facts as real.

Neural correlates of novelty and appropriateness processing in externally induced constraint relaxation.

PubMed

Huang, Furong; Tang, Shuang; Sun, Pei; Luo, Jing

2018-05-15

Novelty and appropriateness are considered the two fundamental features of creative thinking, including insight problem solving, which can be performed through chunk decomposition and constraint relaxation. Based on a previous study that separated the neural bases of novelty and appropriateness in chunk decomposition, in this study, we used event-related functional magnetic resonance imaging (fMRI) to further dissociate these mechanisms in constraint relaxation. Participants were guided to mentally represent the method of problem solving according to the externally provided solutions that were elaborately prepared in advance and systematically varied in their novelty and appropriateness for the given problem situation. The results showed that novelty processing was completed by the temporoparietal junction (TPJ) and regions in the executive system (dorsolateral prefrontal cortex [DLPFC]), whereas appropriateness processing was completed by the TPJ and regions in the episodic memory (hippocampus), emotion (amygdala), and reward systems (orbitofrontal cortex [OFC]). These results likely indicate that appropriateness processing can result in a more memorable and richer experience than novelty processing in constraint relaxation. The shared and distinct neural mechanisms of the features of novelty and appropriateness in constraint relaxation are discussed, enriching the representation of the change theory of insight. Copyright © 2018 Elsevier Inc. All rights reserved.

Multilevel selection and social evolution of insect societies

NASA Astrophysics Data System (ADS)

Korb, Judith; Heinze, Jürgen

How sterile, altruistic worker castes have evolved in social insects and how they are maintained have long been central topics in evolutionary biology. With the advance of kin selection theory, insect societies, in particular those of haplodiploid bees, ants, and wasps, have become highly suitable model systems for investigating the details of social evolution and recently also how within-group conflicts are resolved. Because insect societies typically do not consist of clones, conflicts among nestmates arise, for example about the partitioning of reproduction and the allocation of resources towards male and female sexuals. Variation in relatedness among group members therefore appears to have a profound influence on the social structure of groups. However, insect societies appear to be remarkably robust against such variation: division of labor and task allocation are often organized in more or less the same way in societies with high as in those with very low nestmate relatedness. To explain the discrepancy between predictions from kin structure and empirical data, it was suggested that constraints-such as the lack of power or information-prevent individuals from pursuing their own selfish interests. Applying a multilevel selection approach shows that these constraints are in fact group-level adaptation preventing or resolving intracolonial conflict. The mechanisms of conflict resolution in insect societies are similar to those at other levels in the biological hierarchy (e.g., in the genome or multicellular organisms): alignment of interests, fair lottery, and social control. Insect societies can thus be regarded as a level of selection with novelties that provide benefits beyond the scope of a solitary life. Therefore, relatedness is less important for the maintenance of insect societies, although it played a fundamental role in their evolution.

Evolutionary adaptations: theoretical and practical implications for visual ergonomics.

PubMed

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

2014-01-01

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

Characterizing behavioural ‘characters’: an evolutionary framework

PubMed Central

Araya-Ajoy, Yimen G.; Dingemanse, Niels J.

2014-01-01

Biologists often study phenotypic evolution assuming that phenotypes consist of a set of quasi-independent units that have been shaped by selection to accomplish a particular function. In the evolutionary literature, such quasi-independent functional units are called ‘evolutionary characters’, and a framework based on evolutionary principles has been developed to characterize them. This framework mainly focuses on ‘fixed’ characters, i.e. those that vary exclusively between individuals. In this paper, we introduce multi-level variation and thereby expand the framework to labile characters, focusing on behaviour as a worked example. We first propose a concept of ‘behavioural characters’ based on the original evolutionary character concept. We then detail how integration of variation between individuals (cf. ‘personality’) and within individuals (cf. ‘individual plasticity’) into the framework gives rise to a whole suite of novel testable predictions about the evolutionary character concept. We further propose a corresponding statistical methodology to test whether observed behaviours should be considered expressions of a hypothesized evolutionary character. We illustrate the application of our framework by characterizing the behavioural character ‘aggressiveness’ in wild great tits, Parus major. PMID:24335984

The Cyborg Astrobiologist: testing a novelty detection algorithm on two mobile exploration systems at Rivas Vaciamadrid in Spain and at the Mars Desert Research Station in Utah

NASA Astrophysics Data System (ADS)

McGuire, P. C.; Gross, C.; Wendt, L.; Bonnici, A.; Souza-Egipsy, V.; Ormö, J.; Díaz-Martínez, E.; Foing, B. H.; Bose, R.; Walter, S.; Oesker, M.; Ontrup, J.; Haschke, R.; Ritter, H.

2010-01-01

In previous work, a platform was developed for testing computer-vision algorithms for robotic planetary exploration. This platform consisted of a digital video camera connected to a wearable computer for real-time processing of images at geological and astrobiological field sites. The real-time processing included image segmentation and the generation of interest points based upon uncommonness in the segmentation maps. Also in previous work, this platform for testing computer-vision algorithms has been ported to a more ergonomic alternative platform, consisting of a phone camera connected via the Global System for Mobile Communications (GSM) network to a remote-server computer. The wearable-computer platform has been tested at geological and astrobiological field sites in Spain (Rivas Vaciamadrid and Riba de Santiuste), and the phone camera has been tested at a geological field site in Malta. In this work, we (i) apply a Hopfield neural-network algorithm for novelty detection based upon colour, (ii) integrate a field-capable digital microscope on the wearable computer platform, (iii) test this novelty detection with the digital microscope at Rivas Vaciamadrid, (iv) develop a Bluetooth communication mode for the phone-camera platform, in order to allow access to a mobile processing computer at the field sites, and (v) test the novelty detection on the Bluetooth-enabled phone camera connected to a netbook computer at the Mars Desert Research Station in Utah. This systems engineering and field testing have together allowed us to develop a real-time computer-vision system that is capable, for example, of identifying lichens as novel within a series of images acquired in semi-arid desert environments. We acquired sequences of images of geologic outcrops in Utah and Spain consisting of various rock types and colours to test this algorithm. The algorithm robustly recognized previously observed units by their colour, while requiring only a single image or a few images to learn colours as familiar, demonstrating its fast learning capability.

Bidirectional Modulation of Recognition Memory

PubMed Central

Ho, Jonathan W.; Poeta, Devon L.; Jacobson, Tara K.; Zolnik, Timothy A.; Neske, Garrett T.; Connors, Barry W.

2015-01-01

Perirhinal cortex (PER) has a well established role in the familiarity-based recognition of individual items and objects. For example, animals and humans with perirhinal damage are unable to distinguish familiar from novel objects in recognition memory tasks. In the normal brain, perirhinal neurons respond to novelty and familiarity by increasing or decreasing firing rates. Recent work also implicates oscillatory activity in the low-beta and low-gamma frequency bands in sensory detection, perception, and recognition. Using optogenetic methods in a spontaneous object exploration (SOR) task, we altered recognition memory performance in rats. In the SOR task, normal rats preferentially explore novel images over familiar ones. We modulated exploratory behavior in this task by optically stimulating channelrhodopsin-expressing perirhinal neurons at various frequencies while rats looked at novel or familiar 2D images. Stimulation at 30–40 Hz during looking caused rats to treat a familiar image as if it were novel by increasing time looking at the image. Stimulation at 30–40 Hz was not effective in increasing exploration of novel images. Stimulation at 10–15 Hz caused animals to treat a novel image as familiar by decreasing time looking at the image, but did not affect looking times for images that were already familiar. We conclude that optical stimulation of PER at different frequencies can alter visual recognition memory bidirectionally. SIGNIFICANCE STATEMENT Recognition of novelty and familiarity are important for learning, memory, and decision making. Perirhinal cortex (PER) has a well established role in the familiarity-based recognition of individual items and objects, but how novelty and familiarity are encoded and transmitted in the brain is not known. Perirhinal neurons respond to novelty and familiarity by changing firing rates, but recent work suggests that brain oscillations may also be important for recognition. In this study, we showed that stimulation of the PER could increase or decrease exploration of novel and familiar images depending on the frequency of stimulation. Our findings suggest that optical stimulation of PER at specific frequencies can predictably alter recognition memory. PMID:26424881

The orientating reflex: the "targeting reaction" and "searchlight of attention".

PubMed

Sokolov, E N; Nezlina, N I; Polyanskii, V B; Evtikhin, D V

2002-01-01

A concept of the orientating reflex is presented, based on the principle of vector coding of cognitive and executive processes. The orientating reflex is a complex of orientating reactions of motor, autonomic, and subjective types, accentuating new and significant stimuli. Two main systems form the orientating reflex: the "targeting reaction" and the "searchlight of attention:" In the visual system, the targeting reaction ensures that the image of the object falls onto the fovea; this is mediated by involvement of premotor neurons which are excited by saccade command neurons in the superior colliculi. The "searchlight of attention" is activated as a result of resonance within the gamma frequency range, selectively enhancing cortical detectors and involving the reticular nucleus of the thalamus. Novelty signals arise in novelty neurons of the hippocampus. The synaptic weightings of neocortical detectors for hippocampal novelty neurons is initially characterized by high efficiency, which assigns a significant level of excitation of these neurons to the new stimulus. During repeated stimulation, the synaptic weightings of all the detectors representing a given stimulus decrease, with the result that the novelty signal becomes weaker. When the stimulus changes, it acts on other detectors, whose weightings for novelty neurons remain high, which strengthens the novelty signal. Decreases in the synaptic weightings on repetition of a standard stimulus form a trace of this stimulus in the novelty neurons - this is the "neural model of the stimulus." The novelty signal is determined by the non-concordance of the new stimulus with this "neural model," which is formed under the influence of the standard stimulus. The greater the difference between the new stimulus and the previously formed neural model, the stronger the novelty signal.

Role of hippocampal β-adrenergic and glucocorticoid receptors in the novelty-induced enhancement of fear extinction.

PubMed

Liu, Jian-Feng; Yang, Chang; Deng, Jia-Hui; Yan, Wei; Wang, Hui-Min; Luo, Yi-Xiao; Shi, Hai-Shui; Meng, Shi-Qiu; Chai, Bai-Sheng; Fang, Qin; Chai, Ning; Xue, Yan-Xue; Sun, Jia; Chen, Chen; Wang, Xue-Yi; Wang, Ji-Shi; Lu, Lin

2015-05-27

Fear extinction forms a new memory but does not erase the original fear memory. Exposure to novelty facilitates transfer of short-term extinction memory to long-lasting memory. However, the underlying cellular and molecular mechanisms are still unclear. Using a classical contextual fear-conditioning model, we investigated the effect of novelty on long-lasting extinction memory in rats. We found that exposure to a novel environment but not familiar environment 1 h before or after extinction enhanced extinction long-term memory (LTM) and reduced fear reinstatement. However, exploring novelty 6 h before or after extinction had no such effect. Infusion of the β-adrenergic receptor (βAR) inhibitor propranolol and glucocorticoid receptor (GR) inhibitor RU486 into the CA1 area of the dorsal hippocampus before novelty exposure blocked the effect of novelty on extinction memory. Propranolol prevented activation of the hippocampal PKA-CREB pathway, and RU486 prevented activation of the hippocampal extracellular signal-regulated kinase 1/2 (Erk1/2)-CREB pathway induced by novelty exposure. These results indicate that the hippocampal βAR-PKA-CREB and GR-Erk1/2-CREB pathways mediate the extinction-enhancing effect of novelty exposure. Infusion of RU486 or the Erk1/2 inhibitor U0126, but not propranolol or the PKA inhibitor Rp-cAMPS, into the CA1 before extinction disrupted the formation of extinction LTM, suggesting that hippocampal GR and Erk1/2 but not βAR or PKA play critical roles in this process. These results indicate that novelty promotes extinction memory via hippocampal βAR- and GR-dependent pathways, and Erk1/2 may serve as a behavioral tag of extinction. Copyright © 2015 the authors 0270-6474/15/358308-14$15.00/0.

Multi-objective optimization of an arch dam shape under static loads using an evolutionary game method

NASA Astrophysics Data System (ADS)

Meng, Rui; Cheong, Kang Hao; Bao, Wei; Wong, Kelvin Kian Loong; Wang, Lu; Xie, Neng-gang

2018-06-01

This article attempts to evaluate the safety and economic performance of an arch dam under the action of static loads. The geometric description of a crown cantilever section and the horizontal arch ring is presented. A three-objective optimization model of arch dam shape is established based on the arch dam volume, maximum principal tensile stress and total strain energy. The evolutionary game method is then applied to obtain the optimal solution. In the evolutionary game technique, a novel and more efficient exploration method of the game players' strategy space, named the 'sorting partition method under the threshold limit', is presented, with the game profit functions constructed according to both competitive and cooperative behaviour. By way of example, three optimization goals have all shown improvements over the initial solutions. In particular, the evolutionary game method has potentially faster convergence. This demonstrates the preliminary proof of principle of the evolutionary game method.

Evolutionary genetics of plant adaptation.

PubMed

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

2011-07-01

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

Dynamic multipopulation and density dependent evolutionary games related to replicator dynamics. A metasimplex concept.

PubMed

Argasinski, Krzysztof

2006-07-01

This paper contains the basic extensions of classical evolutionary games (multipopulation and density dependent models). It is shown that classical bimatrix approach is inconsistent with other approaches because it does not depend on proportion between populations. The main conclusion is that interspecific proportion parameter is important and must be considered in multipopulation models. The paper provides a synthesis of both extensions (a metasimplex concept) which solves the problem intrinsic in the bimatrix model. It allows us to model interactions among any number of subpopulations including density dependence effects. We prove that all modern approaches to evolutionary games are closely related. All evolutionary models (except classical bimatrix approaches) can be reduced to a single population general model by a simple change of variables. Differences between classic bimatrix evolutionary games and a new model which is dependent on interspecific proportion are shown by examples.

A Philosophical Perspective on Evolutionary Systems Biology

PubMed Central

Soyer, Orkun S.; Siegal, Mark L.

2015-01-01

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

Novelty helmet use and motorcycle rider fatality

PubMed Central

Rice, Thomas M.; Troszak, Lara; Erhardt, Taryn; Trent, Roger B.; Zhu, Motao

2018-01-01

Objectives To compare the risk of fatal injury across helmet types among collision-involved motorcyclists. Methods We used data from a cohort of motorcyclists involved in police-reported traffic collisions. Eighty-four law enforcement agencies in California collected detailed information on helmet and rider characteristics during collision investigations in June 2012 through July 2013. Multiply-adjusted risk ratios were estimated with log-binomial regression. Results The adjusted fatal injury risk ratio for novelty helmets was 1.95 (95% CI 1.11–3.40, p 0.019), comparing novelty helmets with full-face helmets. The risk ratios for modular, open-face, and half-helmets, compared with full-face helmets, were not significant. Conclusions A more complete understanding of the inadequacy of novelty helmets can be used in educational and law enforcement countermeasures to improve helmet use among motorcycling populations in California and other US states. Law enforcement approaches to mitigating novelty helmet use would seem attractive given that novelty helmets can be visually identified by law enforcement officers with sufficient training. PMID:28431344

Development of a population of cancer cells: Observation and modeling by a Mixed Spatial Evolutionary Games approach.

PubMed

Świerniak, Andrzej; Krześlak, Michał; Student, Sebastian; Rzeszowska-Wolny, Joanna

2016-09-21

Living cells, like whole living organisms during evolution, communicate with their neighbors, interact with the environment, divide, change their phenotypes, and eventually die. The development of specific ways of communication (through signaling molecules and receptors) allows some cellular subpopulations to survive better, to coordinate their physiological status, and during embryonal development to create tissues and organs or in some conditions to become tumors. Populations of cells cultured in vitro interact similarly, also competing for space and nutrients and stimulating each other to better survive or to die. The results of these intercellular interactions of different types seem to be good examples of biological evolutionary games, and have been the subjects of simulations by the methods of evolutionary game theory where individual cells are treated as players. Here we present examples of intercellular contacts in a population of living human cancer HeLa cells cultured in vitro and propose an evolutionary game theory approach to model the development of such populations. We propose a new technique termed Mixed Spatial Evolutionary Games (MSEG) which are played on multiple lattices corresponding to the possible cellular phenotypes which gives the possibility of simulating and investigating the effects of heterogeneity at the cellular level in addition to the population level. Analyses performed with MSEG suggested different ways in which cellular populations develop in the case of cells communicating directly and through factors released to the environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Exploration of a novel object in late adolescence predicts novelty-seeking behavior in adulthood: Associations among behavioral responses in four novelty-seeking tests.

PubMed

Cuenya, Lucas; Sabariego, Marta; Donaire, Rocío; Callejas-Aguilera, José Enrique; Torres, Carmen; Fernández-Teruel, Alberto

2016-04-01

The sensation/novelty seeking behavioral trait refers to the exploration/preference for a novel environment. Novelty seeking increases during late adolescence and it has been associated with several neurobehavioral disorders. In this experiment, we asked whether inbred Roman high- and low-avoidance (RHA-I, RLA-I) rats (1) differ in novelty seeking in late adolescence and (2) whether late adolescent novelty seeking predicts this trait in adulthood. Thirty six male RHA-I and 36 RLA-I rats were exposed to a novel object exploration (NOE) test during late adolescence (pnd: 52-59; contact latency, contact time, contact frequency). Head-dipping (hole-board, HB), time and visits to a novel-arm (Y-maze), and latency-in and emergence latency (emergence test) were registered in adulthood (pnd: 83-105). The results showed strain differences in all these tests (RHA-I>RLA-I). Factor analysis (RHA-I+RLA-I) revealed two clusters. The first one grouped HB and emergence test measures. The second one grouped NOE and Y-maze variables. Time exploring a novel object (NOE) was a significant predictor of novel arm time (RHA-I+RLA, RHA-I); contact latency was a significant predictor of novel arm frequency (RLA-I). Present results show consistent behavioral associations across four novelty-seeking tests and suggest that late adolescent novelty seeking predicts this genetically-influenced temperamental trait in adult Roman rats. Copyright © 2016 Elsevier B.V. All rights reserved.

Evolutionary cognitive therapy versus standard cognitive therapy for depression: a protocol for a blinded, randomized, superiority clinical trial.

PubMed

Giosan, Cezar; Cobeanu, Oana; Mogoase, Cristina; Muresan, Vlad; Malta, Loretta S; Wyka, Katarzyna; Szentagotai, Aurora

2014-03-19

Depression is estimated to become the leading cause of disease burden globally by 2030. Despite existing efficacious treatments (both medical and psychotherapeutic), a large proportion of patients do not respond to therapy. Recent insights from evolutionary psychology suggest that, in addition to targeting the proximal causes of depression (for example, targeting dysfunctional beliefs by cognitive behavioral therapy), the distal or evolutionary causes (for example, inclusive fitness) should also be addressed. A randomized superiority trial is conducted to develop and test an evolutionary-driven cognitive therapy protocol for depression, and to compare its efficacy against standard cognitive therapy for depression. Romanian-speaking adults (18 years or older) with elevated Beck Depression Inventory (BDI) scores (>13), current diagnosis of major depressive disorder or major depressive episode (MDD or MDE), and MDD with comorbid dysthymia, as evaluated by the Structured Clinical Interview for DSM-IV (SCID), are included in the study. Participants are randomized to one of two conditions: 1) evolutionary-driven cognitive therapy (ED-CT) or 2) cognitive therapy (CT). Both groups undergo 12 psychotherapy sessions, and data are collected at baseline, mid-treatment, post-treatment, and the 3-month follow-up. Primary outcomes are depressive symptomatology and a categorical diagnosis of depression post-treatment. This randomized trial compares the newly proposed ED-CT with a classic CT protocol for depression. To our knowledge, this is the first attempt to integrate insights from evolutionary theories of depression into the treatment of this condition in a controlled manner. This study can thus add substantially to the body of knowledge on validated treatments for depression. Current Controlled Trials ISRCTN64664414The trial was registered in June 2013. The first participant was enrolled on October 3, 2012.

OF TRYPANOSOMATIDS. ENDOTRANSFORMATIONS AND ABERRATIONS].

PubMed

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

2016-01-01

Endotransformations and aberrations of the life cycle in the evolutionary history of trypanosomatids (Kinetoplastea: Trypanosomatidae) are analyzed. We treat the term "endotransformations" as evolutionarily fixed changes of phases and/or developmental stages of parasites. By contrast, we treat aberrations as evolutionary unstable, periodically arising deformations of developmental phases of trypanosomatids, never leading to life cycle changes. Various examples of life cycle endotransformations and aberrations in representatives of the family Trypanosomatidae are discussed.

The coming and going of Batesian mimicry in a Holarctic butterfly clade

PubMed Central

2010-01-01

A study using phylogenetic hypothesis testing, published in BMC Evolutionary Biology, suggests that non-mimetic forms of the North American white admiral butterfly evolved from a mimetic ancestor. This case might provide one of the first examples in which mimicry was gained and then lost again, emphasizing the evolutionary lability of Batesian mimicry. See research article http://www.biomedcentral.com/1471-2148/10/239 PMID:20887635

Hippocampal Networks Habituate as Novelty Accumulates

ERIC Educational Resources Information Center

Murty, Vishnu P.; Ballard, Ian C.; Macduffie, Katherine E.; Krebs, Ruth M.; Adcock, R. Alison

2013-01-01

Novelty detection, a critical computation within the medial temporal lobe (MTL) memory system, necessarily depends on prior experience. The current study used functional magnetic resonance imaging (fMRI) in humans to investigate dynamic changes in MTL activation and functional connectivity as experience with novelty accumulates. fMRI data were…

Type II string theory on Calabi-Yau manifolds with torsion and non-Abelian discrete gauge symmetries

DOE PAGES

Braun, Volker; Cvetič, Mirjam; Donagi, Ron; ...

2017-07-26

Here, we provide the first explicit example of Type IIB string theory compactication on a globally defined Calabi-Yau threefold with torsion which results in a fourdimensional effective theory with a non-Abelian discrete gauge symmetry. Our example is based on a particular Calabi-Yau manifold, the quotient of a product of three elliptic curves by a fixed point free action of Z 2 X Z 2. Its cohomology contains torsion classes in various degrees. The main technical novelty is in determining the multiplicative structure of the (torsion part of) the cohomology ring, and in particular showing that the cup product of secondmore » cohomology torsion elements goes non-trivially to the fourth cohomology. This specifies a non-Abelian, Heisenberg-type discrete symmetry group of the four-dimensional theory.« less

Type II string theory on Calabi-Yau manifolds with torsion and non-Abelian discrete gauge symmetries

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

Braun, Volker; Cvetič, Mirjam; Donagi, Ron

Here, we provide the first explicit example of Type IIB string theory compactication on a globally defined Calabi-Yau threefold with torsion which results in a fourdimensional effective theory with a non-Abelian discrete gauge symmetry. Our example is based on a particular Calabi-Yau manifold, the quotient of a product of three elliptic curves by a fixed point free action of Z 2 X Z 2. Its cohomology contains torsion classes in various degrees. The main technical novelty is in determining the multiplicative structure of the (torsion part of) the cohomology ring, and in particular showing that the cup product of secondmore » cohomology torsion elements goes non-trivially to the fourth cohomology. This specifies a non-Abelian, Heisenberg-type discrete symmetry group of the four-dimensional theory.« less

Something Old, Something New: Conserved Enzymes and the Evolution of Novelty in Plant Specialized Metabolism1

PubMed Central

Moghe, Gaurav D.; Last, Robert L.

2015-01-01

Plants produce hundreds of thousands of small molecules known as specialized metabolites, many of which are of economic and ecological importance. This remarkable variety is a consequence of the diversity and rapid evolution of specialized metabolic pathways. These novel biosynthetic pathways originate via gene duplication or by functional divergence of existing genes, and they subsequently evolve through selection and/or drift. Studies over the past two decades revealed that diverse specialized metabolic pathways have resulted from the incorporation of primary metabolic enzymes. We discuss examples of enzyme recruitment from primary metabolism and the variety of paths taken by duplicated primary metabolic enzymes toward integration into specialized metabolism. These examples provide insight into processes by which plant specialized metabolic pathways evolve and suggest approaches to discover enzymes of previously uncharacterized metabolic networks. PMID:26276843

The genome of the Gulf pipefish enables understanding of evolutionary innovations.

PubMed

Small, C M; Bassham, S; Catchen, J; Amores, A; Fuiten, A M; Brown, R S; Jones, A G; Cresko, W A

2016-12-20

Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution. We explored the genome of the Gulf pipefish (Syngnathus scovelli), which belongs to family Syngnathidae (pipefishes, seahorses, and seadragons). These fishes have dramatically derived bodies and a remarkable novelty among vertebrates, the male brood pouch. We produce a reference genome, condensed into chromosomes, for the Gulf pipefish. Gene losses and other changes have occurred in pipefish hox and dlx clusters and in the tbx and pitx gene families, candidate mechanisms for the evolution of syngnathid traits, including an elongated axis and the loss of ribs, pelvic fins, and teeth. We measure gene expression changes in pregnant versus non-pregnant brood pouch tissue and characterize the genomic organization of duplicated metalloprotease genes (patristacins) recruited into the function of this novel structure. Phylogenetic inference using ultraconserved sequences provides an alternative hypothesis for the relationship between orders Syngnathiformes and Scombriformes. Comparisons of chromosome structure among percomorphs show that chromosome number in a pipefish ancestor became reduced via chromosomal fusions. The collected findings from this first syngnathid reference genome open a window into the genomic underpinnings of highly derived morphologies, demonstrating that de novo production of high quality and useful reference genomes is within reach of even small research groups.

Novelties of the flowering plant pollen tube underlie diversification of a key life history stage.

PubMed

Williams, Joseph H

2008-08-12

The origin and rapid diversification of flowering plants has puzzled evolutionary biologists, dating back to Charles Darwin. Since that time a number of key life history and morphological traits have been proposed as developmental correlates of the extraordinary diversity and ecological success of angiosperms. Here, I identify several innovations that were fundamental to the evolutionary lability of angiosperm reproduction, and hence to their diversification. In gymnosperms pollen reception must be near the egg largely because sperm swim or are transported by pollen tubes that grow at very slow rates (< approximately 20 microm/h). In contrast, pollen tube growth rates of taxa in ancient angiosperm lineages (Amborella, Nuphar, and Austrobaileya) range from approximately 80 to 600 microm/h. Comparative analyses point to accelerated pollen tube growth rate as a critical innovation that preceded the origin of the true closed carpel, long styles, multiseeded ovaries, and, in monocots and eudicots, much faster pollen tube growth rates. Ancient angiosperm pollen tubes all have callosic walls and callose plugs (in contrast, no gymnosperms have these features). The early association of the callose-walled growth pattern with accelerated pollen tube growth rate underlies a striking repeated pattern of faster and longer-distance pollen tube growth often within solid pathways in phylogenetically derived angiosperms. Pollen tube innovations are a key component of the spectacular diversification of carpel (flower and fruit) form and reproductive cycles in flowering plants.

Fossil evidence for key innovations in the evolution of insect diversity.

PubMed

Nicholson, David B; Ross, Andrew J; Mayhew, Peter J

2014-10-22

Explaining the taxonomic richness of the insects, comprising over half of all described species, is a major challenge in evolutionary biology. Previously, several evolutionary novelties (key innovations) have been posited to contribute to that richness, including the insect bauplan, wings, wing folding and complete metamorphosis, but evidence over their relative importance and modes of action is sparse and equivocal. Here, a new dataset on the first and last occurrences of fossil hexapod (insects and close relatives) families is used to show that basal families of winged insects (Palaeoptera, e.g. dragonflies) show higher origination and extinction rates in the fossil record than basal wingless groups (Apterygota, e.g. silverfish). Origination and extinction rates were maintained at levels similar to Palaeoptera in the more derived Polyneoptera (e.g. cockroaches) and Paraneoptera (e.g. true bugs), but extinction rates subsequently reduced in the very rich group of insects with complete metamorphosis (Holometabola, e.g. beetles). Holometabola show evidence of a recent slow-down in their high net diversification rate, whereas other winged taxa continue to diversify at constant but low rates. These data suggest that wings and complete metamorphosis have had the most effect on family-level insect macroevolution, and point to specific mechanisms by which they have influenced insect diversity through time. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Revisiting the Novelty Effect: When Familiarity, Not Novelty, Enhances Memory

ERIC Educational Resources Information Center

Poppenk, J.; Kohler, S.; Moscovitch, M.

2010-01-01

Reports of superior memory for novel relative to familiar material have figured prominently in recent theories of memory. However, such "novelty effects" are incongruous with long-standing observations that familiar items are remembered better. In 2 experiments, we explored whether this discrepancy was explained by differences in the…

Novelty, Age, and IQ: A Theoretical Look at Human Preference for Novelty.

ERIC Educational Resources Information Center

Eaves, Ronald C.; Glen, Roderick

1996-01-01

A study of 86 children (ages 5-16) investigated the relationship between age, IQ, and preferences for novelty. Children with higher IQs spent significantly more time responding to novel items than lower-IQ children. Older children with high IQs showed the most interest in novel items. (CR)

The Novelty Exploration Bonus and Its Attentional Modulation

ERIC Educational Resources Information Center

Krebs, Ruth M.; Schott, Bjorn H.; Schutze, Hartmut; Duzel, Emrah

2009-01-01

We hypothesized that novel stimuli represent salient learning signals that can motivate "exploration" in search for potential rewards. In computational theories of reinforcement learning, this is referred to as the novelty "exploration bonus" for rewards. If true, stimulus novelty should enhance the reward anticipation signals in brain areas that…

Children's understandings and motivations surrounding novelty sweets: a qualitative study.

PubMed

Stewart, Kate F; Fairchild, Ruth M; Jones, Rhiannon J; Hunter, Lindsay; Harris, Carole; Morgan, Maria Z

2013-11-01

Novelty sweets resemble or can be used as toys, are brightly coloured, with striking imagery, and sold at pocket money prices. They encourage regular consumption as packaging can be resealed, leading to prolonged exposure of these high-sugar and low pH products to the oral tissues, risk factors for dental caries and erosion, respectively. To determine how children conceptualise novelty sweets and their motivations for buying and consuming them. Focus groups conducted using a brief schedule of open-ended questions, supported by novelty sweets used as prompts in the latter stages. Participants were school children (aged 9-10) from purposively selected state primary schools in Cardiff, UK. Key findings related to the routine nature of sweet eating; familiarity with and availability of novelty sweets; parental awareness and control; lack of awareness of health consequences; and the overall appeal of novelty sweets. Parents reported vagueness regarding consumption habits and permissiveness about any limits they set may have diluted the concept of treats. Flexible permissiveness to sweet buying applied to sweets of all kinds. Parents' reported lack of familiarity with novelty sweets combined with their low cost, easy availability, high sugar content, and acidity give cause for concern. © 2012 John Wiley & Sons Ltd, BSPD and IAPD.

Evolutionary Science as a Method to Facilitate Higher Level Thinking and Reasoning in Medical Training.

PubMed

Graves, Joseph L; Reiber, Chris; Thanukos, Anna; Hurtado, Magdalena; Wolpaw, Terry

2016-10-15

Evolutionary science is indispensable for understanding biological processes. Effective medical treatment must be anchored in sound biology. However, currently the insights available from evolutionary science are not adequately incorporated in either pre-medical or medical school curricula. To illuminate how evolution may be helpful in these areas, examples in which the insights of evolutionary science are already improving medical treatment and ways in which evolutionary reasoning can be practiced in the context of medicine are provided. In order to facilitate the learning of evolutionary principles, concepts derived from evolutionary science that medical students and professionals should understand are outlined. These concepts are designed to be authoritative and at the same time easily accessible for anyone with the general biological knowledge of a first-year medical student. Thus we conclude that medical practice informed by evolutionary principles will be more effective and lead to better patient outcomes.Furthermore, it is argued that evolutionary medicine complements general medical training because it provides an additional means by which medical students can practice the critical thinking skills that will be important in their future practice. We argue that core concepts from evolutionary science have the potential to improve critical thinking and facilitate more effective learning in medical training. © The Author(s) 2016. Published by Oxford University Press on behalf of the Foundation for Evolution, Medicine, and Public Health.

Implicit Interaction: A Modality for Ambient Exercise Monitoring

NASA Astrophysics Data System (ADS)

Wan, J.; O'Grady, M. J.; O'Hare, G. M. P.

Ambient Exercise refers to the implicit exercise that people undertake in the course of their everyday duties - a simple example being climbing stairs. Increasing awareness of the potential health benefits of such activities may well contribute to an increase in a person’s well-being. Initially, it is necessary to monitor and quantify such exercise so that personalized fitness plans may be constructed. In this paper, the implicit interaction modality is harnessed to enable the capturing of ambient exercise activity thereby facilitating its subsequent quantification and interpretation. The novelty of the solution proposed lies in its ubiquity and transparency.

Social Novelty Investigation in the Juvenile Rat: Modulation by the μ-Opioid System.

PubMed

Smith, C J W; Wilkins, K B; Mogavero, J N; Veenema, A H

2015-10-01

The drive to approach and explore novel conspecifics is inherent to social animals and may promote optimal social functioning. Juvenile animals seek out interactions with novel peers more frequently and find these interactions to be more rewarding than their adult counterparts. In the present study, we aimed to establish a behavioural paradigm to measure social novelty-seeking in juvenile rats and to determine the involvement of the opioid, dopamine, oxytocin and vasopressin systems in this behaviour. To this end, we developed the social novelty preference test to assess the preference of a juvenile rat to investigate a novel over a familiar (cage mate) conspecific. We show that across the juvenile period both male and female rats spend more time investigating a novel conspecific than a cage mate, independent of subject sex or repeated exposure to the test. We hypothesised that brain systems subserving social information processing and social motivation/reward (i.e. the opioid, dopamine, oxytocin, vasopressin systems) might support social novelty preference. To test this, receptor antagonists of each of these systems were administered i.c.v. prior to exposure to the social novelty preference test and, subsequently, to the social preference test, to examine the specificity of these effects. We find that μ-opioid receptor antagonism reduces novel social investigation in both the social novelty preference and social preference tests while leaving the investigation of a cage mate (social novelty preference test) or an object (social preference test) unaffected. In contrast, central blockade of dopamine D2 receptors (with eticlopride), oxytocin receptors (with des-Gly-NH2,d(CH2)5[Tyr(Me)2,Thr4]OVT) or vasopressin V1a receptors [with (CH2)5Tyr(Me2)AVP] failed to alter social novelty preference or social preference. Overall, we have established a new behavioural test to study social novelty-seeking behaviour in the juvenile rat and show that the μ-opioid system facilitates this behaviour, possibly by reducing risk avoidance and enhancing the hedonic and/or motivational value of social novelty. © 2015 British Society for Neuroendocrinology.

["Long-branch Attraction" artifact in phylogenetic reconstruction].

PubMed

Li, Yi-Wei; Yu, Li; Zhang, Ya-Ping

2007-06-01

Phylogenetic reconstruction among various organisms not only helps understand their evolutionary history but also reveal several fundamental evolutionary questions. Understanding of the evolutionary relationships among organisms establishes the foundation for the investigations of other biological disciplines. However, almost all the widely used phylogenetic methods have limitations which fail to eliminate systematic errors effectively, preventing the reconstruction of true organismal relationships. "Long-branch Attraction" (LBA) artifact is one of the most disturbing factors in phylogenetic reconstruction. In this review, the conception and analytic method as well as the avoidance strategy of LBA were summarized. In addition, several typical examples were provided. The approach to avoid and resolve LBA artifact has been discussed.

Research on Duplication Dynamics and Evolutionary Stable of Reverse Supply Chain

NASA Astrophysics Data System (ADS)

Huizhong, Dong; Hongli, Song

An evolutionary game model of Reverse Supply Chain(RSC) is established based on duplication dynamics function and evolutionary stable strategy. Using the model framework, this paper provides insights into a deeper understanding on how each supplier make strategic decision independently in reverse supply chain to determine their performance. The main conclusion is as follow: Under the market mechanism, not unless the extra income derived from the implementation of RSC exceeds zero point would the suppliers implement RSC strategy. When those suppliers are passive to RSC, the effective solution is that the government takes macro-control measures, for example, to force those suppliers implement RSC through punishment mechanism.

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

PubMed Central

Bartlett, Madelaine E.; Whipple, Clinton J.

2013-01-01

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

Novelty Enhances Visual Salience Independently of Reward in the Parietal Lobe

PubMed Central

Foley, Nicholas C.; Jangraw, David C.; Peck, Christopher

2014-01-01

Novelty modulates sensory and reward processes, but it remains unknown how these effects interact, i.e., how the visual effects of novelty are related to its motivational effects. A widespread hypothesis, based on findings that novelty activates reward-related structures, is that all the effects of novelty are explained in terms of reward. According to this idea, a novel stimulus is by default assigned high reward value and hence high salience, but this salience rapidly decreases if the stimulus signals a negative outcome. Here we show that, contrary to this idea, novelty affects visual salience in the monkey lateral intraparietal area (LIP) in ways that are independent of expected reward. Monkeys viewed peripheral visual cues that were novel or familiar (received few or many exposures) and predicted whether the trial will have a positive or a negative outcome—i.e., end in a reward or a lack of reward. We used a saccade-based assay to detect whether the cues automatically attracted or repelled attention from their visual field location. We show that salience—measured in saccades and LIP responses—was enhanced by both novelty and positive reward associations, but these factors were dissociable and habituated on different timescales. The monkeys rapidly recognized that a novel stimulus signaled a negative outcome (and withheld anticipatory licking within the first few presentations), but the salience of that stimulus remained high for multiple subsequent presentations. Therefore, novelty can provide an intrinsic bonus for attention that extends beyond the first presentation and is independent of physical rewards. PMID:24899716

Disentangling the effects of novelty, valence and trait anxiety in the bed nucleus of the stria terminalis, amygdala and hippocampus with high resolution 7T fMRI.

PubMed

Pedersen, Walker S; Muftuler, L Tugan; Larson, Christine L

2017-08-01

The hippocampus and amygdala exhibit sensitivity to stimulus novelty that is reduced in participants with inhibited temperament, which is related to trait anxiety. Although the bed nucleus of the stria terminalis (BNST) is highly connected to the amygdala and is implicated in anxiety, whether the BNST responds to novelty remains unstudied, as well as how trait anxiety may modulate this response. Additionally how novelty, stimulus negativity and trait anxiety interact to affect activity in these areas is also unclear. To address these questions, we presented participants with novel and repeated, fearful and neutral faces, while measuring brain activity via fMRI, and also assessed participants' self-reported trait anxiety. As the small size of the BNST makes assessing its activity at typical fMRI resolution difficult, we employed high resolution 7 Tesla scanning. Our results replicate findings of novelty sensitivity that is independent of valence in the hippocampus. Our results also provide novel evidence for a BNST novelty response toward neutral, but not fearful faces. We also found that the novelty response in the hippocampus and BNST was blunted in participants with high trait anxiety. Additionally, we found left amygdala sensitivity to stimulus negativity that was blunted for high trait anxiety participants. These findings extend past research on the response to novel stimuli in the hippocampus and amygdala at high resolution, and are the first to demonstrate trait anxiety modulated novelty sensitivity in the BNST that is dependent on stimulus valence. Copyright © 2017 Elsevier Inc. All rights reserved.

Novelty enhances visual salience independently of reward in the parietal lobe.

PubMed

Foley, Nicholas C; Jangraw, David C; Peck, Christopher; Gottlieb, Jacqueline

2014-06-04

Novelty modulates sensory and reward processes, but it remains unknown how these effects interact, i.e., how the visual effects of novelty are related to its motivational effects. A widespread hypothesis, based on findings that novelty activates reward-related structures, is that all the effects of novelty are explained in terms of reward. According to this idea, a novel stimulus is by default assigned high reward value and hence high salience, but this salience rapidly decreases if the stimulus signals a negative outcome. Here we show that, contrary to this idea, novelty affects visual salience in the monkey lateral intraparietal area (LIP) in ways that are independent of expected reward. Monkeys viewed peripheral visual cues that were novel or familiar (received few or many exposures) and predicted whether the trial will have a positive or a negative outcome--i.e., end in a reward or a lack of reward. We used a saccade-based assay to detect whether the cues automatically attracted or repelled attention from their visual field location. We show that salience--measured in saccades and LIP responses--was enhanced by both novelty and positive reward associations, but these factors were dissociable and habituated on different timescales. The monkeys rapidly recognized that a novel stimulus signaled a negative outcome (and withheld anticipatory licking within the first few presentations), but the salience of that stimulus remained high for multiple subsequent presentations. Therefore, novelty can provide an intrinsic bonus for attention that extends beyond the first presentation and is independent of physical rewards. Copyright © 2014 the authors 0270-6474/14/347947-11$15.00/0.

The interaction between hippocampal GABA-B and cannabinoid receptors upon spatial change and object novelty discrimination memory function.

PubMed

Nasehi, Mohammad; Alaghmandan-Motlagh, Niyousha; Ebrahimi-Ghiri, Mohaddeseh; Nami, Mohammad; Zarrindast, Mohammad-Reza

2017-10-01

Previous studies have postulated functional links between GABA and cannabinoid systems in the hippocampus. The aim of the present study was to investigate any possible interaction between these systems in spatial change and object novelty discrimination memory consolidation in the dorsal hippocampus (CA1 region) of NMRI mice. Assessment of the spatial change and object novelty discrimination memory function was carried out in a non-associative task. The experiment comprised mice exposure to an open field containing five objects followed by the examination of their reactivity to object displacement (spatial change) and object substitution (object novelty) after three sessions of habituation. Our results showed that the post-training intraperitoneal administration of the higher dose of ACPA (0.02 mg/kg) impaired both spatial change and novelty discrimination memory functions. Meanwhile, the higher dose of GABA-B receptor agonist, baclofen, impaired the spatial change memory by itself. Moreover, the post-training intra-CA1 microinjection of a subthreshold dose of baclofen increased the ACPA effect on spatial change and novelty discrimination memory at a lower and higher dose, respectively. On the other hand, the lower and higher but not mid-level doses of GABA-B receptor antagonist, phaclofen, could reverse memory deficits induced by ACPA. However, phaclofen at its mid-level dose impaired the novelty discrimination memory and whereas the higher dose impaired the spatial change memory. Based on our findings, GABA-B receptors in the CA1 region appear to modulate the ACPA-induced cannabinoid CB1 signaling upon spatial change and novelty discrimination memory functions.

Predatory Odor Disrupts Social Novelty Preference in Long-Evans Rats

ERIC Educational Resources Information Center

Anderson, Matthew J.; Layton, William B.

2012-01-01

The present study examined the effects of predatory odor (cat urine) on social novelty preference in Long-Evans rats. Adult male subjects encountered a juvenile conspecific at training, were exposed to either clean cat litter (control) or litter soiled with cat urine (predatory odor), and were tested for social novelty preference. While the…

Redundancy and Novelty Mining in the Business Blogosphere

ERIC Educational Resources Information Center

Tsai, Flora S.; Chan, Kap Luk

2010-01-01

Purpose: The paper aims to explore the performance of redundancy and novelty mining in the business blogosphere, which has not been studied before. Design/methodology/approach: Novelty mining techniques are implemented to single out novel information out of a massive set of text documents. This paper adopted the mixed metric approach which…

Short- and long-lasting consequences of novelty, deviance and surprise on brain and cognition.

PubMed

Schomaker, J; Meeter, M

2015-08-01

When one encounters a novel stimulus this sets off a cascade of brain responses, activating several neuromodulatory systems. As a consequence novelty has a wide range of effects on cognition; improving perception and action, increasing motivation, eliciting exploratory behavior, and promoting learning. Here, we review these benefits and how they may arise in the brain. We propose a framework that organizes novelty's effects on brain and cognition into three groups. First, novelty can transiently enhance perception. This effect is proposed to be mediated by novel stimuli activating the amygdala and enhancing early sensory processing. Second, novel stimuli can increase arousal, leading to short-lived effects on action in the first hundreds of milliseconds after presentation. We argue that these effects are related to deviance, rather than to novelty per se, and link them to activation of the locus-coeruleus norepinephrine system. Third, spatial novelty may trigger the dopaminergic mesolimbic system, promoting dopamine release in the hippocampus, having longer-lasting effects, up to tens of minutes, on motivation, reward processing, and learning and memory. Copyright © 2015 Elsevier Ltd. All rights reserved.

Striatal Activity Underlies Novelty-Based Choice in Humans

PubMed Central

Wittmann, Bianca C.; Daw, Nathaniel D.; Seymour, Ben; Dolan, Raymond J.

2008-01-01

Summary The desire to seek new and unfamiliar experiences is a fundamental behavioral tendency in humans and other species. In economic decision making, novelty seeking is often rational, insofar as uncertain options may prove valuable and advantageous in the long run. Here, we show that, even when the degree of perceptual familiarity of an option is unrelated to choice outcome, novelty nevertheless drives choice behavior. Using functional magnetic resonance imaging (fMRI), we show that this behavior is specifically associated with striatal activity, in a manner consistent with computational accounts of decision making under uncertainty. Furthermore, this activity predicts interindividual differences in susceptibility to novelty. These data indicate that the brain uses perceptual novelty to approximate choice uncertainty in decision making, which in certain contexts gives rise to a newly identified and quantifiable source of human irrationality. PMID:18579085

Novelty Detection Classifiers in Weed Mapping: Silybum marianum Detection on UAV Multispectral Images.

PubMed

Alexandridis, Thomas K; Tamouridou, Afroditi Alexandra; Pantazi, Xanthoula Eirini; Lagopodi, Anastasia L; Kashefi, Javid; Ovakoglou, Georgios; Polychronos, Vassilios; Moshou, Dimitrios

2017-09-01

In the present study, the detection and mapping of Silybum marianum (L.) Gaertn. weed using novelty detection classifiers is reported. A multispectral camera (green-red-NIR) on board a fixed wing unmanned aerial vehicle (UAV) was employed for obtaining high-resolution images. Four novelty detection classifiers were used to identify S. marianum between other vegetation in a field. The classifiers were One Class Support Vector Machine (OC-SVM), One Class Self-Organizing Maps (OC-SOM), Autoencoders and One Class Principal Component Analysis (OC-PCA). As input features to the novelty detection classifiers, the three spectral bands and texture were used. The S. marianum identification accuracy using OC-SVM reached an overall accuracy of 96%. The results show the feasibility of effective S. marianum mapping by means of novelty detection classifiers acting on multispectral UAV imagery.

The Human Frontal Lobes and Frontal Network Systems: An Evolutionary, Clinical, and Treatment Perspective

PubMed Central

Hoffmann, Michael

2013-01-01

Frontal lobe syndromes, better termed as frontal network systems, are relatively unique in that they may manifest from almost any brain region, due to their widespread connectivity. The understandings of the manifold expressions seen clinically are helped by considering evolutionary origins, the contribution of the state-dependent ascending monoaminergic neurotransmitter systems, and cerebral connectivity. Hence, the so-called networktopathies may be a better term for the syndromes encountered clinically. An increasing array of metric tests are becoming available that complement that long standing history of qualitative bedside assessments pioneered by Alexander Luria, for example. An understanding of the vast panoply of frontal systems' syndromes has been pivotal in understanding and diagnosing the most common dementia syndrome under the age of 60, for example, frontotemporal lobe degeneration. New treatment options are also progressively becoming available, with recent evidence of dopaminergic augmentation, for example, being helpful in traumatic brain injury. The latter include not only psychopharmacological options but also device-based therapies including mirror visual feedback therapy. PMID:23577266

40 CFR 405.80 - Applicability; description of the ice cream, frozen desserts, novelties and other dairy desserts...

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 29 2011-07-01 2009-07-01 true Applicability; description of the ice... PRODUCTS PROCESSING POINT SOURCE CATEGORY Ice Cream, Frozen Desserts, Novelties and Other Dairy Desserts Subcategory § 405.80 Applicability; description of the ice cream, frozen desserts, novelties and other dairy...

40 CFR 405.80 - Applicability; description of the ice cream, frozen desserts, novelties and other dairy desserts...

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 30 2012-07-01 2012-07-01 false Applicability; description of the ice... PRODUCTS PROCESSING POINT SOURCE CATEGORY Ice Cream, Frozen Desserts, Novelties and Other Dairy Desserts Subcategory § 405.80 Applicability; description of the ice cream, frozen desserts, novelties and other dairy...

40 CFR 405.80 - Applicability; description of the ice cream, frozen desserts, novelties and other dairy desserts...

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 29 2014-07-01 2012-07-01 true Applicability; description of the ice... PRODUCTS PROCESSING POINT SOURCE CATEGORY Ice Cream, Frozen Desserts, Novelties and Other Dairy Desserts Subcategory § 405.80 Applicability; description of the ice cream, frozen desserts, novelties and other dairy...

40 CFR 405.80 - Applicability; description of the ice cream, frozen desserts, novelties and other dairy desserts...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 28 2010-07-01 2010-07-01 true Applicability; description of the ice... PRODUCTS PROCESSING POINT SOURCE CATEGORY Ice Cream, Frozen Desserts, Novelties and Other Dairy Desserts Subcategory § 405.80 Applicability; description of the ice cream, frozen desserts, novelties and other dairy...

40 CFR 405.80 - Applicability; description of the ice cream, frozen desserts, novelties and other dairy desserts...

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 30 2013-07-01 2012-07-01 true Applicability; description of the ice... PRODUCTS PROCESSING POINT SOURCE CATEGORY Ice Cream, Frozen Desserts, Novelties and Other Dairy Desserts Subcategory § 405.80 Applicability; description of the ice cream, frozen desserts, novelties and other dairy...

Novelty exposure overcomes foot shock-induced spatial-memory impairment by processes of synaptic-tagging in rats.

PubMed

Almaguer-Melian, William; Bergado-Rosado, Jorge; Pavón-Fuentes, Nancy; Alberti-Amador, Esteban; Mercerón-Martínez, Daymara; Frey, Julietta U

2012-01-17

Novelty processing can transform short-term into long-term memory. We propose that this memory-reinforcing effect of novelty could be explained by mechanisms outlined in the "synaptic tagging hypothesis." Initial short-term memory is sustained by a transient plasticity change at activated synapses and sets synaptic tags. These tags are later able to capture and process the plasticity-related proteins (PRPs), which are required to transform a short-term synaptic change into a long-term one. Novelty is involved in inducing the synthesis of PRPs [Moncada D, et al. (2011) Proc Natl Acad Sci USA 108:12937-12936], which are then captured by the tagged synapses, consolidating memory. In contrast to novelty, stress can impair learning, memory, and synaptic plasticity. Here, we address questions as to whether novelty-induced PRPs are able to prevent the loss of memory caused by stress and if the latter would not interact with the tag-setting process. We used water-maze (WM) training as a spatial learning paradigm to test our hypothesis. Stress was induced by a strong foot shock (FS; 5 × 1 mA, 2 s) applied 5 min after WM training. Our data show that FS reduced long-term but not short-term memory in the WM paradigm. This negative effect on memory consolidation was time- and training-dependent. Interestingly, novelty exposure prevented the stress-induced memory loss of the spatial task and increased BDNF and Arc expression. This rescuing effect was blocked by anisomycin, suggesting that WM-tagged synapses were not reset by FS and were thus able to capture the novelty-induced PRPs, re-establishing FS-impaired long-term memory.

A circuit-based mechanism underlying familiarity signaling and the preference for novelty

PubMed Central

Molas, Susanna; Zhao-Shea, Rubing; Liu, Liwang; DeGroot, Steven R.; Gardner, Paul D.; Tapper, Andrew R.

2017-01-01

Novelty preference (NP) is an evolutionarily conserved, essential survival mechanism often dysregulated in neuropsychiatric disorders. NP is mediated by a motivational dopamine signal that increases in response to novel stimuli thereby driving exploration. However, the mechanism by which once novel stimuli transitions to familiar stimuli is unknown. Here we describe a neuroanatomical substrate for familiarity signaling, the interpeduncular nucleus (IPN) of the midbrain, which is activated as novel stimuli become familiar with multiple exposures. Optogenetic silencing of IPN neurons increases salience of and interaction with familiar stimuli without affecting novelty responses; whereas, photo-activation of the same neurons reduces exploration of novel stimuli mimicking familiarity. Bi-directional control of NP by the IPN depends on familiarity- and novelty-signals arising from excitatory habenula and dopaminergic ventral tegmental area inputs, which activate and reduce IPN activity, respectively. These results demonstrate that familiarity signals through unique IPN circuitry that opposes novelty seeking to control NP. PMID:28714952

A circuit-based mechanism underlying familiarity signaling and the preference for novelty.

PubMed

Molas, Susanna; Zhao-Shea, Rubing; Liu, Liwang; DeGroot, Steven R; Gardner, Paul D; Tapper, Andrew R

2017-09-01

Novelty preference (NP) is an evolutionarily conserved, essential survival mechanism often dysregulated in neuropsychiatric disorders. NP is mediated by a motivational dopamine signal that increases in response to novel stimuli, thereby driving exploration. However, the mechanism by which once-novel stimuli transition to familiar stimuli is unknown. Here we describe a neuroanatomical substrate for familiarity signaling, the interpeduncular nucleus (IPN) of the midbrain, which is activated as novel stimuli become familiar with multiple exposures. In mice, optogenetic silencing of IPN neurons increases salience of and interaction with familiar stimuli without affecting novelty responses, whereas photoactivation of the same neurons reduces exploration of novel stimuli mimicking familiarity. Bidirectional control of NP by the IPN depends on familiarity signals and novelty signals arising from excitatory habenula and dopaminergic ventral tegmentum inputs, which activate and reduce IPN activity, respectively. These results demonstrate that familiarity signals through unique IPN circuitry that opposes novelty seeking to control NP.

Unique deep-water ecosystems off the southeastern United States

USGS Publications Warehouse

Ross, Steve W.

2007-01-01

If nothing else, research in deep-sea environments teaches us how little we know about such important and productive habitats. The relatively recent discovery of hydrothermal-vent and cold-seep ecosystems illustrates this paucity of knowledge, and the subsequent explosion of research on these systems is a good example of the impact such concentrated efforts can have on marine sciences (see the March 2007 special issue of Oceanography on InterRidge, and Levin et al., 2007). The recent surge of interest in deep-sea corals is another example of how focused research on a particular subject can result in new perspectives on continental slope biotopes. Although deep-sea corals have been known for over 200 years, they were viewed as somewhat of a novelty, and research on them was sporadic, typically geologic, and usually only documented their occurrences (e.g., Stetson et al., 1962; Neumann et al., 1977; Paull et al., 2000).

Happier, faster: Developmental changes in the effects of mood and novelty on responses.

PubMed

Schomaker, Judith; Rangel-Gomez, Mauricio; Meeter, Martijn

2016-01-01

Positive mood ameliorates several cognitive processes: It can enhance cognitive control, increase flexibility, and promote variety seeking in decision making. These effects of positive mood have been suggested to depend on frontostriatal dopamine, which is also associated with the detection of novelty. This suggests that positive mood could also affect novelty detection. In the present study, children and adults saw either a happy or a neutral movie to induce a positive or neutral mood. After that, they were shown novel and familiar images. On some trials a beep was presented over headphones either at the same time as the image or at a 200-ms stimulus onset asynchrony (SOA), and the task of the participant was to detect these auditory targets. Children were slower in responding than adults. Positive mood, however, speeded responses, especially in children, and induced facilitatory effects of novelty. These effects were consistent with increased arousal. Although effects of novelty were more consistent with an attentional response, in children who had watched a happy movie the novel images evoked a more liberal response criterion, suggestive of increased arousal. This suggests that mood and novelty may affect response behaviour stronger in children than in adults.

On the numerical treatment of selected oscillatory evolutionary problems

NASA Astrophysics Data System (ADS)

Cardone, Angelamaria; Conte, Dajana; D'Ambrosio, Raffaele; Paternoster, Beatrice

2017-07-01

We focus on evolutionary problems whose qualitative behaviour is known a-priori and exploited in order to provide efficient and accurate numerical schemes. For classical numerical methods, depending on constant coefficients, the required computational effort could be quite heavy, due to the necessary employ of very small stepsizes needed to accurately reproduce the qualitative behaviour of the solution. In these situations, it may be convenient to use special purpose formulae, i.e. non-polynomially fitted formulae on basis functions adapted to the problem (see [16, 17] and references therein). We show examples of special purpose strategies to solve two families of evolutionary problems exhibiting periodic solutions, i.e. partial differential equations and Volterra integral equations.

Pancreatic cancer biology and genetics from an evolutionary perspective

PubMed Central

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

2017-01-01

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

Evolutionary perspectives on stress and affective disorder.

PubMed

Gardner, R

2001-01-01

Three general approaches to evolutionary perspectives in psychiatry include the following domains. (1) information from general medicine and physiology that involves defenses against infectious disease and predators, with obsessive compulsive disorder and posttraumatic stress disorder (PTSD) amongst the psychiatric results of this. (2) Sociophysiology assumes that normal brain functions mediate social interactions, including social rank hierarchy, in-out group formation, and family bonding. At times these function maladroitly resulting in psychiatric symptoms, for example, mania, persecutory delusions, and depression. (3) Evolutionary psychology explains self-sacrificing and generous behavior despite how genes act selfishly in natural selection theory, via the helping of relatives, reciprocal altruism, and manipulation of social contracts. Copyright 2001 by W.B. Saunders Company

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

PubMed

Bentley, R Alexander

2008-08-27

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

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

PubMed Central

Bentley, R. Alexander

2008-01-01

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

The contribution of statistical physics to evolutionary biology.

PubMed

de Vladar, Harold P; Barton, Nicholas H

2011-08-01

Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time. Copyright © 2011 Elsevier Ltd. All rights reserved.

Blue Tigers, Black Tapirs, & the Pied Raven of the Faroe Islands: Teaching Genetic Drift Using Real-Life Animal Examples

ERIC Educational Resources Information Center

Robischon, Marcel

2015-01-01

Genetic drift is a concept of population genetics that is central to understanding evolutionary processes and aspects of conservation biology. It is frequently taught using rather abstract representations. I introduce three real-life zoological examples, based on historical and recent color morphs of tigers, tapirs, and ravens, that can complement…

Neurogenomics and the role of a large mutational target on rapid behavioral change.

PubMed

Stanley, Craig E; Kulathinal, Rob J

2016-11-08

Behavior, while complex and dynamic, is among the most diverse, derived, and rapidly evolving traits in animals. The highly labile nature of heritable behavioral change is observed in such evolutionary phenomena as the emergence of converged behaviors in domesticated animals, the rapid evolution of preferences, and the routine development of ethological isolation between diverging populations and species. In fact, it is believed that nervous system development and its potential to evolve a seemingly infinite array of behavioral innovations played a major role in the successful diversification of metazoans, including our own human lineage. However, unlike other rapidly evolving functional systems such as sperm-egg interactions and immune defense, the genetic basis of rapid behavioral change remains elusive. Here we propose that the rapid divergence and widespread novelty of innate and adaptive behavior is primarily a function of its genomic architecture. Specifically, we hypothesize that the broad diversity of behavioral phenotypes present at micro- and macroevolutionary scales is promoted by a disproportionately large mutational target of neurogenic genes. We present evidence that these large neuro-behavioral targets are significant and ubiquitous in animal genomes and suggest that behavior's novelty and rapid emergence are driven by a number of factors including more selection on a larger pool of variants, a greater role of phenotypic plasticity, and/or unique molecular features present in large genes. We briefly discuss the origins of these large neurogenic genes, as they relate to the remarkable diversity of metazoan behaviors, and highlight key consequences on both behavioral traits and neurogenic disease across, respectively, evolutionary and ontogenetic time scales. Current approaches to studying the genetic mechanisms underlying rapid phenotypic change primarily focus on identifying signatures of Darwinian selection in protein-coding regions. In contrast, the large mutational target hypothesis places genomic architecture and a larger allelic pool at the forefront of rapid evolutionary change, particularly in genetic systems that are polygenic and regulatory in nature. Genomic data from brain and neural tissues in mammals as well as a preliminary survey of neurogenic genes from comparative genomic data support this hypothesis while rejecting both positive and relaxed selection on proteins or higher mutation rates. In mammals and invertebrates, neurogenic genes harbor larger protein-coding regions and possess a richer regulatory repertoire of miRNA targets and transcription factor binding sites. Overall, neurogenic genes cover a disproportionately large genomic fraction, providing a sizeable substrate for evolutionary, genetic, and molecular mechanisms to act upon. Readily available comparative and functional genomic data provide unexplored opportunities to test whether a distinct neurogenomic architecture can promote rapid behavioral change via several mechanisms unique to large genes, and which components of this large footprint are uniquely metazoan. The large mutational target hypothesis highlights the eminent roles of mutation and functional genomic architecture in generating rapid developmental and evolutionary change. It has broad implications on our understanding of the genetics of complex adaptive traits such as behavior by focusing on the importance of mutational input, from SNPs to alternative transcripts to transposable elements, on driving evolutionary rates of functional systems. Such functional divergence has important implications in promoting behavioral isolation across short- and long-term timescales. Due to genome-scaled polygenic adaptation, the large target effect also contributes to our inability to identify adapted behavioral candidate genes. The presence of large neurogenic genes, particularly in the mammalian brain and other neural tissues, further offers emerging insight into the etiology of neurodevelopmental and neurodegenerative diseases. The well-known correlation between neurological spectrum disorders in children and paternal age may simply be a direct result of aging fathers accumulating mutations across these large neurodevelopmental genes. The large mutational target hypothesis can also explain the rapid evolution of other functional systems covering a large genomic fraction such as male fertility and its preferential association with hybrid male sterility among closely related taxa. Overall, a focus on mutational potential may increase our power in understanding the genetic basis of complex phenotypes such as behavior while filling a general gap in understanding their evolution.

Hippocampus duality: Memory and novelty detection are subserved by distinct mechanisms.

PubMed

Barbeau, Emmanuel J; Chauvel, Patrick; Moulin, Christopher J A; Regis, Jean; Liégeois-Chauvel, Catherine

2017-04-01

The hippocampus plays a pivotal role both in novelty detection and in long-term memory. The physiological mechanisms underlying these behaviors have yet to be understood in humans. We recorded intracerebral evoked potentials within the hippocampus of epileptic patients (n = 10) during both memory and novelty detection tasks (targets in oddball tasks). We found that memory and detection tasks elicited late local field potentials in the hippocampus during the same period, but of opposite polarity (negative during novelty detection tasks, positive during memory tasks, ∼260-600 ms poststimulus onset, P < 0.05). Critically, these potentials had maximal amplitude on the same contact in the hippocampus for each patient. This pattern did not depend on the task as different types of memory and novelty detection tasks were used. It did not depend on the novelty of the stimulus or the difficulty of the task either. Two different hypotheses are discussed to account for this result: it is either due to the activation of CA1 pyramidal neurons by two different pathways such as the monosynaptic and trisynaptic entorhinal-hippocampus pathways, or to the activation of different neuronal populations, that is, differing either functionally (e.g., novelty/familiarity neurons) or located in different regions of the hippocampus (e.g., CA1/subiculum). In either case, these activities may integrate the activity of two distinct large-scale networks implementing externally or internally oriented, mutually exclusive, brain states. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A neurocomputational account of reward and novelty processing and effects of psychostimulants in attention deficit hyperactivity disorder.

PubMed

Sethi, Arjun; Voon, Valerie; Critchley, Hugo D; Cercignani, Mara; Harrison, Neil A

2018-05-01

Computational models of reinforcement learning have helped dissect discrete components of reward-related function and characterize neurocognitive deficits in psychiatric illnesses. Stimulus novelty biases decision-making, even when unrelated to choice outcome, acting as if possessing intrinsic reward value to guide decisions toward uncertain options. Heightened novelty seeking is characteristic of attention deficit hyperactivity disorder, yet how this influences reward-related decision-making is computationally encoded, or is altered by stimulant medication, is currently uncertain. Here we used an established reinforcement-learning task to model effects of novelty on reward-related behaviour during functional MRI in 30 adults with attention deficit hyperactivity disorder and 30 age-, sex- and IQ-matched control subjects. Each participant was tested on two separate occasions, once ON and once OFF stimulant medication. OFF medication, patients with attention deficit hyperactivity disorder showed significantly impaired task performance (P = 0.027), and greater selection of novel options (P = 0.004). Moreover, persistence in selecting novel options predicted impaired task performance (P = 0.025). These behavioural deficits were accompanied by a significantly lower learning rate (P = 0.011) and heightened novelty signalling within the substantia nigra/ventral tegmental area (family-wise error corrected P < 0.05). Compared to effects in controls, stimulant medication improved attention deficit hyperactivity disorder participants' overall task performance (P = 0.011), increased reward-learning rates (P = 0.046) and enhanced their ability to differentiate optimal from non-optimal novel choices (P = 0.032). It also reduced substantia nigra/ventral tegmental area responses to novelty. Preliminary cross-sectional evidence additionally suggested an association between long-term stimulant treatment and a reduction in the rewarding value of novelty. These data suggest that aberrant substantia nigra/ventral tegmental area novelty processing plays an important role in the suboptimal reward-related decision-making characteristic of attention deficit hyperactivity disorder. Compared to effects in controls, abnormalities in novelty processing and reward-related learning were improved by stimulant medication, suggesting that they may be disorder-specific targets for the pharmacological management of attention deficit hyperactivity disorder symptoms.

Fuzzy multi objective transportation problem – evolutionary algorithm approach

NASA Astrophysics Data System (ADS)

Karthy, T.; Ganesan, K.

2018-04-01

This paper deals with fuzzy multi objective transportation problem. An fuzzy optimal compromise solution is obtained by using Fuzzy Genetic Algorithm. A numerical example is provided to illustrate the methodology.

Evolutionary Debunking Arguments

PubMed Central

Kahane, Guy

2011-01-01

Evolutionary debunking arguments (EDAs) are arguments that appeal to the evolutionary origins of evaluative beliefs to undermine their justification. This paper aims to clarify the premises and presuppositions of EDAs—a form of argument that is increasingly put to use in normative ethics. I argue that such arguments face serious obstacles. It is often overlooked, for example, that they presuppose the truth of metaethical objectivism. More importantly, even if objectivism is assumed, the use of EDAs in normative ethics is incompatible with a parallel and more sweeping global evolutionary debunking argument that has been discussed in recent metaethics. After examining several ways of responding to this global debunking argument, I end by arguing that even if we could resist it, this would still not rehabilitate the current targeted use of EDAs in normative ethics given that, if EDAs work at all, they will in any case lead to a truly radical revision of our evaluative outlook. PMID:21949447

Evolutionary developmental biology: its concepts and history with a focus on Russian and German contributions

NASA Astrophysics Data System (ADS)

Olsson, Lennart; Levit, Georgy S.; Hoßfeld, Uwe

2010-11-01

Evolutionary theory has been likened to a “universal acid” (Dennett 1995) that eats its way into more and more areas of science. Recently, developmental biology has been infused by evolutionary concepts and perspectives, and a new field of research—evolutionary developmental biology—has been created and is often called EvoDevo for short. However, this is not the first attempt to make a synthesis between these two areas of biology. In contrast, beginning right after the publication of Darwin’s Origin in 1859, Ernst Haeckel formulated his biogenetic law in 1872, famously stating that ontogeny recapitulates phylogeny. Haeckel was in his turn influenced by pre-Darwinian thinkers such as Karl Ernst von Baer, who had noted that earlier developmental stages show similarities not seen in the adults. In this review, written for an audience of non-specialists, we first give an overview of the history of EvoDevo, especially the tradition emanating from Haeckel and other comparative embryologists and morphologists, which has often been neglected in discussions about the history of EvoDevo and evolutionary biology. Here we emphasize contributions from Russian and German scientists to compensate for the Anglo-American bias in the literature. In Germany, the direct influence of Ernst Haeckel was felt particularly in Jena, where he spent his entire career as a professor, and we give an overview of the “Jena school” of evolutionary morphology, with protagonists such as Oscar Hertwig, Ludwig Plate, and Victor Franz, who all developed ideas that we would nowadays think of as belonging to EvoDevo. Franz ideas about “biometabolic modi” are similar to those of a Russian comparative morphologist that visited Jena repeatedly, A. N. Sewertzoff, who made important contributions to what we now call heterochrony research—heterochrony meaning changes in the relative timing of developmental events. His student I. I. Schmalhausen became an important contributor to the synthetic theory of evolution in Russia and is only partly known outside of the Russian-reading world because only one of his many books was translated into English early on. He made many important contributions to evolutionary theory and we point out the important parallels between Schmalhausen’s ideas (stabilizing selection, autonomization) and C. H. Waddington’s (canalization, genetic assimilation). This is one of the many parallels that have contributed to an increased appreciation of the internationality of progress in evolutionary thinking in the first half of the twentieth century. A direct link between German and Russian evolutionary biology is provided by N. V. Timoféeff-Ressovsky, whose work on, e.g., fly genetics in Berlin is a crucial part of the history of evo-devo. To emphasize the international nature of heterochrony research as predecessor to the modern era of EvoDevo, we include Sir G. R. de Beer’s work in the UK. This historical part is followed by a short review of the discovery and importance of homeobox genes and of some of the major concepts that form the core of modern EvoDevo, such as modularity, constraints, and evolutionary novelties. Major trends in contemporary EvoDevo are then outlined, such as increased use of genomics and molecular genetics, computational and bioinformatics approaches, ecological developmental biology (eco-devo), and phylogenetically informed comparative embryology. Based on our survey, we end the review with an outlook on future trends and important issues in EvoDevo.

Evolutionary developmental biology: its concepts and history with a focus on Russian and German contributions.

PubMed

Olsson, Lennart; Levit, Georgy S; Hossfeld, Uwe

2010-11-01

Evolutionary theory has been likened to a "universal acid" (Dennett 1995) that eats its way into more and more areas of science. Recently, developmental biology has been infused by evolutionary concepts and perspectives, and a new field of research--evolutionary developmental biology--has been created and is often called EvoDevo for short. However, this is not the first attempt to make a synthesis between these two areas of biology. In contrast, beginning right after the publication of Darwin's Origin in 1859, Ernst Haeckel formulated his biogenetic law in 1872, famously stating that ontogeny recapitulates phylogeny. Haeckel was in his turn influenced by pre-Darwinian thinkers such as Karl Ernst von Baer, who had noted that earlier developmental stages show similarities not seen in the adults. In this review, written for an audience of non-specialists, we first give an overview of the history of EvoDevo, especially the tradition emanating from Haeckel and other comparative embryologists and morphologists, which has often been neglected in discussions about the history of EvoDevo and evolutionary biology. Here we emphasize contributions from Russian and German scientists to compensate for the Anglo-American bias in the literature. In Germany, the direct influence of Ernst Haeckel was felt particularly in Jena, where he spent his entire career as a professor, and we give an overview of the "Jena school" of evolutionary morphology, with protagonists such as Oscar Hertwig, Ludwig Plate, and Victor Franz, who all developed ideas that we would nowadays think of as belonging to EvoDevo. Franz ideas about "biometabolic modi" are similar to those of a Russian comparative morphologist that visited Jena repeatedly, A. N. Sewertzoff, who made important contributions to what we now call heterochrony research--heterochrony meaning changes in the relative timing of developmental events. His student I. I. Schmalhausen became an important contributor to the synthetic theory of evolution in Russia and is only partly known outside of the Russian-reading world because only one of his many books was translated into English early on. He made many important contributions to evolutionary theory and we point out the important parallels between Schmalhausen's ideas (stabilizing selection, autonomization) and C. H. Waddington's (canalization, genetic assimilation). This is one of the many parallels that have contributed to an increased appreciation of the internationality of progress in evolutionary thinking in the first half of the twentieth century. A direct link between German and Russian evolutionary biology is provided by N. V. Timoféeff-Ressovsky, whose work on, e.g., fly genetics in Berlin is a crucial part of the history of evo-devo. To emphasize the international nature of heterochrony research as predecessor to the modern era of EvoDevo, we include Sir G. R. de Beer's work in the UK. This historical part is followed by a short review of the discovery and importance of homeobox genes and of some of the major concepts that form the core of modern EvoDevo, such as modularity, constraints, and evolutionary novelties. Major trends in contemporary EvoDevo are then outlined, such as increased use of genomics and molecular genetics, computational and bioinformatics approaches, ecological developmental biology (eco-devo), and phylogenetically informed comparative embryology. Based on our survey, we end the review with an outlook on future trends and important issues in EvoDevo.

Developmental and evolutionary novelty in the serrated teeth of theropod dinosaurs.

PubMed

Brink, K S; Reisz, R R; LeBlanc, A R H; Chang, R S; Lee, Y C; Chiang, C C; Huang, T; Evans, D C

2015-07-28

Tooth morphology and development can provide valuable insights into the feeding behaviour and evolution of extinct organisms. The teeth of Theropoda, the only clade of predominantly predatory dinosaurs, are characterized by ziphodonty, the presence of serrations (denticles) on their cutting edges. Known today only in varanid lizards, ziphodonty is much more pervasive in the fossil record. Here we present the first model for the development of ziphodont teeth in theropods through histological, SEM, and SR-FTIR analyses, revealing that structures previously hypothesized to prevent tooth breakage instead first evolved to shape and maintain the characteristic denticles through the life of the tooth. We show that this novel complex of dental morphology and tissues characterizes Theropoda, with the exception of species with modified feeding behaviours, suggesting that these characters are important for facilitating the hypercarnivorous diet of most theropods. This adaptation may have played an important role in the initial radiation and subsequent success of theropods as terrestrial apex predators.

Homologies of the meningeal-orbital arteries of humans: a reappraisal.

PubMed Central

Diamond, M K

1991-01-01

Two arteries connect the anterior branch of the middle meningeal artery to the lacrimal artery. One vessel, the sphenoidal artery, passes through the superior orbital fissure. The other vessel, the meningolacrimal artery, passes through the cranio-orbital foramen. An analysis of data derived from embryology, comparative anatomy, and patterns of adult variation indicates that the meningolacrimal artery is homologous with the ramus superior of the stapedial artery, an embryologically and phylogenetically primitive vessel. The sphenoidal artery probably forms late in human ontogeny and represents an evolutionary novelty. Its distribution is probably restricted to hominoids and may be exclusive to humans and orangutans (Pongo pygmaeus). The sphenoidal artery is associated with three other derived features: the sphenoparietal sinus and sulcus and a laterally expanded superior orbital fissure. The high frequency of the sphenoidal artery in Homo and Pongo probably represents a case of parallelism. The earliest paleontological evidence of an enlarged sphenoidal artery in the Hominidae occurs in Indonesian Homo erectus (Sangiran VI). PMID:1810930

Developmental and evolutionary novelty in the serrated teeth of theropod dinosaurs

PubMed Central

Brink, K. S.; Reisz, R. R.; LeBlanc, A. R. H.; Chang, R. S.; Lee, Y. C.; Chiang, C. C.; Huang, T.; Evans, D. C.

2015-01-01

Tooth morphology and development can provide valuable insights into the feeding behaviour and evolution of extinct organisms. The teeth of Theropoda, the only clade of predominantly predatory dinosaurs, are characterized by ziphodonty, the presence of serrations (denticles) on their cutting edges. Known today only in varanid lizards, ziphodonty is much more pervasive in the fossil record. Here we present the first model for the development of ziphodont teeth in theropods through histological, SEM, and SR-FTIR analyses, revealing that structures previously hypothesized to prevent tooth breakage instead first evolved to shape and maintain the characteristic denticles through the life of the tooth. We show that this novel complex of dental morphology and tissues characterizes Theropoda, with the exception of species with modified feeding behaviours, suggesting that these characters are important for facilitating the hypercarnivorous diet of most theropods. This adaptation may have played an important role in the initial radiation and subsequent success of theropods as terrestrial apex predators. PMID:26216577

Phylogenetic relatedness and leaf functional traits, not introduced status, influence community assembly.

PubMed

Lemoine, Nathan P; Shue, Jessica; Verrico, Brittany; Erickson, David; Kress, W John; Parker, John D

2015-10-01

Considerable debate focuses on whether invasive species establish and become abundant by being functionally and phylogenetically distinct from native species, leading to a host of invasion-specific hypotheses of community assembly. Few studies, however, have quantitatively assessed whether similar patterns of phylogenetic and functional similarity explain local abundance of both native and introduced species, which would suggest similar assembly mechanisms regardless of origin. Using a chronosequence of invaded temperate forest stands, we tested whether the occurrence and abundance of both introduced and native species were predicted by phylogenetic relatedness, functional overlap, and key environmental characteristics including forest age. Environmental filtering against functionally and phylogenetically distinct species strongly dictated the occurrence and abundance of both introduced and native species, with slight modifications of these patterns according to forest age. Thus, once functional and evolutionary novelty were quantified, introduced status provided little information about species' presence or abundance, indicating largely similar sorting mechanisms for both native and introduced species.

"Not a very nice subject." Changing views of parasites and parasitology in the twentieth century.

PubMed

Vickerman, Keith

2009-10-01

The man in-the-street who frequently asks the question "Why am I here?" finds even more difficulty with the question "Why are parasites here?" The public's distaste for parasites (and by implication, for parasitologists!) is therefore understandable, as maybe was the feeling of early 20th century biologists that parasites were a puzzle because they did not conform to the then widely held association between evolution and progress, let alone the reason why a benevolent Creator should have created them. In mid-century, the writer, contemplating a career in parasitology was taken aback when he found that extolled contemporary biologists disdained parasites or thought little of parasitology as an intellectual subject. These attitudes reflected a lack of appreciation of the important role of parasites in generating evolutionary novelty and speciation, also unawareness of the value of parasite life-cycle studies for formulating questions of wider significance in biology, deficiencies which were gratifyingly beginning to be remedied in the latter half of the century.

[Long-term memory, neurogenesis and novelty signal].

PubMed

Sokolova, E N; Nezlina, N I

2003-01-01

In accordance with the advanced hypothesis the long-term memory is a collection of "gnostic units" selectively tuned to experienced events. The long-term memory is continuously supplemented by new neurons differentiated from stem cells during neurogenesis (particularly, in adults). The transformation of neuronal progenitors into event-selective gnostic units is accomplished with participation of hippocampal "novelty neurons" emphasizing information inputs to be stored in the long-term memory. The formation of the gnostic units is preceded by informational processes occurring in the ventral ("what?") and dorsal ("where?") systems. The formation of a new gnostic unit selectively tuned to a particular event is a result of combination of feature-detector excitation and novelty signal generated by hippocampal novelty neurons.

Philosophy and Sociology of Science Evolution and History

NASA Astrophysics Data System (ADS)

Rosen, Joe

The following sections are included: * Concrete Versus Abstract Theoretical Models * Introduction: concrete and abstract in kepler's contribution * Einstein's theory of gravitation and mach's principle * Unitary symmetry and the structure of hadrons * Conclusion * Dedication * Symmetry, Entropy and Complexity * Introduction * Symmetry Implies Abstraction and Loss of Information * Broken Symmetries - Imposed or Spontaneous * Symmetry, Order and Information * References * Cosmological Surrealism: More Than "Eternal Reality" Is Needed * Pythagoreanism in atomic, nuclear and particle physics * Introduction: Pythagoreanism as part of the Greek scientific world view — and the three questions I will tackle * Point 1: the impact of Gersonides and Crescas, two scientific anti-Aristotelian rebels * Point 2: Kepler's spheres to Bohr's orbits — Pythagoreanisms at last! * Point 3: Aristotle to Maupertuis, Emmy Noether, Schwinger * References * Paradigm Completion For Generalized Evolutionary Theory With Application To Epistemology * Evolution Fully Generalized * Entropy: Gravity as Model * Evolution and Entropy: Measures of Complexity * Extinctions and a Balanced Evolutionary Paradigm * The Evolution of Human Society - the Age of Information as example * High-Energy Physics and the World Wide Web * Twentieth Century Epistemology has Strong (de facto) Evolutionary Elements * The discoveries towards the beginning of the XXth Century * Summary and Conclusions * References * Evolutionary Epistemology and Invalidation * Introduction * Extinctions and A New Evolutionary Paradigm * Evolutionary Epistemology - Active Mutations * Evolutionary Epistemology: Invalidation as An Extinction * References

Ecological and evolutionary consequences of niche construction for its agent.

PubMed

Kylafis, Grigoris; Loreau, Michel

2008-10-01

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

Evolutionary biology: variation isn't always sexy.

PubMed

Safran, Rebecca J; Hauber, Mark E

2007-05-15

A recent study has found that differences in a male trait, considered a textbook example of sexual selection, are in fact due to naturally selected variation in the aerodynamic optimum for each individual.

Ogasawara Islands, Japan

NASA Image and Video Library

2012-11-12

This image, acquired by NASA Terra spacecraft, is of the volcanic Ogasawara Islands. The islands were listed as a UNESCO World Heritage site, in recognition of an outstanding example of ongoing evolutionary processes in oceanic island ecosystems.

Evolutionary change in physiological phenotypes along the human lineage

PubMed Central

Vining, Alexander Q.; Nunn, Charles L.

2016-01-01

Background and Objectives: Research in evolutionary medicine provides many examples of how evolution has shaped human susceptibility to disease. Traits undergoing rapid evolutionary change may result in associated costs or reduce the energy available to other traits. We hypothesize that humans have experienced more such changes than other primates as a result of major evolutionary change along the human lineage. We investigated 41 physiological traits across 50 primate species to identify traits that have undergone marked evolutionary change along the human lineage. Methodology: We analysed the data using two Bayesian phylogenetic comparative methods. One approach models trait covariation in non-human primates and predicts human phenotypes to identify whether humans are evolutionary outliers. The other approach models adaptive shifts under an Ornstein-Uhlenbeck model of evolution to assess whether inferred shifts are more common on the human branch than on other primate lineages. Results: We identified four traits with strong evidence for an evolutionary increase on the human lineage (amylase, haematocrit, phosphorus and monocytes) and one trait with strong evidence for decrease (neutrophilic bands). Humans exhibited more cases of distinct evolutionary change than other primates. Conclusions and Implications: Human physiology has undergone increased evolutionary change compared to other primates. Long distance running may have contributed to increases in haematocrit and mean corpuscular haemoglobin concentration, while dietary changes are likely related to increases in amylase. In accordance with the pathogen load hypothesis, human monocyte levels were increased, but many other immune-related measures were not. Determining the mechanisms underlying conspicuous evolutionary change in these traits may provide new insights into human disease. PMID:27615376

Novelties of the flowering plant pollen tube underlie diversification of a key life history stage

PubMed Central

Williams, Joseph H.

2008-01-01

The origin and rapid diversification of flowering plants has puzzled evolutionary biologists, dating back to Charles Darwin. Since that time a number of key life history and morphological traits have been proposed as developmental correlates of the extraordinary diversity and ecological success of angiosperms. Here, I identify several innovations that were fundamental to the evolutionary lability of angiosperm reproduction, and hence to their diversification. In gymnosperms pollen reception must be near the egg largely because sperm swim or are transported by pollen tubes that grow at very slow rates (< ≈20 μm/h). In contrast, pollen tube growth rates of taxa in ancient angiosperm lineages (Amborella, Nuphar, and Austrobaileya) range from ≈80 to 600 μm/h. Comparative analyses point to accelerated pollen tube growth rate as a critical innovation that preceded the origin of the true closed carpel, long styles, multiseeded ovaries, and, in monocots and eudicots, much faster pollen tube growth rates. Ancient angiosperm pollen tubes all have callosic walls and callose plugs (in contrast, no gymnosperms have these features). The early association of the callose-walled growth pattern with accelerated pollen tube growth rate underlies a striking repeated pattern of faster and longer-distance pollen tube growth often within solid pathways in phylogenetically derived angiosperms. Pollen tube innovations are a key component of the spectacular diversification of carpel (flower and fruit) form and reproductive cycles in flowering plants. PMID:18678915

History, biology, and health inequities: emergent embodied phenotypes and the illustrative case of the breast cancer estrogen receptor.

PubMed

Krieger, Nancy

2013-01-01

How we think about biology--in historical, ecological, and societal context--matters for framing causes of and solutions to health inequities. Drawing on new insights from ecological evolutionary developmental biology and ecosocial theory, I question dominant gene-centric and ultimately static approaches to conceptualizing biology, using the example of the breast cancer estrogen receptor (ER). Analyzed in terms of its 4 histories--societal, individual (life course), tumor (cellular pathology), and evolutionary--the ER is revealed as a flexible characteristic of cells, tumors, individuals, and populations, with magnitudes of health inequities tellingly changing over time. This example suggests our science will likely be better served by conceptualizing disease and its biomarkers, along with changing magnitudes of health inequities, as embodied history--that is, emergent embodied phenotype, not innate biology.

Quantitative evolutionary design

PubMed Central

Diamond, Jared

2002-01-01

The field of quantitative evolutionary design uses evolutionary reasoning (in terms of natural selection and ultimate causation) to understand the magnitudes of biological reserve capacities, i.e. excesses of capacities over natural loads. Ratios of capacities to loads, defined as safety factors, fall in the range 1.2-10 for most engineered and biological components, even though engineered safety factors are specified intentionally by humans while biological safety factors arise through natural selection. Familiar examples of engineered safety factors include those of buildings, bridges and elevators (lifts), while biological examples include factors of bones and other structural elements, of enzymes and transporters, and of organ metabolic performances. Safety factors serve to minimize the overlap zone (resulting in performance failure) between the low tail of capacity distributions and the high tail of load distributions. Safety factors increase with coefficients of variation of load and capacity, with capacity deterioration with time, and with cost of failure, and decrease with costs of initial construction, maintenance, operation, and opportunity. Adaptive regulation of many biological systems involves capacity increases with increasing load; several quantitative examples suggest sublinear increases, such that safety factors decrease towards 1.0. Unsolved questions include safety factors of series systems, parallel or branched pathways, elements with multiple functions, enzyme reaction chains, and equilibrium enzymes. The modest sizes of safety factors imply the existence of costs that penalize excess capacities. Those costs are likely to involve wasted energy or space for large or expensive components, but opportunity costs of wasted space at the molecular level for minor components. PMID:12122135

Dimensions of novelty: a social representation approach to new foods.

PubMed

Bäckström, A; Pirttilä-Backman, A-M; Tuorila, H

2003-06-01

Social representations of new foods were examined with a total of 44 subjects in nine focus groups. Each group was homogenous, defined by age, gender and educational background. Halfway through the interview, commercial packages of functional, genetically modified, organic, nutritionally modified and ethnic foods were presented as visual stimuli for discussion. Thematic and content analyses of the interview data showed that five dichotomies characterized the social representation: trust/distrust, safe/unsafe, natural/artificial, pleasure/necessity, and past/present. Many metaphors were used, with functional products being associated metaphorically with, for example, medicine and genetically modified products being associated with death and terrorism. Chronological references focused on the development of cuisine. The perceived unsafety of new foods was an important argument for women but not for men. The difference between age groups was in relating the discussion to either present time (young subjects) or past time (older subjects). Level of education affected the content of argumentation. In the context of new foods, social representations are formed to cope with the feeling of strangeness evoked by the novelties. They also have a role in cultural acceptance of new products by making them familiar. Overall, the results reflect the development of a new common sense in which popularized scientific notions are anchored in the process of urbanization.

Detecting and discriminating novel objects: The impact of perirhinal cortex disconnection on hippocampal activity patterns

PubMed Central

Amin, Eman; Olarte‐Sánchez, Cristian M.; Aggleton, John P.

2016-01-01

ABSTRACT Perirhinal cortex provides object‐based information and novelty/familiarity information for the hippocampus. The necessity of these inputs was tested by comparing hippocampal c‐fos expression in rats with or without perirhinal lesions. These rats either discriminated novel from familiar objects (Novel‐Familiar) or explored pairs of novel objects (Novel‐Novel). Despite impairing Novel‐Familiar discriminations, the perirhinal lesions did not affect novelty detection, as measured by overall object exploration levels (Novel‐Novel condition). The perirhinal lesions also largely spared a characteristic network of linked c‐fos expression associated with novel stimuli (entorhinal cortex→CA3→distal CA1→proximal subiculum). The findings show: I) that perirhinal lesions preserve behavioral sensitivity to novelty, whilst still impairing the spontaneous ability to discriminate novel from familiar objects, II) that the distinctive patterns of hippocampal c‐fos activity promoted by novel stimuli do not require perirhinal inputs, III) that entorhinal Fos counts (layers II and III) increase for novelty discriminations, IV) that hippocampal c‐fos networks reflect proximal‐distal connectivity differences, and V) that discriminating novelty creates different pathway interactions from merely detecting novelty, pointing to top‐down effects that help guide object selection. © 2016 The Authors Hippocampus Published by Wiley Periodicals, Inc. PMID:27398938

Programming social, cognitive, and neuroendocrine development by early exposure to novelty.

PubMed

Tang, Akaysha C; Akers, Katherine G; Reeb, Bethany C; Romeo, Russell D; McEwen, Bruce S

2006-10-17

Mildly stressful early life experiences can potentially impact a broad range of social, cognitive, and physiological functions in humans, nonhuman primates, and rodents. Recent rodent studies favor a maternal-mediation hypothesis that considers maternal-care differences induced by neonatal stimulation as the cause of individual differences in offspring development. Using neonatal novelty exposure, a neonatal stimulation paradigm that dissociates maternal individual differences from a direct stimulation effect on the offspring, we investigated the effect of early exposures to novelty on a diverse range of psychological functions using several assessment paradigms. Pups that received brief neonatal novelty exposures away from the home environment showed enhancement in spatial working memory, social competition, and corticosterone response to surprise during adulthood compared with their home-staying siblings. These functional enhancements in novelty-exposed rats occurred despite evidence that maternal care was directed preferentially toward home-staying instead of novelty-exposed pups, indicating that greater maternal care is neither necessary nor sufficient for these early stimulation-induced functional enhancements. We suggest a unifying maternal-modulation hypothesis, which distinguishes itself from the maternal-mediation hypothesis in that (i) neonatal stimulation can have direct effects on pups, cumulatively leading to long-term improvement in adult offspring; and (ii) maternal behavior can attenuate or potentiate these effects, thereby decreasing or increasing this long-term functional improvement.

Novelty Seeking and Drug Addiction in Humans and Animals: From Behavior to Molecules

PubMed Central

Wingo, Taylor; Nesil, Tanseli; Choi, Jung-Seok; Li, Ming D.

2015-01-01

Global treatment of drug addiction costs society billions of dollars annually, but current psychopharmacological therapies have not been successful at desired rates. The increasing number of individuals suffering from substance abuse has turned attention to what makes some people more vulnerable to drug addiction than others. One personality trait that stands out as a contributing factor is novelty seeking. Novelty seeking, affected by both genetic and environmental factors, is defined as the tendency to desire novel stimuli and environments. It can be measured in humans through questionnaires and in rodents using behavioral tasks. On the behavioral level, both human and rodent studies demonstrate that high novelty seeking can predict the initiation of drug use and a transition to compulsive drug use and create a propensity to relapse. These predictions are valid for several drugs of abuse, such as alcohol, nicotine, cocaine, amphetamine, and opiates. On the molecular level, both novelty seeking and addiction are modulated by the central reward system in the brain. Dopamine is the primary neurotransmitter involved in the overlapping neural substrates of both parameters. In sum, the novelty-seeking trait can be valuable for predicting individual vulnerability to drug addiction and for generating successful treatment for patients with substance abuse disorders. PMID:26481371

Novelty Seeking and Drug Addiction in Humans and Animals: From Behavior to Molecules.

PubMed

Wingo, Taylor; Nesil, Tanseli; Choi, Jung-Seok; Li, Ming D

2016-09-01

Global treatment of drug addiction costs society billions of dollars annually, but current psychopharmacological therapies have not been successful at desired rates. The increasing number of individuals suffering from substance abuse has turned attention to what makes some people more vulnerable to drug addiction than others. One personality trait that stands out as a contributing factor is novelty seeking. Novelty seeking, affected by both genetic and environmental factors, is defined as the tendency to desire novel stimuli and environments. It can be measured in humans through questionnaires and in rodents using behavioral tasks. On the behavioral level, both human and rodent studies demonstrate that high novelty seeking can predict the initiation of drug use and a transition to compulsive drug use and create a propensity to relapse. These predictions are valid for several drugs of abuse, such as alcohol, nicotine, cocaine, amphetamine, and opiates. On the molecular level, both novelty seeking and addiction are modulated by the central reward system in the brain. Dopamine is the primary neurotransmitter involved in the overlapping neural substrates of both parameters. In sum, the novelty-seeking trait can be valuable for predicting individual vulnerability to drug addiction and for generating successful treatment for patients with substance abuse disorders.

Evolutionary foundations for cancer biology.

PubMed

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.

Evolutionary foundations for cancer biology

PubMed Central

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. PMID:23396885

An Evolutionary Framework for Understanding the Origin of Eukaryotes.

PubMed

Blackstone, Neil W

2016-04-27

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

Adaptive Prompts for Learning Evolution with Worked Examples--Highlighting the Students between the "Novices" and the "Experts" in a Classroom

ERIC Educational Resources Information Center

Neubrand, Charlotte; Borzikowsky, Christoph; Harms, Ute

2016-01-01

Evolutionary theory constitutes the overarching concept in biology. There is hardly any other concept that is more complex, and causes more difficulties in learning and teaching. One instructional approach in optimizing the learning of complex topics is to use worked examples combined with self-explanation prompts that fit to the prior knowledge…

Novelty response and 50 kHz ultrasonic vocalizations: Differential prediction of locomotor and affective response to amphetamine in Sprague-Dawley rats.

PubMed

Garcia, Erik J; Cain, Mary E

2016-02-01

Novelty and sensation seeking (NSS) predisposes humans and rats to experiment with psychostimulants. In animal models, different tests of NSS predict different phases of drug dependence. Ultrasonic vocalizations (USVs) are evoked by psychomotor stimulants and measure the affective/motivation response to stimuli, yet the role NSS has on USVs in response to amphetamine is not determined. The aim of the present study was to determine if individual differences in NSS and USVs can predict locomotor and USV response to amphetamine (0.0, 0.3, and 1.0 mg/kg) after acute and chronic exposure. Thirty male rats were tested for their response to novelty (IEN), choice to engage in novelty (NPP), and heterospecific play (H-USV). Rats were administered non-contingent amphetamine or saline for seven exposures, and USVs and locomotor activity were measured. After a 14-day rest, rats were administered a challenge dose of amphetamine. Regression analyses indicated that amphetamine dose-dependently increased locomotor activity and the NPP test negatively predicted treatment-induced locomotor activity. The H-USV test predicted treatment-induced frequency-modulated (FM) USVs, but the strength of prediction depended on IEN response. Results provide evidence that locomotor activity and FM USVs induced by amphetamine represent different behavioral responses. The prediction of amphetamine-induced FM USVs by the H-USV screen was changed by the novelty response, indicating that the affective value of amphetamine-measured by FM USVs-depends on novelty response. This provides evidence that higher novelty responders may develop a tolerance faster and may escalate intake faster.

Taxonomy and systematics are key to biological information: Arabidopsis, Eutrema (Thellungiella), Noccaea and Schrenkiella (Brassicaceae) as examples

PubMed Central

Koch, Marcus A.; German, Dmitry A.

2013-01-01

Taxonomy and systematics provide the names and evolutionary framework for any biological study. Without these names there is no access to a biological context of the evolutionary processes which gave rise to a given taxon: close relatives and sister species (hybridization), more distantly related taxa (ancestral states), for example. This is not only true for the single species a research project is focusing on, but also for its relatives, which might be selected for comparative approaches and future research. Nevertheless, taxonomical and systematic knowledge is rarely fully explored and considered across biological disciplines. One would expect the situation to be more developed with model organisms such as Noccaea, Arabidopsis, Schrenkiella and Eutrema (Thellungiella). However, we show the reverse. Using Arabidopsis halleri and Noccaea caerulescens, two model species among metal accumulating taxa, we summarize and reflect past taxonomy and systematics of Arabidopsis and Noccaea and provide a modern synthesis of taxonomic, systematic and evolutionary perspectives. The same is presented for several species of Eutrema s. l. and Schrenkiella recently appeared as models for studying stress tolerance in plants and widely known under the name Thellungiella. PMID:23914192

Morphogenesis and mechanostabilization of complex natural and 3D printed shapes

PubMed Central

Tiwary, Chandra Sekhar; Kishore, Sharan; Sarkar, Suman; Mahapatra, Debiprosad Roy; Ajayan, Pulickel M.; Chattopadhyay, Kamanio

2015-01-01

The natural selection and the evolutionary optimization of complex shapes in nature are closely related to their functions. Mechanostabilization of shape of biological structure via morphogenesis has several beautiful examples. With the help of simple mechanics-based modeling and experiments, we show an important causality between natural shape selection as evolutionary outcome and the mechanostabilization of seashells. The effect of biological growth on the mechanostabilization process is identified with examples of two natural shapes of seashells, one having a diametrically converging localization of stresses and the other having a helicoidally concentric localization of stresses. We demonstrate how the evolved shape enables predictable protection of soft body parts of the species. The effect of bioavailability of natural material is found to be a secondary factor compared to shape selectivity, where material microstructure only acts as a constraint to evolutionary optimization. This is confirmed by comparing the mechanostabilization behavior of three-dimensionally printed synthetic polymer structural shapes with that of natural seashells consisting of ceramic and protein. This study also highlights interesting possibilities in achieving a new design of structures made of ordinary materials which have bio-inspired optimization objectives. PMID:26601170

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

PubMed

Furlong, Michael; Seong, Jae Young

2017-01-01

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

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

PubMed Central

Furlong, Michael; Seong, Jae Young

2017-01-01

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

Sentence Level Information Patterns for Novelty Detection

DTIC Science & Technology

2006-07-01

had new discourse entities that were not found in the growing history list of discourse entities. Eichmann et al [38] considered the number of new...TREC2002: Question Answering and Novelty Tracks”, TREC 2002. [10] D. Eichmann and P. Srinivasan. “Novel Results and Some Answers, The University...D. Eichmann , P. Srinivasan, M. Light, H. Wang, X. Y. Qiu, R. J. Arens, and A. Sehgal, “Experiments in Novelty, Genes and Questions at the

Optimality and stability of symmetric evolutionary games with applications in genetic selection.

PubMed

Huang, Yuanyuan; Hao, Yiping; Wang, Min; Zhou, Wen; Wu, Zhijun

2015-06-01

Symmetric evolutionary games, i.e., evolutionary games with symmetric fitness matrices, have important applications in population genetics, where they can be used to model for example the selection and evolution of the genotypes of a given population. In this paper, we review the theory for obtaining optimal and stable strategies for symmetric evolutionary games, and provide some new proofs and computational methods. In particular, we review the relationship between the symmetric evolutionary game and the generalized knapsack problem, and discuss the first and second order necessary and sufficient conditions that can be derived from this relationship for testing the optimality and stability of the strategies. Some of the conditions are given in different forms from those in previous work and can be verified more efficiently. We also derive more efficient computational methods for the evaluation of the conditions than conventional approaches. We demonstrate how these conditions can be applied to justifying the strategies and their stabilities for a special class of genetic selection games including some in the study of genetic disorders.

Evolutionary genetics of the Drosophila alcohol dehydrogenase gene-enzyme system.

PubMed

Heinstra, P W

1993-01-01

Evolutionary genetics embodies a broad research area that ranges from the DNA level to studies of genetic aspects in populations. In all cases the purpose is to determine the impact of genetic variation on evolutionary change. The broad range of evolutionary genetics requires the involvement of a diverse group of researchers: molecular biologists, (population) geneticists, biochemists, physiologists, ecologists, ethologists and theorists, each of which has its own insights and interests. For example, biochemists are often not concerned with the physiological function of a protein (with respect to pH, substrates, temperature, etc.), while ecologists, in turn, are often not interested in the biochemical-physiological aspects underlying the traits they study. This review deals with several evolutionary aspects of the Drosophila alcohol dehydrogenase gene-enzyme system, and includes my own personal viewpoints. I have tried to condense and integrate the current knowledge in this field as it has developed since the comprehensive review by van Delden (1982). Details on specific issues may be gained from Sofer and Martin (1987), Sullivan, Atkinson and Starmer (1990); Chambers (1988, 1991); Geer, Miller and Heinstra (1991); and Winberg and McKinley-McKee (1992).

The fossil Osmundales (Royal Ferns)—a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes

PubMed Central

2017-01-01

The Osmundales (Royal Fern order) originated in the late Paleozoic and is the most ancient surviving lineage of leptosporangiate ferns. In contrast to its low diversity today (less than 20 species in six genera), it has the richest fossil record of any extant group of ferns. The structurally preserved trunks and rhizomes alone are referable to more than 100 fossil species that are classified in up to 20 genera, four subfamilies, and two families. This diverse fossil record constitutes an exceptional source of information on the evolutionary history of the group from the Permian to the present. However, inconsistent terminology, varying formats of description, and the general lack of a uniform taxonomic concept renders this wealth of information poorly accessible. To this end, we provide a comprehensive review of the diversity of structural features of osmundalean axes under a standardized, descriptive terminology. A novel morphological character matrix with 45 anatomical characters scored for 15 extant species and for 114 fossil operational units (species or specimens) is analysed using networks in order to establish systematic relationships among fossil and extant Osmundales rooted in axis anatomy. The results lead us to propose an evolutionary classification for fossil Osmundales and a revised, standardized taxonomy for all taxa down to the rank of (sub)genus. We introduce several nomenclatural novelties: (1) a new subfamily Itopsidemoideae (Guaireaceae) is established to contain Itopsidema, Donwelliacaulis, and Tiania; (2) the thamnopteroid genera Zalesskya, Iegosigopteris, and Petcheropteris are all considered synonymous with Thamnopteris; (3) 12 species of Millerocaulis and Ashicaulis are assigned to modern genera (tribe Osmundeae); (4) the hitherto enigmatic Aurealcaulis is identified as an extinct subgenus of Plenasium; and (5) the poorly known Osmundites tuhajkulensis is assigned to Millerocaulis. In addition, we consider Millerocaulis stipabonettiorum a possible member of Palaeosmunda and Millerocaulis estipularis as probably constituting the earliest representative of the (Todea-)Leptopteris lineage (subtribe Todeinae) of modern Osmundoideae. PMID:28713650

The fossil Osmundales (Royal Ferns)-a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes.

PubMed

Bomfleur, Benjamin; Grimm, Guido W; McLoughlin, Stephen

2017-01-01

The Osmundales (Royal Fern order) originated in the late Paleozoic and is the most ancient surviving lineage of leptosporangiate ferns. In contrast to its low diversity today (less than 20 species in six genera), it has the richest fossil record of any extant group of ferns. The structurally preserved trunks and rhizomes alone are referable to more than 100 fossil species that are classified in up to 20 genera, four subfamilies, and two families. This diverse fossil record constitutes an exceptional source of information on the evolutionary history of the group from the Permian to the present. However, inconsistent terminology, varying formats of description, and the general lack of a uniform taxonomic concept renders this wealth of information poorly accessible. To this end, we provide a comprehensive review of the diversity of structural features of osmundalean axes under a standardized, descriptive terminology. A novel morphological character matrix with 45 anatomical characters scored for 15 extant species and for 114 fossil operational units (species or specimens) is analysed using networks in order to establish systematic relationships among fossil and extant Osmundales rooted in axis anatomy. The results lead us to propose an evolutionary classification for fossil Osmundales and a revised, standardized taxonomy for all taxa down to the rank of (sub)genus. We introduce several nomenclatural novelties: (1) a new subfamily Itopsidemoideae (Guaireaceae) is established to contain Itopsidema , Donwelliacaulis , and Tiania ; (2) the thamnopteroid genera Zalesskya , Iegosigopteris , and Petcheropteris are all considered synonymous with Thamnopteris ; (3) 12 species of Millerocaulis and Ashicaulis are assigned to modern genera (tribe Osmundeae); (4) the hitherto enigmatic Aurealcaulis is identified as an extinct subgenus of Plenasium ; and (5) the poorly known Osmundites tuhajkulensis is assigned to Millerocaulis . In addition, we consider Millerocaulis stipabonettiorum a possible member of Palaeosmunda and Millerocaulis estipularis as probably constituting the earliest representative of the ( Todea -) Leptopteris lineage (subtribe Todeinae) of modern Osmundoideae.

Decreased plasma ghrelin contributes to anorexia following novelty stress.

PubMed

Saegusa, Yayoi; Takeda, Hiroshi; Muto, Shuichi; Nakagawa, Koji; Ohnishi, Shunsuke; Sadakane, Chiharu; Nahata, Miwa; Hattori, Tomohisa; Asaka, Masahiro

2011-10-01

We hypothesized that anorexia induced by novelty stress caused by exposure to a novel environment may be due to activation of corticotropin-releasing factor (CRF) and subsequently mediated by decreasing peripheral ghrelin concentration via serotonin (5-HT) and melanocortin-4 receptors (MC4R). Each mouse was transferred from group-housed cages to individual cages to establish the novelty stress. We observed the effect of changes in feeding behavior in a novel environment using the method of transferring group-housed mice to individual cages. We investigated the effect of an intracerebroventricular injection of antagonists/agonists of CRF1/2 receptors (CRF1/2Rs), 5-HT(1B)/(2C) receptors (5-HT(1B)/(2C)R), and MC4R to clarify the role of each receptor on the decrease in food intake. Plasma ghrelin levels were also measured. The novelty stress caused a reduction in food intake that was abolished by administering a CRF1R antagonist. Three hours after the novelty stress, appetite reduction was associated with reduced levels of neuropeptide Y/agouti-related peptide mRNA, increased levels of proopiomelanocortin mRNA in the hypothalamus, and a decrease in plasma ghrelin level. Administering a CRF1R antagonist, a 5-HT(1B)/(2C)R antagonist, an MC4R antagonist, exogenous ghrelin, and an enhancer of ghrelin secretion, rikkunshito, resolved the reduction in food intake 3 h after the novelty stress by enhancing circulating ghrelin concentrations. We showed that anorexia during a novelty stress is a process in which CRF1R is activated at the early stage of appetite loss and is subsequently activated by a 5-HT(1B)/(2C)R and MC4R stimulus, leading to decreased peripheral ghrelin concentrations.

Nomenclatural and taxonomic problems related to the electronic publication of new nomina and nomenclatural acts in zoology, with brief comments on optical discs and on the situation in botany.

PubMed

Dubois, Alain; Crochet, Pierre-André; Dickinson, Edward C; Nemésio, André; Aescht, Erna; Bauer, Aaron M; Blagoderov, Vladimir; Bour, Roger; De Carvalho, Marcelo R; Desutter-Grandcolas, Laure; Frétey, Thierry; Jäger, Peter; Koyamba, Victoire; Lavilla, Esteban O; Löbl, Ivan; Louchart, Antoine; Malécot, Valéry; Schatz, Heinrich; Ohler, Annemarie

2013-11-11

In zoological nomenclature, to be potentially valid, nomenclatural novelties (i.e., new nomina and nomenclatural acts) need first to be made available, that is, published in works qualifying as publications as defined by the International Code of zoological Nomenclature ("the Code"). In September 2012, the Code was amended in order to allow the recognition of works electronically published online after 2011 as publications available for the purpose of zoological nomenclature, provided they meet several conditions, notably a preregistration of the work in ZooBank. Despite these new Rules, several of the long-discussed problems concerning the electronic publication of new nomina and nomenclatural acts have not been resolved. The publication of this amendment provides an opportunity to discuss some of these in detail. It is important to note that: (1) all works published only online before 2012 are nomenclaturally unavailable; (2) printed copies of the PDFs of works which do not have their own ISSN or ISBN, and which are not obtainable free of charge or by purchase, do not qualify as publications but must be seen as facsimiles of unavailable works and are unable to provide nomenclatural availability to any nomenclatural novelties they may contain; (3) prepublications online of later released online publications are unavailable, i.e., they do not advance the date of publication; (4) the publication dates of works for which online prepublications had been released are not those of these prepublications and it is critical that the real release date of such works appear on the actual final electronic publication, but this is not currently the case in electronic periodicals that distribute such online prepublications and which still indicate on their websites and PDFs the date of release of prepublication as that of publication of the work; (5) supplementary online materials and subsequent formal corrections of either paper or electronic publications distributed only online are nomenclaturally unavailable; (6) nomenclatural information provided on online websites that do not have a fixed content and format, with ISSN or ISBN, is unavailable. We give precise examples of many of these nomenclatural problems. Several of them, when they arise, are due to the fact that the availability of nomenclatural novelties now depends on information that will have to be sought not from the work itself but from extrinsic evidence. As shown by several examples discussed here, an electronic document can be modified while keeping the same DOI and publication date, which is not compatible with the requirements of zoological nomenclature. Therefore, another system of registration of electronic documents as permanent and inalterable will have to be devised. ZooBank also clearly needs to be improved in several respects. Mention in a work of its registration number (LSID) in ZooBank would seem to be possible only if this registration has occurred previously, but some works that have purportedly been registered in ZooBank are in fact missing on this web application. In conclusion, we offer recommendations to authors, referees, editors, publishers, libraries and the International Commission on Zoological Nomenclature, in the hope that such problems can be limited along with the potential chaos in zoological nomenclature that could result, if careful attention is not paid to the problems we highlight here, from a somewhat misplaced, and perhaps now widespread, understanding that electronic publication of nomenclatural novelties is now allowed and straightforward. We suggest that, as long as the problematic points linked to the new amendment and to electronic publication as a whole are not resolved, nomenclatural novelties continue to be published in paper-printed journals that have so far shown editorial competence regarding taxonomy and nomenclature, which is not the case of several recent electronic-only published journals.

The awareness of novelty for strangely familiar words: a laboratory analogue of the déjà vu experience.

PubMed

Urquhart, Josephine A; O'Connor, Akira R

2014-01-01

Déjà vu is a nebulous memory experience defined by a clash between evaluations of familiarity and novelty for the same stimulus. We sought to generate it in the laboratory by pairing a DRM recognition task, which generates erroneous familiarity for critical words, with a monitoring task by which participants realise that some of these erroneously familiar words are in fact novel. We tested 30 participants in an experiment in which we varied both participant awareness of stimulus novelty and erroneous familiarity strength. We found that déjà vu reports were most frequent for high novelty critical words (∼25%), with low novelty critical words yielding only baseline levels of déjà vu report frequency (∼10%). There was no significant variation in déjà vu report frequency according to familiarity strength. Discursive accounts of the experimentally-generated déjà vu experience suggest that aspects of the naturalistic déjà vu experience were captured by this analogue, but that the analogue was also limited in its focus and prone to influence by demand characteristics. We discuss theoretical and methodological considerations relevant to further development of this procedure and propose that verifiable novelty is an important component of both naturalistic and experimental analogues of déjà vu.

The awareness of novelty for strangely familiar words: a laboratory analogue of the déjà vu experience

PubMed Central

Urquhart, Josephine A.

2014-01-01

Déjà vu is a nebulous memory experience defined by a clash between evaluations of familiarity and novelty for the same stimulus. We sought to generate it in the laboratory by pairing a DRM recognition task, which generates erroneous familiarity for critical words, with a monitoring task by which participants realise that some of these erroneously familiar words are in fact novel. We tested 30 participants in an experiment in which we varied both participant awareness of stimulus novelty and erroneous familiarity strength. We found that déjà vu reports were most frequent for high novelty critical words (∼25%), with low novelty critical words yielding only baseline levels of déjà vu report frequency (∼10%). There was no significant variation in déjà vu report frequency according to familiarity strength. Discursive accounts of the experimentally-generated déjà vu experience suggest that aspects of the naturalistic déjà vu experience were captured by this analogue, but that the analogue was also limited in its focus and prone to influence by demand characteristics. We discuss theoretical and methodological considerations relevant to further development of this procedure and propose that verifiable novelty is an important component of both naturalistic and experimental analogues of déjà vu. PMID:25401055

Apathy, Novelty Processing, and the P3 Potential in Parkinson’s Disease

PubMed Central

Kaufman, David A. S.; Bowers, Dawn; Okun, Michael S.; Van Patten, Ryan; Perlstein, William M.

2016-01-01

Parkinson’s disease (PD) is characterized by deficits in goal-directed behavior as well as mood and motivational symptoms, including apathy, depression, and anxiety. The present study investigated novelty processing in PD, using event-related potentials (ERPs) to characterize electrophysiological reflections of visual novelty processing. Since apathy has been associated with decreased novelty processing (P3 potentials) in highly apathetic PD patients, we were particularly interested to see if this relationship exists in a sample of PD patients with heterogeneous levels of apathy. Non-demented patients with PD receiving dopaminergic treatment (n = 14) and healthy control participants (n = 12) completed a three-stimulus oddball task while EEG was recorded. Relative to controls, the PD patients exhibited reductions in centrofrontally distributed P3 potentials when viewing novel distracters during this task. Distracter-related P3 amplitudes evoked by novel distracters were strongly associated with apathy symptoms, even after controlling for the effects of depression, anxiety, and executive function. Executive dysfunction was also predictive of novelty-related P3 processing, yet this relationship was independent from that of apathy. These findings suggest that the brain’s electrophysiological response to novelty is closely related to both motivational and cognitive symptoms in PD, even for patients whose apathy symptoms are not excessive. These results have significant implications for our understanding of non-motor symptoms in this clinical population. PMID:27445962

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly.

PubMed

Hanski, Ilkka A

2011-08-30

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time.

D4 receptor deficiency in mice has limited effects on impulsivity and novelty seeking.

PubMed

Helms, C M; Gubner, N R; Wilhelm, C J; Mitchell, S H; Grandy, D K

2008-09-01

Alleles of the human dopamine D(4) receptor (D(4)R) gene (DRD4.7) have repeatedly been found to correlate with novelty seeking, substance abuse, pathological gambling, and attention-deficit hyperactivity disorder (ADHD). If these various psychopathologies are a result of attenuated D(4)R-mediated signaling, mice lacking D(4)Rs (D(4)KO) should be more impulsive than wild-type (WT) mice and exhibit more novelty seeking. However, in our study, D(4)KO and WT mice showed similar levels of impulsivity as measured by delay discounting performance and response inhibition on a Go/No-go test, suggesting that D(4)R-mediated signaling may not affect impulsivity. D(4)KO mice were more active than WT mice in the first 5 min of a novel open field test, suggesting greater novelty seeking. For both genotypes, more impulsive mice habituated less in the novel open field. These data suggest that the absence of D(4)Rs is not sufficient to cause psychopathologies associated with heightened impulsivity and novelty seeking.

Modularity of mind and the role of incentive motivation in representing novelty.

PubMed

Anselme, Patrick

2012-07-01

Animal and human brains contain a myriad of mental representations that have to be successfully tracked within fractions of a second in a large number of situations. This retrieval process is hard to explain without postulating the massive modularity of cognition. Assuming that the mind is massively modular, it is then necessary to understand how cognitive modules can efficiently represent dynamic environments-in which some modules may have to deal with change-induced novelty and uncertainty. Novelty of a stimulus is a problem for a module when unknown, significant stimuli do not satisfy the module's processing criteria-or domain specificity-and cannot therefore be included in its database. It is suggested that the brain mechanisms of incentive motivation, recruited when faced with novelty and uncertainty, induce transient variations in the domain specificity of cognitive modules in order to allow them to process information they were not prepared to learn. It is hypothesised that the behavioural transitions leading from exploratory activity to habit formation are correlated with (and possibly caused by) the organism's ability to counter novelty-induced uncertainty.

Involvement of the oxytocin system in the nucleus accumbens in the regulation of juvenile social novelty-seeking behavior.

PubMed

Smith, Caroline J W; Mogavero, Jazmin N; Tulimieri, Maxwell T; Veenema, Alexa H

2017-07-01

Exploration of novel environments, stimuli, and conspecifics is highly adaptive during the juvenile period, as individuals transition from immaturity to adulthood. We recently showed that juvenile rats prefer to interact with a novel individual over a familiar cage mate. However, the neural mechanisms underlying this juvenile social novelty-seeking behavior remain largely unknown. One potential candidate is the oxytocin (OXT) system, given its involvement in various motivated social behaviors. Here, we show that administration of the specific oxytocin receptor antagonist desGly-NH 2 ,d(CH 2 ) 5 -[Tyr(Me) 2 ,Thr 4 ]OVT reduces social novelty seeking-behavior in juvenile male rats when injected into the nucleus accumbens (10ng/0.5μl/side). The same drug dose was ineffective at altering social novelty-seeking behavior when administered into the lateral septum or basolateral amygdala. These results are the first to suggest the involvement of the OXT system in the nucleus accumbens in the regulation of juvenile social novelty-seeking behavior. Copyright © 2017 Elsevier Inc. All rights reserved.

Vector Symbolic Spiking Neural Network Model of Hippocampal Subarea CA1 Novelty Detection Functionality.

PubMed

Agerskov, Claus

2016-04-01

A neural network model is presented of novelty detection in the CA1 subdomain of the hippocampal formation from the perspective of information flow. This computational model is restricted on several levels by both anatomical information about hippocampal circuitry and behavioral data from studies done in rats. Several studies report that the CA1 area broadcasts a generalized novelty signal in response to changes in the environment. Using the neural engineering framework developed by Eliasmith et al., a spiking neural network architecture is created that is able to compare high-dimensional vectors, symbolizing semantic information, according to the semantic pointer hypothesis. This model then computes the similarity between the vectors, as both direct inputs and a recalled memory from a long-term memory network by performing the dot-product operation in a novelty neural network architecture. The developed CA1 model agrees with available neuroanatomical data, as well as the presented behavioral data, and so it is a biologically realistic model of novelty detection in the hippocampus, which can provide a feasible explanation for experimentally observed dynamics.

Evolutionary change in physiological phenotypes along the human lineage.

PubMed

Vining, Alexander Q; Nunn, Charles L

2016-01-01

Research in evolutionary medicine provides many examples of how evolution has shaped human susceptibility to disease. Traits undergoing rapid evolutionary change may result in associated costs or reduce the energy available to other traits. We hypothesize that humans have experienced more such changes than other primates as a result of major evolutionary change along the human lineage. We investigated 41 physiological traits across 50 primate species to identify traits that have undergone marked evolutionary change along the human lineage. We analysed the data using two Bayesian phylogenetic comparative methods. One approach models trait covariation in non-human primates and predicts human phenotypes to identify whether humans are evolutionary outliers. The other approach models adaptive shifts under an Ornstein-Uhlenbeck model of evolution to assess whether inferred shifts are more common on the human branch than on other primate lineages. We identified four traits with strong evidence for an evolutionary increase on the human lineage (amylase, haematocrit, phosphorus and monocytes) and one trait with strong evidence for decrease (neutrophilic bands). Humans exhibited more cases of distinct evolutionary change than other primates. Human physiology has undergone increased evolutionary change compared to other primates. Long distance running may have contributed to increases in haematocrit and mean corpuscular haemoglobin concentration, while dietary changes are likely related to increases in amylase. In accordance with the pathogen load hypothesis, human monocyte levels were increased, but many other immune-related measures were not. Determining the mechanisms underlying conspicuous evolutionary change in these traits may provide new insights into human disease. The Author(s) 2016. Published by Oxford University Press on behalf of the Foundation for Evolution, Medicine, and Public Health.

Nonbinary Tree-Based Phylogenetic Networks.

PubMed

Jetten, Laura; van Iersel, Leo

2018-01-01

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can, for example, represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and strictly-tree-based nonbinary phylogenetic networks. We give simple graph-theoretic characterizations of tree-based and strictly-tree-based nonbinary phylogenetic networks. Moreover, we show for each of these two classes that it can be decided in polynomial time whether a given network is contained in the class. Our approach also provides a new view on tree-based binary phylogenetic networks. Finally, we discuss two examples of nonbinary phylogenetic networks in biology and show how our results can be applied to them.

Pharmacogenomic implications of the evolutionary history of infectious diseases in Africa

PubMed Central

Baker, J L; Shriner, D; Bentley, A R; Rotimi, C N

2017-01-01

As the common birthplace of all human populations, modern humans have lived longer on the African continent than in any other geographical region of the world. This long history, along with the evolutionary need to adapt to environmental challenges such as exposure to infectious agents, has led to greater genetic variation in Africans. The vast genetic variation in Africans also extends to genes involved in the absorption, distribution, metabolism and excretion of pharmaceuticals. Ongoing cataloging of these clinically relevant variants reveals huge allele-frequency differences within and between African populations. Here, we examine Africa's large burden of infectious disease, discuss key examples of known genetic variation modulating disease risk, and provide examples of clinically relevant variants critical for establishing dosing guidelines. We propose that a more systematic characterization of the genetic diversity of African ancestry populations is required if the current benefits of precision medicine are to be extended to these populations. PMID:27779243

Long-term memory, neurogenesis, and signal novelty.

PubMed

Sokolov, E N; Nezlina, N I

2004-10-01

According to our suggested hypothesis, long-term memory is a collection of "gnostic units," selectively tuned to past events. The formation of long-term memory occurs with the involvement of constantly appearing new neurons which differentiate from stem cells during the process of neurogenesis, in particular in adults. Conversion of precursor neurons into "gnostic units" selective in relation to ongoing events, supplemented by the involvement of hippocampal "novelty neurons," which increase the flow of information needing to be fixed in long-term memory. "Gnostic units" form before the informational processes occurring in the ventral ("what?") and dorsal ("where?") systems. Formation of new "gnostic units" selectively tuned to a particular event results from the combination of excitation of the detector for stimulus characteristics and the novelty signal generated by "novelty neurons" in the hippocampus.

Multiscale global identification of porous structures

NASA Astrophysics Data System (ADS)

Hatłas, Marcin; Beluch, Witold

2018-01-01

The paper is devoted to the evolutionary identification of the material constants of porous structures based on measurements conducted on a macro scale. Numerical homogenization with the RVE concept is used to determine the equivalent properties of a macroscopically homogeneous material. Finite element method software is applied to solve the boundary-value problem in both scales. Global optimization methods in form of evolutionary algorithm are employed to solve the identification task. Modal analysis is performed to collect the data necessary for the identification. A numerical example presenting the effectiveness of proposed attitude is attached.

Learning, epigenetics, and computation: An extension on Fitch's proposal. Comment on “Toward a computational framework for cognitive biology: Unifying approaches from cognitive neuroscience and comparative cognition” by W. Tecumseh Fitch

NASA Astrophysics Data System (ADS)

Okanoya, Kazuo

2014-09-01

The comparative computational approach of Fitch [1] attempts to renew the classical David Marr paradigm of computation, algorithm, and implementation, by introducing evolutionary view of the relationship between neural architecture and cognition. This comparative evolutionary view provides constraints useful in narrowing down the problem space for both cognition and neural mechanisms. I will provide two examples from our own studies that reinforce and extend Fitch's proposal.

CDMetaPOP: An individual-based, eco-evolutionary model for spatially explicit simulation of landscape demogenetics

USGS Publications Warehouse

Landguth, Erin L; Bearlin, Andrew; Day, Casey; Dunham, Jason B.

2016-01-01

1. Combining landscape demographic and genetics models offers powerful methods for addressing questions for eco-evolutionary applications.2. Using two illustrative examples, we present Cost–Distance Meta-POPulation, a program to simulate changes in neutral and/or selection-driven genotypes through time as a function of individual-based movement, complex spatial population dynamics, and multiple and changing landscape drivers.3. Cost–Distance Meta-POPulation provides a novel tool for questions in landscape genetics by incorporating population viability analysis, while linking directly to conservation applications.

Developmental biology, the stem cell of biological disciplines.

PubMed

Gilbert, Scott F

2017-12-01

Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines." Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding off more disciplines, while retaining its own identity. While its descendant disciplines differentiate into sciences with a restricted set of paradigms, examples, and techniques, developmental biology remains vigorous, pluripotent, and relatively undifferentiated. In many disciplines, especially in evolutionary biology and oncology, the developmental perspective is being reasserted as an important research program.

Modulation of contextual fear conditioning by chronic stress in rats is related to individual differences in behavioral reactivity to novelty.

PubMed

Cordero, M Isabel; Kruyt, Nyika D; Sandi, Carmen

2003-04-25

We investigated whether contextual fear conditioning could be related to the behavioral trait of locomotor reactivity to novelty in undisturbed and chronically stressed rats. Fear conditioning was found to be specifically enhanced in low reactive-stressed animals, as compared to low reactive-undisturbed rats. The results suggest that individuals that display low reactivity to novelty are more susceptible to be influenced by stress exposure to subsequently exhibit potentiated contextual fear conditioning.

The Comet Cometh: Evolving Developmental Systems.

PubMed

Jaeger, Johannes; Laubichler, Manfred; Callebaut, Werner

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

Paleontology at the "high table"? Popularization and disciplinary status in recent paleontology.

PubMed

Sepkoski, David

2014-03-01

This paper examines the way in which paleontologists used "popular books" to call for a broader "expanded synthesis" of evolutionary biology. Beginning in the 1970s, a group of influential paleontologists, including Stephen Jay Gould, Niles Eldredge, David Raup, Steven Stanley, and others, aggressively promoted a new theoretical, evolutionary approach to the fossil record as an important revision of the existing synthetic view of Darwinism. This work had a transformative effect within the discipline of paleontology. However, by the 1980s, paleontologists began making their case to a wider audience, both within evolutionary biology, and to the general public. Many of their books-for example, Eldredge's provocatively-titled Unfinished Synthesis-explicitly argued that the received synthetic view of Darwinian evolution was incomplete, and that paleontological contributions such as punctuated equilibria, the hierarchical model of macroevolution, and the study of mass extinction dynamics offered a substantial corrective to evolutionary theory. This paper argues that books-far from being "mere popularizations" of scientific ideas-played an important role in disciplinary debates surrounding evolutionary theory during the 1980s, and in particular that paleontologists like Gould and Eldredge self-consciously adopted the book format because of the importance of that genre in the history of evolutionary biology. Copyright © 2013 Elsevier Ltd. All rights reserved.

An Evolutionary Framework for Understanding the Origin of Eukaryotes

PubMed Central

Blackstone, Neil W.

2016-01-01

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

High-Novelty-Preference Rats are Predisposed to Compulsive Cocaine Self-administration

PubMed Central

Belin, David; Berson, Nadège; Balado, Eric; Piazza, Pier Vincenzo; Deroche-Gamonet, Véronique

2011-01-01

Sensation/novelty-seeking is amongst the best markers of cocaine addiction in humans. However, its implication in the vulnerability to cocaine addiction is still a matter of debate, as it is unclear whether this trait precedes or follows the development of addiction. Sensation/novelty-seeking trait has been identified in rats on the basis of either novelty-induced locomotor activity (high-responder (HR) trait) or novelty-induced place preference (high-novelty-preference trait (HNP)). HR and HNP traits have been associated with differential sensitivity to psychostimulants. However, it has recently been demonstrated that HR rats do not develop compulsive cocaine self-administration (SA) after protracted exposure to the drug, thereby suggesting that at least one dimension of sensation/novelty seeking in the rat is dissociable from the vulnerability to switch from controlled to compulsive cocaine SA. We therefore investigated whether HNP, as measured as the propensity to choose a new environment in a free choice procedure, as opposed to novelty-induced locomotor activity, predicts the vulnerability to, and the severity of, addiction-like behavior for cocaine. For this, we identified HR/LR rats and HNP/LNP rats before any exposure to cocaine. After 60 days of cocaine SA, each rat was given an addiction score based on three addiction-like behaviors (persistence of responding when the drug is signaled as not available, high breakpoint under progressive ratio schedule and resistance to punishment) that resemble the clinical features of drug addiction, namely inability to refrain from drug seeking, high motivation for the drug and compulsive drug use despite adverse consequences. We show that, as opposed to HR rats, HNP rats represent a sub-population predisposed to compulsive cocaine intake, displaying higher addiction scores than LNP rats. This study thereby provides new insights into the factors predisposing to cocaine addiction, supporting the hypothesis that addiction is sustained by two vulnerable phenotypes: a ‘drug use prone' phenotype such as HR which brings an individual to develop drug use and an ‘addiction prone' phenotype, such as HNP, which facilitates the shift from sustained to compulsive drug intake and addiction. PMID:20980989

Evolution of the indoor biome.

PubMed

Martin, Laura J; Adams, Rachel I; Bateman, Ashley; Bik, Holly M; Hawks, John; Hird, Sarah M; Hughes, David; Kembel, Steven W; Kinney, Kerry; Kolokotronis, Sergios-Orestis; Levy, Gabriel; McClain, Craig; Meadow, James F; Medina, Raul F; Mhuireach, Gwynne; Moreau, Corrie S; Munshi-South, Jason; Nichols, Lauren M; Palmer, Clare; Popova, Laura; Schal, Coby; Täubel, Martin; Trautwein, Michelle; Ugalde, Juan A; Dunn, Robert R

2015-04-01

Few biologists have studied the evolutionary processes at work in indoor environments. Yet indoor environments comprise approximately 0.5% of ice-free land area--an area as large as the subtropical coniferous forest biome. Here we review the emerging subfield of 'indoor biome' studies. After defining the indoor biome and tracing its deep history, we discuss some of its evolutionary dimensions. We restrict our examples to the species found in human houses--a subset of the environments constituting the indoor biome--and offer preliminary hypotheses to advance the study of indoor evolution. Studies of the indoor biome are situated at the intersection of evolutionary ecology, anthropology, architecture, and human ecology and are well suited for citizen science projects, public outreach, and large-scale international collaborations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conservation Evo-Devo: Preserving Biodiversity by Understanding Its Origins.

PubMed

Campbell, Calum S; Adams, Colin E; Bean, Colin W; Parsons, Kevin J

2017-10-01

Unprecedented rates of species extinction increase the urgency for effective conservation biology management practices. Thus, any improvements in practice are vital and we suggest that conservation can be enhanced through recent advances in evolutionary biology, specifically advances put forward by evolutionary developmental biology (i.e., evo-devo). There are strong overlapping conceptual links between conservation and evo-devo whereby both fields focus on evolutionary potential. In particular, benefits to conservation can be derived from some of the main areas of evo-devo research, namely phenotypic plasticity, modularity and integration, and mechanistic investigations of the precise developmental and genetic processes that determine phenotypes. Using examples we outline how evo-devo can expand into conservation biology, an opportunity which holds great promise for advancing both fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

Selection of energy source and evolutionary stable strategies for power plants under financial intervention of government

NASA Astrophysics Data System (ADS)

Hafezalkotob, Ashkan; Mahmoudi, Reza

2017-09-01

Currently, many socially responsible governments adopt economic incentives and deterrents to manage environmental impacts of electricity suppliers. Considering the Stackelberg leadership of the government, the government's role in the competition of power plants in an electricity market is investigated. A one-population evolutionary game model of power plants is developed to study how their production strategy depends on tariffs levied by the government. We establish that a unique evolutionary stable strategy (ESS) for the population exists. Numerical examples demonstrate that revenue maximization and environment protection policies of the government significantly affect the production ESS of competitive power plants. The results reveal that the government can introduce a green energy source as an ESS of the competitive power plants by imposing appropriate tariffs.

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

PubMed

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

2015-11-27

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

SolTrace Background | Concentrating Solar Power | NREL

Science.gov Websites

codes was written to model a very specific optical geometry, and each one built upon the others in an evolutionary way. Examples of such codes include: OPTDSH, a code written to model circular aperture parabolic

Stationary stability for evolutionary dynamics in finite populations

DOE PAGES

Harper, Marc; Fryer, Dashiell

2016-08-25

Here, we demonstrate a vast expansion of the theory of evolutionary stability to finite populations with mutation, connecting the theory of the stationary distribution of the Moran process with the Lyapunov theory of evolutionary stability. We define the notion of stationary stability for the Moran process with mutation and generalizations, as well as a generalized notion of evolutionary stability that includes mutation called an incentive stable state (ISS) candidate. For sufficiently large populations, extrema of the stationary distribution are ISS candidates and we give a family of Lyapunov quantities that are locally minimized at the stationary extrema and at ISSmore » candidates. In various examples, including for the Moran andWright–Fisher processes, we show that the local maxima of the stationary distribution capture the traditionally-defined evolutionarily stable states. The classical stability theory of the replicator dynamic is recovered in the large population limit. Finally we include descriptions of possible extensions to populations of variable size and populations evolving on graphs.« less

Consciousness and the natural method.

PubMed

Flanagan, O

1995-09-01

'Consciousness' is a superordinate term for a heterogeneous array of mental state types. The types share the property of 'being experienced' or 'being experiences'--'of there being something that it is like for the subject to be in one of these states.' I propose that we can only build a theory of consciousness by deploying 'the natural method' of coordinating all relevant informational resources at once, especially phenomenology, cognitive science, neuroscience and evolutionary biology. I'll provide two examples of the natural method in action in mental domains where an adaptationist evolutionary account seems plausible: (i) visual awareness and (ii) conscious event memory. Then I will discuss a case, (iii), dreaming, where I think no adaptationist evolutionary account exists. Beyond whatever interest the particular cases have, the examination will show why I think that a theory of mind, and the role conscious mentation plays in it, will need to be built domain-by-domain with no a priori expectation that there will be a unified account of the causal role or evolutionary history of different domains and competences.

Rule Extraction Based on Extreme Learning Machine and an Improved Ant-Miner Algorithm for Transient Stability Assessment.

PubMed

Li, Yang; Li, Guoqing; Wang, Zhenhao

2015-01-01

In order to overcome the problems of poor understandability of the pattern recognition-based transient stability assessment (PRTSA) methods, a new rule extraction method based on extreme learning machine (ELM) and an improved Ant-miner (IAM) algorithm is presented in this paper. First, the basic principles of ELM and Ant-miner algorithm are respectively introduced. Then, based on the selected optimal feature subset, an example sample set is generated by the trained ELM-based PRTSA model. And finally, a set of classification rules are obtained by IAM algorithm to replace the original ELM network. The novelty of this proposal is that transient stability rules are extracted from an example sample set generated by the trained ELM-based transient stability assessment model by using IAM algorithm. The effectiveness of the proposed method is shown by the application results on the New England 39-bus power system and a practical power system--the southern power system of Hebei province.

Novelty and Promotional Items

EPA Pesticide Factsheets

Small novelty or promotional products, primarily used for outreach and educational purposes, must effectively convey a message, and their purchase will only be allowed if the item will contribute to the accomplishment of the Agency's mission.

Visual novel stimuli in an ERP novelty oddball paradigm: effects of familiarity on repetition and recognition memory.

PubMed

Cycowicz, Yael M; Friedman, David

2007-01-01

The orienting response, the brain's reaction to novel and/or out of context familiar events, is reflected by the novelty P3 of the ERP. Contextually novel events also engender high rates of recognition memory. We examined, under incidental and intentional conditions, the effects of visual symbol familiarity on the novelty P3 recorded during an oddball task and on the parietal episodic memory (EM) effect, an index of recollection. Repetition of familiar, but not unfamiliar, symbols elicited a reduction in the novelty P3. Better recognition performance for the familiar symbols was associated with a robust parietal EM effect, which was absent for the unfamiliar symbols in the incidental task. These data demonstrate that processing of novel events depends on expectation and whether stimuli have preexisting representations in long-term semantic memory.

The neural basis of novelty and appropriateness in processing of creative chunk decomposition.

PubMed

Huang, Furong; Fan, Jin; Luo, Jing

2015-06-01

Novelty and appropriateness have been recognized as the fundamental features of creative thinking. However, the brain mechanisms underlying these features remain largely unknown. In this study, we used event-related functional magnetic resonance imaging (fMRI) to dissociate these mechanisms in a revised creative chunk decomposition task in which participants were required to perform different types of chunk decomposition that systematically varied in novelty and appropriateness. We found that novelty processing involved functional areas for procedural memory (caudate), mental rewarding (substantia nigra, SN), and visual-spatial processing, whereas appropriateness processing was mediated by areas for declarative memory (hippocampus), emotional arousal (amygdala), and orthography recognition. These results indicate that non-declarative and declarative memory systems may jointly contribute to the two fundamental features of creative thinking. Copyright © 2015 Elsevier Inc. All rights reserved.

Improved epileptic seizure detection combining dynamic feature normalization with EEG novelty detection.

PubMed

Bogaarts, J G; Hilkman, D M W; Gommer, E D; van Kranen-Mastenbroek, V H J M; Reulen, J P H

2016-12-01

Continuous electroencephalographic monitoring of critically ill patients is an established procedure in intensive care units. Seizure detection algorithms, such as support vector machines (SVM), play a prominent role in this procedure. To correct for inter-human differences in EEG characteristics, as well as for intra-human EEG variability over time, dynamic EEG feature normalization is essential. Recently, the median decaying memory (MDM) approach was determined to be the best method of normalization. MDM uses a sliding baseline buffer of EEG epochs to calculate feature normalization constants. However, while this method does include non-seizure EEG epochs, it also includes EEG activity that can have a detrimental effect on the normalization and subsequent seizure detection performance. In this study, EEG data that is to be incorporated into the baseline buffer are automatically selected based on a novelty detection algorithm (Novelty-MDM). Performance of an SVM-based seizure detection framework is evaluated in 17 long-term ICU registrations using the area under the sensitivity-specificity ROC curve. This evaluation compares three different EEG normalization methods, namely a fixed baseline buffer (FB), the median decaying memory (MDM) approach, and our novelty median decaying memory (Novelty-MDM) method. It is demonstrated that MDM did not improve overall performance compared to FB (p < 0.27), partly because seizure like episodes were included in the baseline. More importantly, Novelty-MDM significantly outperforms both FB (p = 0.015) and MDM (p = 0.0065).

Environmental stress alters genetic regulation of novelty seeking in vervet monkeys.

PubMed

Fairbanks, L A; Bailey, J N; Breidenthal, S E; Laudenslager, M L; Kaplan, J R; Jorgensen, M J

2011-08-01

Considerable attention has been paid to identifying genetic influences and gene-environment interactions that increase vulnerability to environmental stressors, with promising but inconsistent results. A nonhuman primate model is presented here that allows assessment of genetic influences in response to a stressful life event for a behavioural trait with relevance for psychopathology. Genetic and environmental influences on free-choice novelty seeking behaviour were assessed in a pedigreed colony of vervet monkeys before and after relocation from a low stress to a higher stress environment. Heritability of novelty seeking scores, and genetic correlations within and between environments were conducted using variance components analysis. The results showed that novelty seeking was markedly inhibited in the higher stress environment, with effects persisting across a 2-year period for adults but not for juveniles. There were significant genetic contributions to novelty seeking scores in each year (h(2) = 0.35-0.43), with high genetic correlations within each environment (rhoG > 0.80) and a lower genetic correlation (rhoG = 0.35, non-significant) between environments. There were also significant genetic contributions to individual change scores from before to after the move (h(2) = 0.48). These results indicate that genetic regulation of novelty seeking was modified by the level of environmental stress, and they support a role for gene-environment interactions in a behavioural trait with relevance for mental health. © 2011 The Authors. Genes, Brain and Behavior © 2011 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.

Withdrawal from repeated treatment with amphetamine reduces novelty-seeking behavior and enhances environmental habituation in mice.

PubMed

Fukushiro, Daniela F; Mári-Kawamoto, Elisa; Aramini, Tatiana C F; Saito, Luis P; Costa, Jacqueline M; Josino, Fabiana S; Frussa-Filho, Roberto

2011-11-01

Anhedonia associated with a dysphoric state is an important feature of amphetamine withdrawal in humans. We aimed to investigate the effects of amphetamine withdrawal on two motivation-related behaviors in mice: novelty seeking and environmental habituation. Because anxiety can interfere with the behavioral outcome of other tasks, amphetamine-withdrawn mice were also evaluated in the elevated plus maze. Swiss male mice (three months old) were treated with 2.0mg/kg amphetamine for 13 days, every other day, in their home cages (a total of seven injections). Twenty-four hours after withdrawal from drug treatment, mice were tested in a free-choice novelty apparatus containing one familiar and one novel compartment or in the elevated plus maze. Novelty-seeking behavior was assessed by comparing the time spent in the novel compartment vs. the familiar compartment, whereas environmental habituation was concomitantly evaluated by the time-response curve of total locomotion (novel+familiar). Novelty seeking was decreased during amphetamine withdrawal, and this result was not associated with changes in the anxiety-like behavior of mice. Additionally, amphetamine withdrawal enhanced environmental habituation. The concomitant decrease in novelty seeking and the increase in environmental habituation seem to be related to amphetamine withdrawal-induced anhedonia. Thus, the model proposed here could be used as a tool for the study of mechanisms and potential treatment of the anhedonic behavioral consequences of psychostimulant withdrawal. Copyright © 2011 Elsevier Inc. All rights reserved.

Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene

PubMed Central

Bumaschny, Viviana F; Low, Malcolm J; Rubinstein, Marcelo

2007-01-01

The proopiomelanocortin gene (POMC) is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5′ distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE) retroposons, in particular to MAR1 retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE retroposon. In addition, we found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution. PMID:17922573

Comparable Ages for the Independent Origins of Electrogenesis in African and South American Weakly Electric Fishes

PubMed Central

Lavoué, Sébastien; Miya, Masaki; Arnegard, Matthew E.; Sullivan, John P.; Hopkins, Carl D.; Nishida, Mutsumi

2012-01-01

One of the most remarkable examples of convergent evolution among vertebrates is illustrated by the independent origins of an active electric sense in South American and African weakly electric fishes, the Gymnotiformes and Mormyroidea, respectively. These groups independently evolved similar complex systems for object localization and communication via the generation and reception of weak electric fields. While good estimates of divergence times are critical to understanding the temporal context for the evolution and diversification of these two groups, their respective ages have been difficult to estimate due to the absence of an informative fossil record, use of strict molecular clock models in previous studies, and/or incomplete taxonomic sampling. Here, we examine the timing of the origins of the Gymnotiformes and the Mormyroidea using complete mitogenome sequences and a parametric Bayesian method for divergence time reconstruction. Under two different fossil-based calibration methods, we estimated similar ages for the independent origins of the Mormyroidea and Gymnotiformes. Our absolute estimates for the origins of these groups either slightly postdate, or just predate, the final separation of Africa and South America by continental drift. The most recent common ancestor of the Mormyroidea and Gymnotiformes was found to be a non-electrogenic basal teleost living more than 85 millions years earlier. For both electric fish lineages, we also estimated similar intervals (16–19 or 22–26 million years, depending on calibration method) between the appearance of electroreception and the origin of myogenic electric organs, providing rough upper estimates for the time periods during which these complex electric organs evolved de novo from skeletal muscle precursors. The fact that the Gymnotiformes and Mormyroidea are of similar age enhances the comparative value of the weakly electric fish system for investigating pathways to evolutionary novelty, as well as the influences of key innovations in communication on the process of species radiation. PMID:22606250

Bipartite life cycle of coral reef fishes promotes increasing shape disparity of the head skeleton during ontogeny: an example from damselfishes (Pomacentridae)

PubMed Central

2011-01-01

Background Quantitative studies of the variation of disparity during ontogeny exhibited by the radiation of coral reef fishes are lacking. Such studies dealing with the variation of disparity, i.e. the diversity of organic form, over ontogeny could be a first step in detecting evolutionary mechanisms in these fishes. The damselfishes (Pomacentridae) have a bipartite life-cycle, as do the majority of demersal coral reef fishes. During their pelagic dispersion phase, all larvae feed on planktonic prey. On the other hand, juveniles and adults associated with the coral reef environment show a higher diversity of diets. Using geometric morphometrics, we study the ontogenetic dynamic of shape disparity of different head skeletal units (neurocranium, suspensorium and opercle, mandible and premaxilla) in this fish family. We expected that larvae of different species might be relatively similar in shapes. Alternatively, specialization may become notable even in the juvenile and adult phase. Results The disparity levels increase significantly throughout ontogeny for each skeletal unit. At settlement, all larval shapes are already species-specific. Damselfishes show high levels of ontogenetic allometry during their post-settlement growth. The divergence of allometric patterns largely explains the changes in patterns and levels of shape disparity over ontogeny. The rate of shape change and the length of ontogenetic trajectories seem to be less variable among species. We also show that the high levels of shape disparity at the adult stage are correlated to a higher level of ecological and functional diversity in this stage. Conclusion Diversification throughout ontogeny of damselfishes results from the interaction among several developmental novelties enhancing disparity. The bipartite life-cycle of damselfishes exemplifies a case where the variation of environmental factors, i.e. the transition from the more homogeneous oceanic environment to the coral reef offering a wide range of feeding habits, promotes increasing shape disparity of the head skeleton over the ontogeny of fishes. PMID:21450094

Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology

PubMed Central

van Belkum, Alex; Struelens, Marc; de Visser, Arjan; Verbrugh, Henri; Tibayrenc, Michel

2001-01-01

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made. PMID:11432813

Reverse Evolution of Armor Plates in the Threespine Stickleback

USGS Publications Warehouse

Kitano, J.; Bolnick, D.I.; Beauchamp, D.A.; Mazur, M.M.; Mori, S.; Nakano, T.; Peichel, C.L.

2008-01-01

Faced with sudden environmental changes, animals must either adapt to novel environments or go extinct. Thus, study of the mechanisms underlying rapid adaptation is crucial not??only for the understanding of natural evolutionary processes but also for the understanding of human-induced evolutionary change, which is an increasingly important problem [1-8]. In the present study, we demonstrate that the frequency of completely plated threespine stickleback fish (Gasterosteus aculeatus) has increased in an urban freshwater lake (Lake Washington, Seattle, Washington) within the last 40 years. This is a dramatic example of "reverse evolution," [9] because the general evolutionary trajectory is toward armor-plate reduction in freshwater sticklebacks [10]. On the basis of our genetic studies and simulations, we propose that the most likely cause of reverse evolution is increased selection for the completely plated morph, which we suggest could result from higher levels of trout predation after a sudden increase in water transparency during the early 1970s. Rapid evolution was facilitated by the existence of standing allelic variation in Ectodysplasin (Eda), the gene that underlies the major plate-morph locus [11]. The Lake Washington stickleback thus provides a novel example of reverse evolution, which is probably caused by a change in allele frequency at the major plate locus in response to a changing predation regime. ?? 2008 Elsevier Ltd. All rights reserved.

Long Distance Dispersal of Zooplankton Endemic to Isolated Mountaintops - an Example of an Ecological Process Operating on an Evolutionary Time Scale

PubMed Central

Vanschoenwinkel, Bram; Mergeay, Joachim; Pinceel, Tom; Waterkeyn, Aline; Vandewaerde, Hanne; Seaman, Maitland; Brendonck, Luc

2011-01-01

Recent findings suggest a convergence of time scales between ecological and evolutionary processes which is usually explained in terms of rapid micro evolution resulting in evolution on ecological time scales. A similar convergence, however, can also emerge when slow ecological processes take place on evolutionary time scales. A good example of such a slow ecological process is the colonization of remote aquatic habitats by passively dispersed zooplankton. Using variation at the protein coding mitochondrial COI gene, we investigated the balance between mutation and migration as drivers of genetic diversity in two Branchipodopsis fairy shrimp species (Crustacea, Anostraca) endemic to remote temporary rock pool clusters at the summit of isolated mountaintops in central South Africa. We showed that both species colonized the region almost simultaneously c. 0.8 My ago, but exhibit contrasting patterns of regional genetic diversity and demographic history. The haplotype network of the common B. cf. wolfi showed clear evidence of 11 long distance dispersal events (up to 140 km) with five haplotypes that are shared among distant inselbergs, as well as some more spatially isolated derivates. Similar patterns were not observed for B. drakensbergensis presumably since this rarer species experienced a genetic bottleneck. We conclude that the observed genetic patterns reflect rare historic colonization events rather than frequent ongoing gene flow. Moreover, the high regional haplotype diversity combined with a high degree of haplotype endemicity indicates that evolutionary- (mutation) and ecological (migration) processes in this system operate on similar time scales. PMID:22102865

Planetary Protection: Two Relevant Terrestrial Examples

NASA Astrophysics Data System (ADS)

Chyba, C.

2002-09-01

Concerns about potential pathogens in returned samples from Mars ("Mars Sample Return: Issues and Recommendations", National Research Council, 1997) or planetary satellites ("Evaluating the Biological Potential in Samples Returned from Planetary Satellites and Small Solar System Bodies", National Research Council, 1998) focus on two potential types of pathogenesis, toxic and infectious. The National Research Council reports cited above state that the chances of extraterrestrial organisms proving either toxic or infectious to humans are extremely low, but cannot be entirely ruled out. Here I discuss recently discovered terrestrial examples relevant to each possibility, in order to make these concerns concrete. The first example concerns the production of hepatotoxins (toxins affecting the liver) and neurotoxins by cyanobacteria in glacial lakes on alpine pastures in Switzerland. In this example, mat-forming benthic cyanobacteria are implicated in a hundred cattle poisonings that have been reported from alpine pasteurs in southeastern Switzerland over the past twenty-five years (e.g. K. Mez et al, Hydrobiologia 368, 1-15 (1998)). It is unlikely that these cyanobacteria evolved the toxins in response to dairy cows; rather the susceptibility of cattle to these toxins seems simply to be an unfortunate coincidence of a toxin working across a large evolutionary distance. The second example concerns the recent demonstration that the decimation of shallow-water Caribbean elkhorn coral is due to infection by a common fecal enterobacterium associated with the human gut (K. L. Patterson et al., PNAS 99, 8725-8730 (2002)). The bacterium, Serratia marcenscens, is also a free-living microbe in water and soil, as well as an opportunistic pathogen in a variety of animal species. The distance between humans and corals emphasizes the possibility that certain organisms may prove pathogenic across a wide evolutionary divide. Of course, in neither of these cases are the evolutionary distances crossed as large as those that would likely exist between any martian organisms and human beings. The possibility that life on the two worlds might share a common ancestor suggests that these distances may not be altogether incomparable, but this remains speculation pending further exploration. This work is supported in part by the NASA Exobiology Program and a Presidential Early Career Award for Scientists and Engineers.

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

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

Resonator memories and optical novelty filters

NASA Astrophysics Data System (ADS)

Anderson, Dana Z.; Erle, Marie C.

Optical resonators having holographic elements are potential candidates for storing information that can be accessed through content addressable or associative recall. Closely related to the resonator memory is the optical novelty filter, which can detect the differences between a test object and a set of reference objects. We discuss implementations of these devices using continuous optical media such as photorefractive materials. The discussion is framed in the context of neural network models. There are both formal and qualitative similarities between the resonator memory and optical novelty filter and network models. Mode competition arises in the theory of the resonator memory, much as it does in some network models. We show that the role of the phenomena of "daydreaming" in the real-time programmable optical resonator is very much akin to the role of "unlearning" in neural network memories. The theory of programming the real-time memory for a single mode is given in detail. This leads to a discussion of the optical novelty filter. Experimental results for the resonator memory, the real-time programmable memory, and the optical tracking novelty filter are reviewed. We also point to several issues that need to be addressed in order to implement more formal models of neural networks.

Resonator Memories And Optical Novelty Filters

NASA Astrophysics Data System (ADS)

Anderson, Dana Z.; Erie, Marie C.

1987-05-01

Optical resonators having holographic elements are potential candidates for storing information that can be accessed through content-addressable or associative recall. Closely related to the resonator memory is the optical novelty filter, which can detect the differences between a test object and a set of reference objects. We discuss implementations of these devices using continuous optical media such as photorefractive ma-terials. The discussion is framed in the context of neural network models. There are both formal and qualitative similarities between the resonator memory and optical novelty filter and network models. Mode competition arises in the theory of the resonator memory, much as it does in some network models. We show that the role of the phenomena of "daydream-ing" in the real-time programmable optical resonator is very much akin to the role of "unlearning" in neural network memories. The theory of programming the real-time memory for a single mode is given in detail. This leads to a discussion of the optical novelty filter. Experimental results for the resonator memory, the real-time programmable memory, and the optical tracking novelty filter are reviewed. We also point to several issues that need to be addressed in order to implement more formal models of neural networks.

Autonomous visual exploration creates developmental change in familiarity and novelty seeking behaviors

PubMed Central

Perone, Sammy; Spencer, John P.

2013-01-01

What motivates children to radically transform themselves during early development? We addressed this question in the domain of infant visual exploration. Over the first year, infants' exploration shifts from familiarity to novelty seeking. This shift is delayed in preterm relative to term infants and is stable within individuals over the course of the first year. Laboratory tasks have shed light on the nature of this familiarity-to-novelty shift, but it is not clear what motivates the infant to change her exploratory style. We probed this by letting a Dynamic Neural Field (DNF) model of visual exploration develop itself via accumulating experience in a virtual world. We then situated it in a canonical laboratory task. Much like infants, the model exhibited a familiarity-to-novelty shift. When we manipulated the initial conditions of the model, the model's performance was developmentally delayed much like preterm infants. This delay was overcome by enhancing the model's experience during development. We also found that the model's performance was stable at the level of the individual. Our simulations indicate that novelty seeking emerges with no explicit motivational source via the accumulation of visual experience within a complex, dynamical exploratory system. PMID:24065948

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly

PubMed Central

Hanski, Ilkka A.

2011-01-01

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time. PMID:21788506

Feeding/nutrition interactions affecting aggression

USDA-ARS?s Scientific Manuscript database

Pigs are social animals. From an evolutionary perspective, being social conveys a number of benefits, but potentially some disadvantages, especially for certain individuals within the group. For example, living in a social group can improve successful foraging in a natural setting, but competition w...

Evolution caused by extreme events.

PubMed

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

2017-06-19

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

Evolutionary systems biology: historical and philosophical perspectives on an emerging synthesis.

PubMed

O'Malley, Maureen A

2012-01-01

Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.

The relative importance of rapid evolution for plant-microbe interactions depends on ecological context.

PubMed

Terhorst, Casey P; Lennon, Jay T; Lau, Jennifer A

2014-06-22

Evolution can occur on ecological time-scales, affecting community and ecosystem processes. However, the importance of evolutionary change relative to ecological processes remains largely unknown. Here, we analyse data from a long-term experiment in which we allowed plant populations to evolve for three generations in dry or wet soils and used a reciprocal transplant to compare the ecological effect of drought and the effect of plant evolutionary responses to drought on soil microbial communities and nutrient availability. Plants that evolved under drought tended to support higher bacterial and fungal richness, and increased fungal : bacterial ratios in the soil. Overall, the magnitudes of ecological and evolutionary effects on microbial communities were similar; however, the strength and direction of these effects depended on the context in which they were measured. For example, plants that evolved in dry environments increased bacterial abundance in dry contemporary environments, but decreased bacterial abundance in wet contemporary environments. Our results suggest that interactions between recent evolutionary history and ecological context affect both the direction and magnitude of plant effects on soil microbes. Consequently, an eco-evolutionary perspective is required to fully understand plant-microbe interactions.

SLiM 2: Flexible, Interactive Forward Genetic Simulations.

PubMed

Haller, Benjamin C; Messer, Philipp W

2017-01-01

Modern population genomic datasets hold immense promise for revealing the evolutionary processes operating in natural populations, but a crucial prerequisite for this goal is the ability to model realistic evolutionary scenarios and predict their expected patterns in genomic data. To that end, we present SLiM 2: an evolutionary simulation framework that combines a powerful, fast engine for forward population genetic simulations with the capability of modeling a wide variety of complex evolutionary scenarios. SLiM achieves this flexibility through scriptability, which provides control over most aspects of the simulated evolutionary scenarios with a simple R-like scripting language called Eidos. An example SLiM simulation is presented to illustrate the power of this approach. SLiM 2 also includes a graphical user interface for simulation construction, interactive runtime control, and dynamic visualization of simulation output, facilitating easy and fast model development with quick prototyping and visual debugging. We conclude with a performance comparison between SLiM and two other popular forward genetic simulation packages. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Drosophila sex combs as a model of evolutionary innovations.

PubMed

Kopp, Artyom

2011-01-01

The diversity of animal and plant forms is shaped by nested evolutionary innovations. Understanding the genetic and molecular changes responsible for these innovations is therefore one of the key goals of evolutionary biology. From the genetic point of view, the origin of novel traits implies the origin of new regulatory pathways to control their development. To understand how these new pathways are assembled in the course of evolution, we need model systems that combine relatively recent innovations with a powerful set of genetic and molecular tools. One such model is provided by the Drosophila sex comb-a male-specific morphological structure that evolved in a relatively small lineage related to the model species D. melanogaster. Our extensive knowledge of sex comb development in D. melanogaster provides the basis for investigating the genetic changes responsible for sex comb origin and diversification. At the same time, sex combs can change on microevolutionary timescales and differ spectacularly among closely related species, providing opportunities for direct genetic analysis and for integrating developmental and population-genetic approaches. Sex comb evolution is associated with the origin of novel interactions between Hox and sex determination genes. Activity of the sex determination pathway was brought under the control of the Hox code to become segment-specific, while Hox gene expression became sexually dimorphic. At the same time, both Hox and sex determination genes were integrated into the intrasegmental spatial patterning network, and acquired new joint downstream targets. Phylogenetic analysis shows that similar sex comb morphologies evolved independently in different lineages. Convergent evolution at the phenotypic level reflects convergent changes in the expression of Hox and sex determination genes, involving both independent gains and losses of regulatory interactions. However, the downstream cell-differentiation programs have diverged between species, and in some lineages, similar adult morphologies are produced by different morphogenetic mechanisms. These features make the sex comb an excellent model for examining not only the genetic changes responsible for its evolution, but also the cellular processes that translate DNA sequence changes into morphological diversity. The origin and diversification of sex combs provides insights into the roles of modularity, cooption, and regulatory changes in evolutionary innovations, and can serve as a model for understanding the origin of the more drastic novelties that define higher order taxa. © 2011 Wiley Periodicals, Inc.

Drosophila Sex Combs as a Model of Evolutionary Innovations

PubMed Central

Kopp, Artyom

2011-01-01

The diversity of animal and plant forms is shaped by nested evolutionary innovations. Understanding the genetic and molecular changes responsible for these innovations is therefore one of the key goals of evolutionary biology. From the genetic point of view, the origin of novel traits implies the origin of new regulatory pathways to control their development. To understand how these new pathways are assembled in the course of evolution, we need model systems that combine relatively recent innovations with a powerful set of genetic and molecular tools. One such model is provided by the Drosophila sex comb – a male-specific morphological structure that evolved in a relatively small lineage related to the model species D. melanogaster. Our extensive knowledge of sex comb development in D. melanogaster provides the basis for investigating the genetic changes responsible for sex comb origin and diversification. At the same time, sex combs can change on microevolutionary timescales and differ spectacularly among closely related species, providing opportunities for direct genetic analysis and for integrating developmental and population-genetic approaches. Sex comb evolution is associated with the origin of novel interactions between HOX and sex determination genes. Activity of the sex determination pathway was brought under the control of the HOX code to become segment-specific, while HOX gene expression became sexually dimorphic. At the same time, both HOX and sex determination genes were integrated into the intrasegmental spatial patterning network, and acquired new joint downstream targets. Phylogenetic analysis shows that similar sex comb morphologies evolved independently in different lineages. Convergent evolution at the phenotypic level reflects convergent changes in the expression of HOX and sex determination genes, involving both independent gains and losses of regulatory interactions. However, the downstream cell differentiation programs have diverged between species, and in some lineages similar adult morphologies are produced by different morphogenetic mechanisms. These features make the sex comb an excellent model for examining not only the genetic changes responsible for its evolution, but also the cellular processes that translate DNA sequence changes into morphological diversity. The origin and diversification of sex combs provides insights into the roles of modularity, cooption, and regulatory changes in evolutionary innovations, and can serve as a model for understanding the origin of the more drastic novelties that define higher-order taxa. PMID:23016935

A constraint-based evolutionary learning approach to the expectation maximization for optimal estimation of the hidden Markov model for speech signal modeling.

PubMed

Huda, Shamsul; Yearwood, John; Togneri, Roberto

2009-02-01

This paper attempts to overcome the tendency of the expectation-maximization (EM) algorithm to locate a local rather than global maximum when applied to estimate the hidden Markov model (HMM) parameters in speech signal modeling. We propose a hybrid algorithm for estimation of the HMM in automatic speech recognition (ASR) using a constraint-based evolutionary algorithm (EA) and EM, the CEL-EM. The novelty of our hybrid algorithm (CEL-EM) is that it is applicable for estimation of the constraint-based models with many constraints and large numbers of parameters (which use EM) like HMM. Two constraint-based versions of the CEL-EM with different fusion strategies have been proposed using a constraint-based EA and the EM for better estimation of HMM in ASR. The first one uses a traditional constraint-handling mechanism of EA. The other version transforms a constrained optimization problem into an unconstrained problem using Lagrange multipliers. Fusion strategies for the CEL-EM use a staged-fusion approach where EM has been plugged with the EA periodically after the execution of EA for a specific period of time to maintain the global sampling capabilities of EA in the hybrid algorithm. A variable initialization approach (VIA) has been proposed using a variable segmentation to provide a better initialization for EA in the CEL-EM. Experimental results on the TIMIT speech corpus show that CEL-EM obtains higher recognition accuracies than the traditional EM algorithm as well as a top-standard EM (VIA-EM, constructed by applying the VIA to EM).

Pristionchus pacificus daf-16 is essential for dauer formation but dispensable for mouth form dimorphism.

PubMed

Ogawa, Akira; Bento, Gilberto; Bartelmes, Gabi; Dieterich, Christoph; Sommer, Ralf J

2011-04-01

The nematode Pristionchus pacificus shows two forms of phenotypic plasticity: dauer formation and dimorphism of mouth form morphologies. It can therefore serve as a model for studying the evolutionary mechanisms that underlie phenotypic plasticity. Formation of dauer larvae is observed in many other species and constitutes one of the most crucial survival strategies in nematodes, whereas the mouth form dimorphism is an evolutionary novelty observed only in P. pacificus and related nematodes. We have previously shown that the same environmental cues and steroid signaling control both dauer formation and mouth form dimorphism. Here, we examine by mutational analysis and whole-genome sequencing the function of P. pacificus (Ppa) daf-16, which encodes a forkhead transcription factor; in C. elegans, daf-16 is the target of insulin signaling and plays important roles in dauer formation. We found that mutations in Ppa-daf-16 cause strong dauer formation-defective phenotypes, suggesting that Ppa-daf-16 represents one of the evolutionarily conserved regulators of dauer formation. Upon strong dauer induction with lophenol, Ppa-daf-16 individuals formed arrested larvae that partially resemble wild-type dauer larvae, indicating that Ppa-daf-16 is also required for dauer morphogenesis. By contrast, regulation of mouth form dimorphism was unaffected by Ppa-daf-16 mutations and mutant animals responded normally to environmental cues. Our results suggest that mechanisms for dauer formation and mouth form regulation overlap partially, but not completely, and one of two key transcriptional regulators of the dauer regulatory network was either independently co-opted for, or subsequently lost by, the mouth form regulatory network.

Opposing Forces of A/T-Biased Mutations and G/C-Biased Gene Conversions Shape the Genome of the Nematode Pristionchus pacificus

PubMed Central

Weller, Andreas M.; Rödelsperger, Christian; Eberhardt, Gabi; Molnar, Ruxandra I.; Sommer, Ralf J.

2014-01-01

Base substitution mutations are a major source of genetic novelty and mutation accumulation line (MAL) studies revealed a nearly universal AT bias in de novo mutation spectra. While a comparison of de novo mutation spectra with the actual nucleotide composition in the genome suggests the existence of general counterbalancing mechanisms, little is known about the evolutionary and historical details of these opposing forces. Here, we correlate MAL-derived mutation spectra with patterns observed from population resequencing. Variation observed in natural populations has already been subject to evolutionary forces. Distinction between rare and common alleles, the latter of which are close to fixation and of presumably older age, can provide insight into mutational processes and their influence on genome evolution. We provide a genome-wide analysis of de novo mutations in 22 MALs of the nematode Pristionchus pacificus and compare the spectra with natural variants observed in resequencing of 104 natural isolates. MALs show an AT bias of 5.3, one of the highest values observed to date. In contrast, the AT bias in natural variants is much lower. Specifically, rare derived alleles show an AT bias of 2.4, whereas common derived alleles close to fixation show no AT bias at all. These results indicate the existence of a strong opposing force and they suggest that the GC content of the P. pacificus genome is in equilibrium. We discuss GC-biased gene conversion as a potential mechanism acting against AT-biased mutations. This study provides insight into genome evolution by combining MAL studies with natural variation. PMID:24414549

Evolutionary computation in zoology and ecology.

PubMed

Boone, Randall B

2017-12-01

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

Evolutionary computation in zoology and ecology

PubMed Central

2017-01-01

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

How hardwired is human behavior?

PubMed

Nicholson, N

1998-01-01

Time and time again managers have tried to eliminate hierarchies, politics, and interorganizational rivalry--but to no avail. Why? Evolutionary psychologists would say that they are working against nature--emotional and behavioral "hardwiring" that is the legacy of our Stone Age ancestors. In this evolutionary psychology primer for executives, Nigel Nicholson explores many of the Science's central tenets. Of course, evolutionary psychology is still an emerging discipline, and its strong connection with the theory of natural selection has sparked significant controversy. But, as Nicholson suggests, evolutionary psychology is now well established enough that its insights into human instinct will prove illuminating to anyone seeking to understand why people act the way they do in organizational settings. Take gossip. According to evolutionary psychology, our Stone Age ancestors needed this skill to survive the socially unpredictable conditions of the Savannah Plain. Thus, over time, the propensity to gossip became part of our mental programming. Executives trying to eradicate gossip at work might as well try to change their employees' musical tastes. Better to put one's energy into making sure the "rumor mill" avoids dishonesty or unkindness as much as possible. Evolutionary psychology also explores the dynamics of the human group. Clans on the Savannah Plain, for example, appear to have had no more than 150 members. The message for managers? People will likely be most effective in small organizational units. As every executive knows, it pays to be an insightful student of human nature. Evolutionary psychology adds another important chapter to consider.

Temperament and character personality dimensions in patients with dental anxiety.

PubMed

Bergdahl, Maud; Bergdahl, Jan

2003-04-01

The aim of the present study was to investigate character and temperament dimensions of personality in six men and 31 women (aged 20-57 yr) with severe dental anxiety, and to evaluate whether these dimensions were associated with the level of dental anxiety. The Dental Anxiety Scale (DAS) and the Temperament and Character Inventory (TCI) were used. High ratings in novelty seeking and female gender predicted high DAS scores. Compared with controls, the patients scored significantly higher on the temperament dimension, novelty seeking. For character dimensions, the patients scored lower on cooperativeness and higher on self-transcendence than controls. Our results indicated that patients with dental anxiety are neurotic extravert (i.e. novelty seekers who experience brief dissociative periods and magical thinking). Furthermore, the combination of the inherited temperament dimension novelty seeking and the social learned character dimension cooperativeness and self-transcendence seem to form a vulnerable personality to develop dental anxiety.

Effects of novelty on behavior in the adolescent and adult rat.

PubMed

Stansfield, Kirstie H; Kirstein, Cheryl L

2006-01-01

Adolescence is a time of high-risk behavior and increased exploration. This developmental period is marked by a greater probability of initiating drug use and is associated with an increased risk to develop addiction and dependency in adulthood. Human adolescents are predisposed towards an increased likelihood of risk taking behaviors (Zuckerman, 1986), including drug use or initiation. The purpose of the study was to examine differences in developmental risk taking behaviors. Adolescent and adult animals were exposed to a novel stimulus in a familiar environment to assess impulsive behaviors, novelty preference, and exploratory behaviors. Adolescent animals had greater novelty-induced locomotor activity, greater novelty preference, and showed higher approach and exploratory behaviors compared to adult animals. These data support the notion that adolescents may be predisposed toward sensation seeking and consequently, are more likely to engage in risk-taking behaviors, such as drug use initiation. Copyright 2005 Wiley Periodicals, Inc.

Computation of direct and inverse mutations with the SEGM web server (Stochastic Evolution of Genetic Motifs): an application to splice sites of human genome introns.

PubMed

Benard, Emmanuel; Michel, Christian J

2009-08-01

We present here the SEGM web server (Stochastic Evolution of Genetic Motifs) in order to study the evolution of genetic motifs both in the direct evolutionary sense (past-present) and in the inverse evolutionary sense (present-past). The genetic motifs studied can be nucleotides, dinucleotides and trinucleotides. As an example of an application of SEGM and to understand its functionalities, we give an analysis of inverse mutations of splice sites of human genome introns. SEGM is freely accessible at http://lsiit-bioinfo.u-strasbg.fr:8080/webMathematica/SEGM/SEGM.html directly or by the web site http://dpt-info.u-strasbg.fr/~michel/. To our knowledge, this SEGM web server is to date the only computational biology software in this evolutionary approach.

Parametric Sensitivity Analysis of Oscillatory Delay Systems with an Application to Gene Regulation.

PubMed

Ingalls, Brian; Mincheva, Maya; Roussel, Marc R

2017-07-01

A parametric sensitivity analysis for periodic solutions of delay-differential equations is developed. Because phase shifts cause the sensitivity coefficients of a periodic orbit to diverge, we focus on sensitivities of the extrema, from which amplitude sensitivities are computed, and of the period. Delay-differential equations are often used to model gene expression networks. In these models, the parametric sensitivities of a particular genotype define the local geometry of the evolutionary landscape. Thus, sensitivities can be used to investigate directions of gradual evolutionary change. An oscillatory protein synthesis model whose properties are modulated by RNA interference is used as an example. This model consists of a set of coupled delay-differential equations involving three delays. Sensitivity analyses are carried out at several operating points. Comments on the evolutionary implications of the results are offered.

[TRANSFORMATIONS OF LIFE CYCLES IN THE EVOLUTIONARY HISTORY OF TRYPANOSOMATIDAE. EXOTRANSFORMATIONS].

PubMed

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

2015-01-01

The present review is devoted to the analysis of exotransformations of life cycles in the evolutionary history of trypanosomatids (Kinetoplastea: Trypanosomatidae). Exotransformations are treated as processes associated with the transition of a trypanosomatid to a new host. The result of these transformations comprises both the inclusion of new hosts in life cycles of parasites and also epy formation of parasitic systems de novo. It is shown that exotransformations are one of the main modi in the evolution of trypanosomatids. Different examples of exotransformations of life cycle in all the taxonomic groups of Trypanosomatidae are given.

In search of a metatheory for cognitive development (or, Piaget is dead and I don't feel so good myself).

PubMed

Bjorklund, D F

1997-02-01

With the waning of influence of Piaget's theory and the shortcomings of information-processing perspectives of cognitive growth, cognitive developmentalists lack a common set of broad, overarching principles and assumptions--a metatheory--to guide their research. Developmental biology is suggested as metatheory for cognitive development. Although it is important for developmentalists to understand proximal biological causes (e.g., brain development), most important for such a metatheory is an evolutionary perspective. Some basic principles of evolutionary psychology are introduced, and examples of contemporary research and theory consistent with these ideas are provided.

On the evolutionary constraint surface of hydra

NASA Technical Reports Server (NTRS)

Slobodkin, L. B.; Dunn, K.

1983-01-01

Food consumption, body size, and budding rate were measured simultaneously in isolated individual hydra of six strains. For each individual hydra the three measurements define a point in the three dimensional space with axes: food consumption, budding rate, and body size. These points lie on a single surface, regardless of species. Floating rate and incidence of sexuality map onto this surface. It is suggested that this surface is an example of a general class of evolutionary constraint surfaces derived from the conjunction of evolutinary theory and the theory of ecological resource budgets. These constraint surfaces correspond to microevolutionary domains.

Geometric morphometrics and virtual anthropology: advances in human evolutionary studies.

PubMed

Rein, Thomas R; Harvati, Katerina

2014-01-01

Geometric morphometric methods have been increasingly used in paleoanthropology in the last two decades, lending greater power to the analysis and interpretation of the human fossil record. More recently the advent of the wide use of computed tomography and surface scanning, implemented in combination with geometric morphometrics (GM), characterizes a new approach, termed Virtual Anthropology (VA). These methodological advances have led to a number of developments in human evolutionary studies. We present some recent examples of GM and VA related research in human evolution with an emphasis on work conducted at the University of Tübingen and other German research institutions.

Isolating Escherichia coli strains for recombinant protein production.

PubMed

Schlegel, Susan; Genevaux, Pierre; de Gier, Jan-Willem

2017-03-01

Escherichia coli has been widely used for the production of recombinant proteins. To improve protein production yields in E. coli, directed engineering approaches have been commonly used. However, there are only few reported examples of the isolation of E. coli protein production strains using evolutionary approaches. Here, we first give an introduction to bacterial evolution and mutagenesis to set the stage for discussing how so far selection- and screening-based approaches have been used to isolate E. coli protein production strains. Finally, we discuss how evolutionary approaches may be used in the future to isolate E. coli strains with improved protein production characteristics.

Personality trait interactions in parents of patients with borderline personality disorder: a controlled study using the Temperament and Character Inventory.

PubMed

Fassino, Secondo; Amianto, Federico; Gastaldi, Filippo; Abbate-Daga, Giovanni; Brambilla, Francesca; Leombruni, Paolo

2009-01-30

Family environment is a pathogenic factor of borderline personality disorder (BPD). However, the personality traits of patients with BPD and their parents have never been assessed using the same instrument and then examined for relationships. In the present study, we explored the temperament and character traits of BPD patients and their parents to investigate possible interactions. In total, 56 patients with BPD and their parents were evaluated with the Temperament and Character Inventory (TCI) and compared with 53 control families. Discriminant and correlation analyses indicated that subjects with BPD displayed higher levels of novelty seeking, harm avoidance, and self-transcendence and lower levels of self-directedness than control subjects. Their fathers displayed higher levels of novelty seeking and lower levels of persistence and self-directedness, and their mothers displayed lower levels of self-directedness compared with levels in control parents. In BPD families, temperament and character traits displayed high levels of discriminatory power. Novelty seeking in offspring with borderline personality disorder was significantly correlated with their mothers' novelty seeking and their fathers' self-transcendence. Self-directedness in borderline offspring was significantly correlated with both their mothers' and fathers' novelty seeking, and their self-transcendence was significantly correlated with their mothers' novelty seeking and harm avoidance. The different correlational pattern for borderline and control families is discussed. Characteristic personality patterns were found in BPD offspring and in both parents. The relationship between personality traits of borderline offspring and those of their parents may be related to both genetic transmission and family dynamics. Ramifications for treatment are discussed.

Multi-Hamiltonian structure of Plebanski's second heavenly equation

NASA Astrophysics Data System (ADS)

Neyzi, F.; Nutku, Y.; Sheftel, M. B.

2005-09-01

We show that Plebanski's second heavenly equation, when written as a first-order nonlinear evolutionary system, admits multi-Hamiltonian structure. Therefore by Magri's theorem it is a completely integrable system. Thus it is an example of a completely integrable system in four dimensions.

Supporting diagnosis of attention-deficit hyperactive disorder with novelty detection.

PubMed

Lee, Hyoung-Joo; Cho, Sungzoon; Shin, Min-Sup

2008-03-01

Computerized continuous performance test (CPT) is a widely used diagnostic tool for attention-deficit hyperactivity disorder (ADHD). It measures the number of correctly detected stimuli as well as response times. Typically, when calculating a cut-off score for discriminating between normal and abnormal, only the normal children's data are collected. Then the average and standard deviation of each measure or variable is computed. If any of variables is larger than 2 sigma above the average, that child is diagnosed as abnormal. We will call this approach as "T-score 70" classifier. However, its performance has a lot to be desired due to a high false negative error. In order to improve the classification accuracy we propose to use novelty detection approaches for supporting ADHD diagnosis. Novelty detection is a model building framework where a classifier is constructed using only one class of training data and a new input pattern is classified according to its similarity to the training data. A total of eight novelty detectors are introduced and applied to our ADHD datasets collected from two modes of tests, visual and auditory. They are evaluated and compared with the T-score model on validation datasets in terms of false positive and negative error rates, and area under receiver operating characteristics curve (AuROC). Experimental results show that the cut-off score of 70 is suboptimal which leads to a low false positive error but a very high false negative error. A few novelty detectors such as Parzen density estimators yield much more balanced classification performances. Moreover, most novelty detectors outperform the T-score method for most age groups statistically with a significance level of 1% in terms of AuROC. In particular, we recommend the Parzen and Gaussian density estimators, kernel principal component analysis, one-class support vector machine, and K-means clustering novelty detector which can improve upon the T-score method on average by at least 30% for the visual test and 40% for the auditory test. In addition, their performances are relatively stable over various parameter values as long as they are within reasonable ranges. The proposed novelty detection approaches can replace the T-score method which has been considered the "gold standard" for supporting ADHD diagnosis. Furthermore, they can be applied to other psychological tests where only normal data are available.

Ion channels in key marine invertebrates; their diversity and potential for applications in biotechnology.

PubMed

Brown, Euan R; Piscopo, Stefania

2011-01-01

Of the intra-membrane proteins, the class that comprises voltage and ligand-gated ion channels represents the major substrate whereby signals pass between and within cells in all organisms. It has been presumed that vertebrate and particularly mammalian ion channels represent the apex of evolutionary complexity and diversity and much effort has been focused on understanding their function. However, the recent availability of cheap high throughput genome sequencing has massively broadened and deepened the quality of information across phylogeny and is radically changing this view. Here we review current knowledge on such channels in key marine invertebrates where physiological evidence is backed up by molecular sequences and expression/functional studies. As marine invertebrates represent a much greater range of phyla than terrestrial vertebrates and invertebrates together, we argue that these animals represent a highly divergent, though relatively underused source of channel novelty. As ion channels are exquisitely selective sensors for voltage and ligands, their potential and actual applications in biotechnology are manifold. Copyright © 2011 Elsevier Inc. All rights reserved.

An overlooked pink species of land iguana in the Galápagos

PubMed Central

Gentile, Gabriele; Fabiani, Anna; Marquez, Cruz; Snell, Howard L.; Snell, Heidi M.; Tapia, Washington; Sbordoni, Valerio

2009-01-01

Despite the attention given to them, the Galápagos have not yet finished offering evolutionary novelties. When Darwin visited the Galápagos, he observed both marine (Amblyrhynchus) and land (Conolophus) iguanas but did not encounter a rare pink black-striped land iguana (herein referred to as “rosada,” meaning “pink” in Spanish), which, surprisingly, remained unseen until 1986. Here, we show that substantial genetic isolation exists between the rosada and syntopic yellow forms and that the rosada is basal to extant taxonomically recognized Galápagos land iguanas. The rosada, whose present distribution is a conundrum, is a relict lineage whose origin dates back to a period when at least some of the present-day islands had not yet formed. So far, this species is the only evidence of ancient diversification along the Galápagos land iguana lineage and documents one of the oldest events of divergence ever recorded in the Galápagos. Conservation efforts are needed to prevent this form, identified by us as a good species, from extinction. PMID:19124773

Animal regeneration: ancestral character or evolutionary novelty?

PubMed

Slack, Jonathan Mw

2017-09-01

An old question about regeneration is whether it is an ancestral character which is a general property of living matter, or whether it represents a set of specific adaptations to the different circumstances faced by different types of animal. In this review, some recent results on regeneration are assessed to see if they can throw any new light on this question. Evidence in favour of an ancestral character comes from the role of Wnt and bone morphogenetic protein signalling in controlling the pattern of whole-body regeneration in acoels, which are a basal group of bilaterian animals. On the other hand, there is some evidence for adaptive acquisition or maintenance of the regeneration of appendages based on the occurrence of severe non-lethal predation, the existence of some novel genes in regenerating organisms, and differences at the molecular level between apparently similar forms of regeneration. It is tentatively concluded that whole-body regeneration is an ancestral character although has been lost from most animal lineages. Appendage regeneration is more likely to represent a derived character resulting from many specific adaptations. © 2017 The Author.

Antibiotic resistance in the wild: an eco-evolutionary perspective.

PubMed

Hiltunen, Teppo; Virta, Marko; Laine, Anna-Liisa

2017-01-19

The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics. Furthermore, antibiotic leakage to natural environments can radically alter bacterial communities. Overall, we argue that eco-evolutionary feedback loops in microbial communities can be modified by residual antibiotics and evolution of antibiotic resistance. The aim of this review is to connect some of the well-established key concepts in evolutionary biology and recent advances in the study of eco-evolutionary dynamics to research on antibiotic resistance. We also identify some key knowledge gaps related to eco-evolutionary dynamics of antibiotic resistance, and review some of the recent technical advantages in molecular microbiology that offer new opportunities for tackling these questions. Finally, we argue that using the full potential of evolutionary theory and active communication across the different fields is needed for solving this global crisis more efficiently.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Authors.

Antibiotic resistance in the wild: an eco-evolutionary perspective

PubMed Central

Virta, Marko

2017-01-01

The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics. Furthermore, antibiotic leakage to natural environments can radically alter bacterial communities. Overall, we argue that eco-evolutionary feedback loops in microbial communities can be modified by residual antibiotics and evolution of antibiotic resistance. The aim of this review is to connect some of the well-established key concepts in evolutionary biology and recent advances in the study of eco-evolutionary dynamics to research on antibiotic resistance. We also identify some key knowledge gaps related to eco-evolutionary dynamics of antibiotic resistance, and review some of the recent technical advantages in molecular microbiology that offer new opportunities for tackling these questions. Finally, we argue that using the full potential of evolutionary theory and active communication across the different fields is needed for solving this global crisis more efficiently. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences'. PMID:27920384

Self-Actualization and the Human Tendency for Varied Experience

ERIC Educational Resources Information Center

Schwartz, Marilyn M.; Gaines, Lawrence S.

1974-01-01

Examines the hypothesis that a significant correlate of self-actualization may be the subjective expression of the tendency towards novelty experiencing and examines the interaction of self-actualization level and specific components of the novelty experiencing construct. (Author/RC)

Social competitiveness and plasticity of neuroendocrine function in old age: influence of neonatal novelty exposure and maternal care reliability.

PubMed

Akers, Katherine G; Yang, Zhen; DelVecchio, Dominic P; Reeb, Bethany C; Romeo, Russell D; McEwen, Bruce S; Tang, Akaysha C

2008-06-30

Early experience is known to have a profound impact on brain and behavioral function later in life. Relatively few studies, however, have examined whether the effects of early experience remain detectable in the aging animal. Here, we examined the effects of neonatal novelty exposure, an early stimulation procedure, on late senescent rats' ability to win in social competition. During the first 3 weeks of life, half of each litter received daily 3-min exposures to a novel environment while the other half stayed in the home cage. At 24 months of age, pairs of rats competed against each other for exclusive access to chocolate rewards. We found that novelty-exposed rats won more rewards than home-staying rats, indicating that early experience exerts a life-long effect on this aspect of social dominance. Furthermore, novelty-exposed but not home-staying rats exhibited habituation of corticosterone release across repeated days of social competition testing, suggesting that early experience permanently enhances plasticity of the stress response system. Finally, we report a surprising finding that across individual rat families, greater effects of neonatal novelty exposure on stress response plasticity were found among families whose dams provided more reliable, instead of a greater total quantity of, maternal care.

Aesthetic Emotions and Aesthetic People: Openness Predicts Sensitivity to Novelty in the Experiences of Interest and Pleasure

PubMed Central

Fayn, Kirill; MacCann, Carolyn; Tiliopoulos, Niko; Silvia, Paul J.

2015-01-01

There is a stable relationship between the Openness/Intellect domain of personality and aesthetic engagement. However, neither of these are simple constructs and while the relationship exists, process based evidence explaining the relationship is still lacking. This research sought to clarify the relationship by evaluating the influence of the Openness and Intellect aspects on several different aesthetic emotions. Two studies looked at the between- and within-person differences in arousal and the emotions of interest, pleasure and confusion in response to visual art. The results suggest that Openness, as opposed to Intellect, was predictive of greater arousal, interest and pleasure, while both aspects explained less confusion. Differences in Openness were associated with within-person emotion appraisal contingencies, particularly greater novelty-interest and novelty-pleasure relationships. Those higher in Openness were particularly influenced by novelty in artworks. For pleasure this relationship suggested a different qualitative structure of appraisals. The appraisal of novelty is part of the experience of pleasure for those high in Openness, but not those low in Openness. This research supports the utility of studying Openness and Intellect as separate aspects of the broad domain and clarifies the relationship between Openness and aesthetic states in terms of within-person appraisal processes. PMID:26696940

Aesthetic Emotions and Aesthetic People: Openness Predicts Sensitivity to Novelty in the Experiences of Interest and Pleasure.

PubMed

Fayn, Kirill; MacCann, Carolyn; Tiliopoulos, Niko; Silvia, Paul J

2015-01-01

There is a stable relationship between the Openness/Intellect domain of personality and aesthetic engagement. However, neither of these are simple constructs and while the relationship exists, process based evidence explaining the relationship is still lacking. This research sought to clarify the relationship by evaluating the influence of the Openness and Intellect aspects on several different aesthetic emotions. Two studies looked at the between- and within-person differences in arousal and the emotions of interest, pleasure and confusion in response to visual art. The results suggest that Openness, as opposed to Intellect, was predictive of greater arousal, interest and pleasure, while both aspects explained less confusion. Differences in Openness were associated with within-person emotion appraisal contingencies, particularly greater novelty-interest and novelty-pleasure relationships. Those higher in Openness were particularly influenced by novelty in artworks. For pleasure this relationship suggested a different qualitative structure of appraisals. The appraisal of novelty is part of the experience of pleasure for those high in Openness, but not those low in Openness. This research supports the utility of studying Openness and Intellect as separate aspects of the broad domain and clarifies the relationship between Openness and aesthetic states in terms of within-person appraisal processes.

[Orienting reflex: "targeting reaction" and "searchlight of attention"].

PubMed

Sokolov, E N; Nezlina, N I; Polianskiĭ, V B; Evtikhin, D V

2001-01-01

The concept of orienting reflex based on the principle of vector coding of cognitive and executive processes is proposed. The orienting reflex to non-signal and signal stimuli is a set of orienting reactions: motor, autonomic, neuronal, and subjective emphasizing new and significant stimuli. Two basic mechanisms can be identified within the orienting reflex: a "targeting reaction" and a "searchlight of attention". In the visual system the first one consists in a foveation of a target stimulus. The foveation is performed with participation of premotor neurons excited by saccadic command neurons of the superior colliculi. The "searchlight of attention" is based on the resonance of gamma-oscillations in the reticular thalamus selectively enhancing responses of cortical neurons (involuntary attention). The novelty signal is generated in novelty neurons of the hippocampus, which are selectively tuned to a repeatedly presented standard stimulus. The selective tuning is caused by the depression of plastic synapses representing a "neuronal model" of the standard stimulus. A mismatch of the novel stimulus with the established neuronal model gives rise to a "novelty signal" enhancing the novel input. The novelty signal inhibits current conditioned reflexes (external inhibition) contributing to redirecting the behavior. By triggering the expression of early genes the novelty signal initiates the formation of the long-term memory connected with neoneurogenesis.

DECOY: Documenting Experiences with Cigarettes and Other Tobacco in Young Adults

PubMed Central

Berg, Carla J.; Haardörfer, Regine; Lewis, Michael; Getachew, Betelihem; Lloyd, Steven A.; Thomas, Sarah Fretti; Lanier, Angela; Trepanier, Kelleigh; Johnston, Teresa; Grimsley, Linda; Foster, Bruce; Benson, Stephanie; Smith, Alicia; Barr, Dana Boyd; Windle, Michael

2016-01-01

Objectives We examined psychographic characteristics associated with tobacco use among Project DECOY participants. Methods Project DECOY is a 2-year longitudinal mixed-methods study examining risk for tobacco use among 3418 young adults across 7 Georgia colleges/universities. Baseline measures included sociodemographics, tobacco use, and psychographics using the Values, Attitudes, and Lifestyle Scale. Bivariate and multivariable analyses were conducted to identify correlates of tobacco use. Results Past 30-day use prevalence was: 13.3% cigarettes; 11.3% little cigars/cigarillos (LCCs); 3.6% smokeless tobacco; 10.9% e-cigarettes; and 12.2% hookah. Controlling for sociodemographics, correlates of cigarette use included greater novelty seeking (p < .001) and intellectual curiosity (p = .010) and less interest in tangible creation (p = .002) and social conservatism (p < .001). Correlates of LCC use included greater novelty seeking (p < .001) and greater fashion orientation (p = .007). Correlates of smokeless tobacco use included greater novelty seeking (p = .006) and less intellectual curiosity (p < .001). Correlates of e-cigarette use included greater novelty seeking (p < .001) and less social conservatism (p = .002). Correlates of hookah use included greater novelty seeking (p < .001), fashion orientation (p = .044), and self-focused thinking (p = .002), and less social conservatism (p < .001). Conclusions Psychographic characteristics distinguish users of different tobacco products. PMID:27103410

Modern meta-heuristics based on nonlinear physics processes: A review of models and design procedures

NASA Astrophysics Data System (ADS)

Salcedo-Sanz, S.

2016-10-01

Meta-heuristic algorithms are problem-solving methods which try to find good-enough solutions to very hard optimization problems, at a reasonable computation time, where classical approaches fail, or cannot even been applied. Many existing meta-heuristics approaches are nature-inspired techniques, which work by simulating or modeling different natural processes in a computer. Historically, many of the most successful meta-heuristic approaches have had a biological inspiration, such as evolutionary computation or swarm intelligence paradigms, but in the last few years new approaches based on nonlinear physics processes modeling have been proposed and applied with success. Non-linear physics processes, modeled as optimization algorithms, are able to produce completely new search procedures, with extremely effective exploration capabilities in many cases, which are able to outperform existing optimization approaches. In this paper we review the most important optimization algorithms based on nonlinear physics, how they have been constructed from specific modeling of a real phenomena, and also their novelty in terms of comparison with alternative existing algorithms for optimization. We first review important concepts on optimization problems, search spaces and problems' difficulty. Then, the usefulness of heuristics and meta-heuristics approaches to face hard optimization problems is introduced, and some of the main existing classical versions of these algorithms are reviewed. The mathematical framework of different nonlinear physics processes is then introduced as a preparatory step to review in detail the most important meta-heuristics based on them. A discussion on the novelty of these approaches, their main computational implementation and design issues, and the evaluation of a novel meta-heuristic based on Strange Attractors mutation will be carried out to complete the review of these techniques. We also describe some of the most important application areas, in broad sense, of meta-heuristics, and describe free-accessible software frameworks which can be used to make easier the implementation of these algorithms.

THE EVOLUTION OF SCHOOL MATHEMATICS.

ERIC Educational Resources Information Center

DAVIS, ROBERT B.

ACTION AND PLANS OF THE MADISON PROJECT TO GIVE RATIONAL GUIDANCE TO EVOLUTIONARY CHANGES IN SCHOOL MATHEMATICS ARE DESCRIBED. THE PROJECT ATTEMPTS TO CONTRIBUTE TO RATIONAL GUIDANCE OF EDUCATIONAL EVOLUTION BY MAKING "THRUSTS AND PROBES" INTO THE UNKNOWN POTENTIAL OF MATHEMATICS LEARNING. EXAMPLES ARE--INTRODUCING THE ARITHMETIC OF…

Darwin's Natural Selection in the Classroom.

ERIC Educational Resources Information Center

Lovely, Deborah

Resuscitating Charles Darwin's language from historians' emphatic denigration of the written word serves as an example to demonstrate what the English discipline can accomplish in recovering cultural heritage. Michael Ghiselin, an evolutionary anatomist, suggests that scholars must concentrate on the ideas, not the language, Darwin employed. Yet…

Knowledge: Genuine and Bogus

ERIC Educational Resources Information Center

Bunge, Mario

2011-01-01

Pseudoscience is error, substantive or methodological, parading as science. Obvious examples are parapsychology, "intelligent design," and homeopathy. Psychoanalysis and pop evolutionary psychology are less obvious, yet no less flawed in both method and doctrine. The fact that science can be faked to the point of deceiving science lovers suggests…

Using a two-phase evolutionary framework to select multiple network spreaders based on community structure

NASA Astrophysics Data System (ADS)

Fu, Yu-Hsiang; Huang, Chung-Yuan; Sun, Chuen-Tsai

2016-11-01

Using network community structures to identify multiple influential spreaders is an appropriate method for analyzing the dissemination of information, ideas and infectious diseases. For example, data on spreaders selected from groups of customers who make similar purchases may be used to advertise products and to optimize limited resource allocation. Other examples include community detection approaches aimed at identifying structures and groups in social or complex networks. However, determining the number of communities in a network remains a challenge. In this paper we describe our proposal for a two-phase evolutionary framework (TPEF) for determining community numbers and maximizing community modularity. Lancichinetti-Fortunato-Radicchi benchmark networks were used to test our proposed method and to analyze execution time, community structure quality, convergence, and the network spreading effect. Results indicate that our proposed TPEF generates satisfactory levels of community quality and convergence. They also suggest a need for an index, mechanism or sampling technique to determine whether a community detection approach should be used for selecting multiple network spreaders.

Bi-directional evolutionary structural optimization for strut-and-tie modelling of three-dimensional structural concrete

NASA Astrophysics Data System (ADS)

Shobeiri, Vahid; Ahmadi-Nedushan, Behrouz

2017-12-01

This article presents a method for the automatic generation of optimal strut-and-tie models in reinforced concrete structures using a bi-directional evolutionary structural optimization method. The methodology presented is developed for compliance minimization relying on the Abaqus finite element software package. The proposed approach deals with the generation of truss-like designs in a three-dimensional environment, addressing the design of corbels and joints as well as bridge piers and pile caps. Several three-dimensional examples are provided to show the capabilities of the proposed framework in finding optimal strut-and-tie models in reinforced concrete structures and verifying its efficiency to cope with torsional actions. Several issues relating to the use of the topology optimization for strut-and-tie modelling of structural concrete, such as chequerboard patterns, mesh-dependency and multiple load cases, are studied. In the last example, a design procedure for detailing and dimensioning of the strut-and-tie models is given according to the American Concrete Institute (ACI) 318-08 provisions.

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

NASA Astrophysics Data System (ADS)

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

2014-07-01

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

Interolog interfaces in protein–protein docking

PubMed Central

Alsop, James D.

2015-01-01

ABSTRACT Proteins are essential elements of biological systems, and their function typically relies on their ability to successfully bind to specific partners. Recently, an emphasis of study into protein interactions has been on hot spots, or residues in the binding interface that make a significant contribution to the binding energetics. In this study, we investigate how conservation of hot spots can be used to guide docking prediction. We show that the use of evolutionary data combined with hot spot prediction highlights near‐native structures across a range of benchmark examples. Our approach explores various strategies for using hot spots and evolutionary data to score protein complexes, using both absolute and chemical definitions of conservation along with refinements to these strategies that look at windowed conservation and filtering to ensure a minimum number of hot spots in each binding partner. Finally, structure‐based models of orthologs were generated for comparison with sequence‐based scoring. Using two data sets of 22 and 85 examples, a high rate of top 10 and top 1 predictions are observed, with up to 82% of examples returning a top 10 hit and 35% returning top 1 hit depending on the data set and strategy applied; upon inclusion of the native structure among the decoys, up to 55% of examples yielded a top 1 hit. The 20 common examples between data sets show that more carefully curated interolog data yields better predictions, particularly in achieving top 1 hits. Proteins 2015; 83:1940–1946. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:25740680

Taking Research Experiences for Undergraduates Online

NASA Astrophysics Data System (ADS)

Hubenthal, Michael; Judge, Jasmeet

2013-04-01

To today's budding scientists, the notion of sharing experiences and working collaboratively with distant peers is not a novelty. Instead, this is what most young scientists expect to achieve through the Internet portals they carry in their pockets and backpacks. They have never known a world without information and communication technologies (ICT) such as laptops, mobile phones, text messaging, and the Internet. As a result, they have grown to rely on uninterrupted access to the Internet for a range of information-gathering and communication activities. Further, this generation of students has fully embraced structured online learning opportunities. For example, in 2011 more than 6.7 million U.S. students in higher education took at least one online course [Allen and Seaman, 2013].

Considerations associated with the introduction of female crewmembers in spacecraft and space stations

NASA Technical Reports Server (NTRS)

Brown, J. W.

1979-01-01

This paper examines considerations of inclusion of female crewmembers in spacecraft and space stations. The anthropometric and physiological differences between males and females as related to spaceflight such as body dimensions, muscle strength characteristics, body posture, reach, and physiological differences are discussed. Crew provisions including inflight garments, hair style, cosmetics, personal hygiene, waste management, and personal privacy are described. Impacts on hardware design and crew performance, examples of effects on Orbiter systems, data on females and their performance under conditions analogous to spaceflight, and earth-based simulation experience are examined. It is concluded that no major problems have been found which would preclude females from space, and in the future the novelty of mixed crews will significantly decrease.

Modelling and temporal performances evaluation of networked control systems using (max, +) algebra

NASA Astrophysics Data System (ADS)

Ammour, R.; Amari, S.

2015-01-01

In this paper, we address the problem of temporal performances evaluation of producer/consumer networked control systems. The aim is to develop a formal method for evaluating the response time of this type of control systems. Our approach consists on modelling, using Petri nets classes, the behaviour of the whole architecture including the switches that support multicast communications used by this protocol. (max, +) algebra formalism is then exploited to obtain analytical formulas of the response time and the maximal and minimal bounds. The main novelty is that our approach takes into account all delays experienced at the different stages of networked automation systems. Finally, we show how to apply the obtained results through an example of networked control system.

On the tsunami wave-submerged breakwater interaction

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

Filianoti, P.; Piscopo, R.

The tsunami wave loads on a submerged rigid breakwater are inertial. It is the result arising from the simple calculation method here proposed, and it is confirmed by the comparison with results obtained by other researchers. The method is based on the estimate of the speed drop of the tsunami wave passing over the breakwater. The calculation is rigorous for a sinusoidal wave interacting with a rigid submerged obstacle, in the framework of the linear wave theory. This new approach gives a useful and simple tool for estimating tsunami loads on submerged breakwaters.An unexpected novelty come out from a workedmore » example: assuming the same wave height, storm waves are more dangerous than tsunami waves, for the safety against sliding of submerged breakwaters.« less

Complexity as AN Epistemic Revolution: Considerations on the New Science in the Context of Western Intellectual History

NASA Astrophysics Data System (ADS)

Popolo, Damian

The paper will seek to present a genesis of complexity in European philosophical thought. Following the works of Gleick and Hobsbawn it is possible to discern the emergence of complexity's ethos in the `age of revolutions'. Gleick, for example, has noted the influence of natural philosophy on the first precursors of chaos theory. Natural philosophy itself was deeply anchored in German romanticism. The paper will thus seek to present, following Foucault, an `Archaeology of Complexity' which considers Foucault's definition of epistemes as evolving modes of thought. In particular, the paper will seek to use Foucault's description of the modern episteme in order to detect the novelty inherent within the ethos of Complexity.

Quantification provides a conceptual basis for convergent evolution.

PubMed

Speed, Michael P; Arbuckle, Kevin

2017-05-01

While much of evolutionary biology attempts to explain the processes of diversification, there is an important place for the study of phenotypic similarity across life forms. When similar phenotypes evolve independently in different lineages this is referred to as convergent evolution. Although long recognised, evolutionary convergence is receiving a resurgence of interest. This is in part because new genomic data sets allow detailed and tractable analysis of the genetic underpinnings of convergent phenotypes, and in part because of renewed recognition that convergence may reflect limitations in the diversification of life. In this review we propose that although convergent evolution itself does not require a new evolutionary framework, none the less there is room to generate a more systematic approach which will enable evaluation of the importance of convergent phenotypes in limiting the diversity of life's forms. We therefore propose that quantification of the frequency and strength of convergence, rather than simply identifying cases of convergence, should be considered central to its systematic comprehension. We provide a non-technical review of existing methods that could be used to measure evolutionary convergence, bringing together a wide range of methods. We then argue that quantification also requires clear specification of the level at which the phenotype is being considered, and argue that the most constrained examples of convergence show similarity both in function and in several layers of underlying form. Finally, we argue that the most important and impressive examples of convergence are those that pertain, in form and function, across a wide diversity of selective contexts as these persist in the likely presence of different selection pressures within the environment. © 2016 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Flower color as a model system for studies of plant evo-devo.

PubMed

Sobel, James M; Streisfeld, Matthew A

2013-01-01

Even though pigmentation traits have had substantial impacts on the field of animal evolutionary developmental biology, they have played only relatively minor roles in plant evo-devo. This is surprising given the often direct connection between flower color and fitness variation mediated through the effects of pollinators. At the same time, ecological and evolutionary genetic studies have utilized the molecular resources available for the anthocyanin pathway to generate several examples of the molecular basis of putatively adaptive transitions in flower color. Despite this opportunity to synthesize experimental approaches in ecology, evolution, and developmental biology, the investigation of many fundamental questions in evo-devo using this powerful model is only at its earliest stages. For example, a long-standing question is whether predictable genetic changes accompany the repeated evolution of a trait. Due to the conserved nature of the biochemical and regulatory control of anthocyanin biosynthesis, it has become possible to determine whether, and under what circumstances, different types of mutations responsible for flower color variation are preferentially targeted by natural selection. In addition, because plants use anthocyanin and related compounds in vegetative tissue for other important physiological functions, the identification of naturally occurring transitions from unpigmented to pigmented flowers provides the opportunity to examine the mechanisms by which regulatory networks are co-opted into new developmental domains. Here, we review what is known about the ecological and molecular basis of anthocyanic flower color transitions in natural systems, focusing on the evolutionary and developmental features involved. In doing so, we provide suggestions for future work on this trait and suggest that there is still much to be learned from the evolutionary development of flower color transitions in nature.

Randomness and arbitrary coordination in the reactive ultimatum game

NASA Astrophysics Data System (ADS)

da Silva, Roberto; Valverde, Pablo; Lamb, Luis C.

2016-07-01

Darwin's theory of evolution - as introduced in game theory by Maynard Smith - is not the only important evolutionary aspect in an evolutionary dynamics, since complex interdependencies, competition, and growth should be modeled by, for example, reactive aspects. In the ultimatum game, the reciprocity and the fifty-fifty partition seems to be a deviation from rational behavior of the players under the light of Nash equilibrium. Such equilibrium emerges, for example, from the punishment of the responder who generally tends to refuse unfair proposals. In the iterated version of the game, the proposers are able to improve their proposals by adding a value thus making fairer proposals. Such evolutionary aspects are not properly Darwinian-motivated, but they are endowed with a fundamental aspect: they reflect their actions according to value of the offers. Recently, a reactive version of the ultimatum game where acceptance occurs with fixed probability was proposed. In this paper, we aim at exploring this reactive version of the ultimatum game where the acceptance by players depends on the offer. In order to do so, we analyze two situations: (i) mean field and (ii) we consider players inserted within the networks with arbitrary coordination. We then show that the reactive aspect, here studied, thus far not analyzed in the evolutionary game theory literature can unveil an essential feature for the convergence to fifty-fifty split. Moreover we also analyze populations under four different polices ranging from a highly conservative to a moderate one, with respect to the decision in changing the proposal based on acceptances. We show that the idea of gaining less more times added to the reciprocity of the players is highly relevant to the concept of ;healthy; societies population bargaining.

Resistance and relatedness on an evolutionary graph

PubMed Central

Maciejewski, Wes

2012-01-01

When investigating evolution in structured populations, it is often convenient to consider the population as an evolutionary graph—individuals as nodes, and whom they may act with as edges. There has, in recent years, been a surge of interest in evolutionary graphs, especially in the study of the evolution of social behaviours. An inclusive fitness framework is best suited for this type of study. A central requirement for an inclusive fitness analysis is an expression for the genetic similarity between individuals residing on the graph. This has been a major hindrance for work in this area as highly technical mathematics are often required. Here, I derive a result that links genetic relatedness between haploid individuals on an evolutionary graph to the resistance between vertices on a corresponding electrical network. An example that demonstrates the potential computational advantage of this result over contemporary approaches is provided. This result offers more, however, to the study of population genetics than strictly computationally efficient methods. By establishing a link between gene transfer and electric circuit theory, conceptualizations of the latter can enhance understanding of the former. PMID:21849384

Evolution: like any other science it is predictable.

PubMed

Morris, Simon Conway

2010-01-12

Evolutionary biology rejoices in the diversity of life, but this comes at a cost: other than working in the common framework of neo-Darwinian evolution, specialists in, for example, diatoms and mammals have little to say to each other. Accordingly, their research tends to track the particularities and peculiarities of a given group and seldom enquires whether there are any wider or deeper sets of explanations. Here, I present evidence in support of the heterodox idea that evolution might look to a general theory that does more than serve as a tautology ('evolution explains evolution'). Specifically, I argue that far from its myriad of products being fortuitous and accidental, evolution is remarkably predictable. Thus, I urge a move away from the continuing obsession with Darwinian mechanisms, which are entirely uncontroversial. Rather, I emphasize why we should seek explanations for ubiquitous evolutionary convergence, as well as the emergence of complex integrated systems. At present, evolutionary theory seems to be akin to nineteenth-century physics, blissfully unaware of the imminent arrival of quantum mechanics and general relativity. Physics had its Newton, biology its Darwin: evolutionary biology now awaits its Einstein.

Evolution: like any other science it is predictable

PubMed Central

Conway Morris, Simon

2010-01-01

Evolutionary biology rejoices in the diversity of life, but this comes at a cost: other than working in the common framework of neo-Darwinian evolution, specialists in, for example, diatoms and mammals have little to say to each other. Accordingly, their research tends to track the particularities and peculiarities of a given group and seldom enquires whether there are any wider or deeper sets of explanations. Here, I present evidence in support of the heterodox idea that evolution might look to a general theory that does more than serve as a tautology (‘evolution explains evolution’). Specifically, I argue that far from its myriad of products being fortuitous and accidental, evolution is remarkably predictable. Thus, I urge a move away from the continuing obsession with Darwinian mechanisms, which are entirely uncontroversial. Rather, I emphasize why we should seek explanations for ubiquitous evolutionary convergence, as well as the emergence of complex integrated systems. At present, evolutionary theory seems to be akin to nineteenth-century physics, blissfully unaware of the imminent arrival of quantum mechanics and general relativity. Physics had its Newton, biology its Darwin: evolutionary biology now awaits its Einstein. PMID:20008391

Evolution of early embryogenesis in rhabditid nematodes

PubMed Central

Brauchle, Michael; Kiontke, Karin; MacMenamin, Philip; Fitch, David H. A.; Piano, Fabio

2009-01-01

The cell biological events that guide early embryonic development occur with great precision within species but can be quite diverse across species. How these cellular processes evolve and which molecular components underlie evolutionary changes is poorly understood. To begin to address these questions, we systematically investigated early embryogenesis, from the one- to the four-cell embryo, in 34 nematode species related to C. elegans. We found 40 cell-biological characters that captured the phenotypic differences between these species. By tracing the evolutionary changes on a molecular phylogeny, we found that these characters evolved multiple times and independently of one another. Strikingly, all these phenotypes are mimicked by single-gene RNAi experiments in C. elegans. We use these comparisons to hypothesize the molecular mechanisms underlying the evolutionary changes. For example, we predict that a cell polarity module was altered during the evolution of the Protorhabditis group and show that PAR-1, a kinase localized asymmetrically in C. elegans early embryos, is symmetrically localized in the one-cell stage of Protorhabditis group species. Our genome-wide approach identifies candidate molecules—and thereby modules—associated with evolutionary changes in cell-biological phenotypes. PMID:19643102

Reinforcement and a cline in mating behaviour evolve in response to secondary contact and hybridization in shield-back katydids (Orthoptera: Tettigoniidae).

PubMed

Cole, J A

2016-09-01

In a dispersal-limited species that has evolved reproductive character displacement at a contact zone, a cline in mating behaviour may result if gene flow diffuses alleles out of the contact zone into allopatric populations. Prior work has found such a clinal pattern in the shield-back katydid Aglaothorax morsei, in which the male calling songs in a sympatric population have a displaced, short interpulse interval that increases in length with increasing distance from the contact zone. In this study, molecular phylogenetic and female preference data show that (1) sympatric populations result from secondary contact, (2) hybridization in sympatry has resulted in unidirectional mitochondrial introgression and (3) female preferences are consistent with reproductive character displacement and could generate a cline in mating behaviour. These data together suggest a history of reinforcement, generally considered rare in acoustically communicating insects; thus, Aglaothorax represents an important example of a rarely documented evolutionary process. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

The Evolution of Altruistic Preferences: Mothers versus Fathers

PubMed Central

Alger, Ingela; Cox, Donald

2013-01-01

What can evolutionary biology tell us about male-female differences in preferences concerning family matters? Might mothers be more solicitous toward offspring than fathers, for example? The economics literature has documented gender differences—children benefit more from money put in the hands of mothers rather than fathers, for example—and these differences are thought to be partly due to preferences. Yet for good reason family economics is mostly concerned with how prices and incomes affect behavior against a backdrop of exogenous preferences. Evolutionary biology complements this approach by treating preferences as the outcome of natural selection. We mine the well-developed biological literature to make a prima facie case for evolutionary roots of parental preferences. We consider the most rudimentary of traits—sex differences in gamete size and internal fertilization—and explain how they have been thought to generate male-female differences in altruism toward children and other preferences related to family behavior. The evolutionary approach to the family illuminates connections between issues typically thought distinct in family economics, such as parental care and marriage markets. PMID:23976890

Human Facial Expressions as Adaptations:Evolutionary Questions in Facial Expression Research

PubMed Central

SCHMIDT, KAREN L.; COHN, JEFFREY F.

2007-01-01

The importance of the face in social interaction and social intelligence is widely recognized in anthropology. Yet the adaptive functions of human facial expression remain largely unknown. An evolutionary model of human facial expression as behavioral adaptation can be constructed, given the current knowledge of the phenotypic variation, ecological contexts, and fitness consequences of facial behavior. Studies of facial expression are available, but results are not typically framed in an evolutionary perspective. This review identifies the relevant physical phenomena of facial expression and integrates the study of this behavior with the anthropological study of communication and sociality in general. Anthropological issues with relevance to the evolutionary study of facial expression include: facial expressions as coordinated, stereotyped behavioral phenotypes, the unique contexts and functions of different facial expressions, the relationship of facial expression to speech, the value of facial expressions as signals, and the relationship of facial expression to social intelligence in humans and in nonhuman primates. Human smiling is used as an example of adaptation, and testable hypotheses concerning the human smile, as well as other expressions, are proposed. PMID:11786989

Evolutionary game theory using agent-based methods.

PubMed

Adami, Christoph; Schossau, Jory; Hintze, Arend

2016-12-01

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

An open future for ecological and evolutionary data?

PubMed

Kenall, Amye; Harold, Simon; Foote, Christopher

2014-04-02

As part of BioMed Central's open science mission, we are pleased to announce that two of our journals have integrated with the open data repository Dryad. Authors submitting their research to either BMC Ecology or BMC Evolutionary Biology will now have the opportunity to deposit their data directly into the Dryad archive and will receive a permanent, citable link to their dataset. Although this does not affect any of our current data deposition policies at these journals, we hope to encourage a more widespread adoption of open data sharing in the fields of ecology and evolutionary biology by facilitating this process for our authors. We also take this opportunity to discuss some of the wider issues that may concern researchers when making their data openly available. Although we offer a number of positive examples from different fields of biology, we also recognise that reticence to data sharing still exists, and that change must be driven from within research communities in order to create future science that is fit for purpose in the digital age. This editorial was published jointly in both BMC Ecology and BMC Evolutionary Biology.

Creativity and Cognition: Producing Effective Novelty.

ERIC Educational Resources Information Center

Cropley, Arthur J.

1999-01-01

Reviews cognitive processes, control mechanisms, and structures in creative thinking, and examines the way these aspects of cognition develop from childhood to adulthood. The cognitive definition of creativity, cognitive approaches to novelty production, creativity and cognitive development, and mechanisms guiding cognitive processes are explored.…

LP-211, a selective 5-HT7 receptor agonist, increases novelty-preference and promotes risk-prone behavior in rats.

PubMed

Beaudet, G; Paizanis, E; Zoratto, F; Lacivita, E; Leopoldo, M; Freret, T; Laviola, G; Boulouard, M; Adriani, W

2017-12-01

Gambling disorder is associated to an increased impulsivity, a high level of novelty-seeking and a dysregulation of the forebrain neurotransmission systems. However, the neurobiological mechanisms of this addictive disorder are not fully understood and no valid pharmacological approach has yet been approved. The present study aimed to investigate the effect of 5-HT7 receptor (5-HT 7 R) stimulation with a brain penetrant and selective agonist, LP-211 (0.25 and 0.50 mg kg -1 i.p.) during post-experience consolidation, (i) acutely in a novelty-preference test (Exp. 1) or (ii) sub-chronically in the Probabilistic-Delivery Task (rPDT, commonly used to measure individual differences in risk proneness of rats; Exp. 2). Results of Exp. 1 showed that 5-HT 7 R activation improves consolidation of chamber-shape memory in the novelty-preference test, leading to significant novelty-induced hyperactivity and recognition, in conditions where controls displayed a null-preference. These results suggest that 5-HT 7 Rs may be involved in the consolidation of information inherent to spatial environments, facilitating the recognition of novelty. Furthermore, in the operant rPDT (Exp. 2), 5-HT 7 R activation shifts the choice towards a larger yet unlikely reward and turns the propensity of rats towards risk-prone behavior. Thus, 5-HT 7 Rs stimulation apparently strengthens the consideration of future, bigger rewards, also enhancing the seeking of it by operant pokes. These effects may well be explained by LP-211 actions on hippocampal versus prefrontal cortex-mediated regulations, leading to improved (though suboptimal) strategy formation. However, further experiments are necessary to determine more in depth the serotonergic pathways involved. © 2017 Wiley Periodicals, Inc.

Withdrawal from repeated treatment with ethanol induces a protracted decrease in novelty-seeking behavior and enhancement of environmental habituation in mice.

PubMed

Fukushiro, Daniela F; Saito, Luis P; Mári-Kawamoto, Elisa; Aramini, Tatiana C F; Costa, Jacqueline M; Josino, Fabiana S; Uehara, Regina A; Frussa-Filho, Roberto

2012-03-01

Ethanol withdrawal syndrome is characterized by somatic and behavioral symptoms, including increased anxiety and anhedonia. In animal models, however, there are many studies on the anxiogenic effects occurring during the first 24h after ethanol withdrawal, while anhedonia has been overlooked. Recently, we have found that amphetamine withdrawal reduced novelty seeking and enhanced environmental habituation in mice, two motivation-related behaviors. We now investigate the effects of withdrawal from ethanol, a drug of abuse with a different pharmacological profile, on these two motivation-related behaviors. Swiss male mice (3months old) were treated with 1.8g/kg ethanol for 21 consecutive days in their home cages. Seven days after ethanol withdrawal, mice were tested in a free-choice novelty apparatus containing one familiar and one novel compartment. Novelty-seeking behavior was assessed by comparing time spent in the novel compartment versus the familiar compartment, whereas environmental habituation was concomitantly evaluated by the time-response curve of total locomotion (novel+familiar). Novelty seeking was decreased and environmental habituation was enhanced during ethanol withdrawal. These anhedonic responses were not associated with concurrent changes in the anxiety-like behavior of mice (as confirmed in the elevated plus-maze test). We propose that the concomitant evaluation of novelty-seeking behavior and environmental habituation can be useful to study the behavioral consequences not only of amphetamine withdrawal but also of ethanol withdrawal. Furthermore, the present data support recent clinical findings that suggest the occurrence of protracted anhedonia well beyond the limited period immediately following the abrupt cessation of ethanol intake. Copyright © 2012. Published by Elsevier Inc.

Neuroendocrine-Immune Circuits, Phenotypes, and Interactions

PubMed Central

Ashley, Noah T.; Demas, Gregory E.

2016-01-01

Multidirectional interactions among the immune, endocrine, and nervous systems have been demonstrated in humans and non-human animal models for many decades by the biomedical community, but ecological and evolutionary perspectives are lacking. Neuroendocrine-immune interactions can be conceptualized using a series of feedback loops, which culminate into distinct neuroendocrine-immune phenotypes. Behavior can exert profound influences on these phenotypes, which can in turn reciprocally modulate behavior. For example, the behavioral aspects of reproduction, including courtship, aggression, mate selection and parental behaviors can impinge upon neuroendocrine-immune interactions. One classic example is the immunocompetence handicap hypothesis (ICHH), which proposes that steroid hormones act as mediators of traits important for female choice while suppressing the immune system. Reciprocally, neuroendocrine-immune pathways can promote the development of altered behavioral states, such as sickness behavior. Understanding the energetic signals that mediate neuroendocrine-immune crosstalk is an active area of research. Although the field of psychoneuroimmunology (PNI) has begun to explore this crosstalk from a biomedical standpoint, the neuroendocrine-immune-behavior nexus has been relatively underappreciated in comparative species. The field of ecoimmunology, while traditionally emphasizing the study of non-model systems from an ecological evolutionary perspective, often under natural conditions, has focused less on the physiological mechanisms underlying behavioral responses. This review summarizes neuroendocrine-immune interactions using a comparative framework to understand the ecological and evolutionary forces that shape these complex physiological interactions. PMID:27765499

Neuroendocrine-immune circuits, phenotypes, and interactions.

PubMed

Ashley, Noah T; Demas, Gregory E

2017-01-01

Multidirectional interactions among the immune, endocrine, and nervous systems have been demonstrated in humans and non-human animal models for many decades by the biomedical community, but ecological and evolutionary perspectives are lacking. Neuroendocrine-immune interactions can be conceptualized using a series of feedback loops, which culminate into distinct neuroendocrine-immune phenotypes. Behavior can exert profound influences on these phenotypes, which can in turn reciprocally modulate behavior. For example, the behavioral aspects of reproduction, including courtship, aggression, mate selection and parental behaviors can impinge upon neuroendocrine-immune interactions. One classic example is the immunocompetence handicap hypothesis (ICHH), which proposes that steroid hormones act as mediators of traits important for female choice while suppressing the immune system. Reciprocally, neuroendocrine-immune pathways can promote the development of altered behavioral states, such as sickness behavior. Understanding the energetic signals that mediate neuroendocrine-immune crosstalk is an active area of research. Although the field of psychoneuroimmunology (PNI) has begun to explore this crosstalk from a biomedical standpoint, the neuroendocrine-immune-behavior nexus has been relatively underappreciated in comparative species. The field of ecoimmunology, while traditionally emphasizing the study of non-model systems from an ecological evolutionary perspective, often under natural conditions, has focused less on the physiological mechanisms underlying behavioral responses. This review summarizes neuroendocrine-immune interactions using a comparative framework to understand the ecological and evolutionary forces that shape these complex physiological interactions. Copyright © 2016 Elsevier Inc. All rights reserved.

Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

NASA Astrophysics Data System (ADS)

Ma, Zhanshan (Sam)

In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three categories of population dynamics models: deterministic modeling with Logistic chaos map as an example, stochastic modeling with spatial distribution patterns as an example, as well as survival analysis and extended evolutionary game theory (EEGT) modeling. Sample experiment results with Genetic algorithms (GA) are presented to demonstrate the applications of these models. The proposed EC population dynamics approach also makes survival selection largely unnecessary or much simplified since the individuals are naturally selected (controlled) by the mathematical models for EC population dynamics.

Linear antenna array optimization using flower pollination algorithm.

PubMed

Saxena, Prerna; Kothari, Ashwin

2016-01-01

Flower pollination algorithm (FPA) is a new nature-inspired evolutionary algorithm used to solve multi-objective optimization problems. The aim of this paper is to introduce FPA to the electromagnetics and antenna community for the optimization of linear antenna arrays. FPA is applied for the first time to linear array so as to obtain optimized antenna positions in order to achieve an array pattern with minimum side lobe level along with placement of deep nulls in desired directions. Various design examples are presented that illustrate the use of FPA for linear antenna array optimization, and subsequently the results are validated by benchmarking along with results obtained using other state-of-the-art, nature-inspired evolutionary algorithms such as particle swarm optimization, ant colony optimization and cat swarm optimization. The results suggest that in most cases, FPA outperforms the other evolutionary algorithms and at times it yields a similar performance.

Regulatory divergence of X-linked genes and hybrid male sterility in mice.

PubMed

Oka, Ayako; Shiroishi, Toshihiko

2014-01-01

Postzygotic reproductive isolation is the reduction of fertility or viability in hybrids between genetically diverged populations. One example of reproductive isolation, hybrid male sterility, may be caused by genetic incompatibility between diverged genetic factors in two distinct populations. Genetic factors involved in hybrid male sterility are disproportionately located on the X chromosome. Recent studies showing the evolutionary divergence in gene regulatory networks or epigenetic effects suggest that the genetic incompatibilities occur at much broader levels than had previously been thought (e.g., incompatibility of protein-protein interactions). The latest studies suggest that evolutionary divergence of transcriptional regulation causes genetic incompatibilities in hybrid animals, and that such incompatibilities preferentially involve X-linked genes. In this review, we focus on recent progress in understanding hybrid sterility in mice, including our studies, and we discuss the evolutionary significance of regulatory divergence for speciation.

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

PubMed Central

Lankau, Richard A; Strauss, Sharon Y

2011-01-01

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

Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein.

PubMed

Clifton, Ben E; Kaczmarski, Joe A; Carr, Paul D; Gerth, Monica L; Tokuriki, Nobuhiko; Jackson, Colin J

2018-04-23

The emergence of enzymes through the neofunctionalization of noncatalytic proteins is ultimately responsible for the extraordinary range of biological catalysts observed in nature. Although the evolution of some enzymes from binding proteins can be inferred by homology, we have a limited understanding of the nature of the biochemical and biophysical adaptations along these evolutionary trajectories and the sequence in which they occurred. Here we reconstructed and characterized evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase. We show how the intrinsic reactivity of a desolvated general acid was harnessed by a series of mutations radiating from the active site, which optimized enzyme-substrate complementarity and transition-state stabilization and minimized sampling of noncatalytic conformations. Our work reveals the molecular evolutionary processes that underlie the emergence of enzymes de novo, which are notably mirrored by recent examples of computational enzyme design and directed evolution.

A survey on evolutionary algorithm based hybrid intelligence in bioinformatics.

PubMed

Li, Shan; Kang, Liying; Zhao, Xing-Ming

2014-01-01

With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs) are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks.

Eocene evolution of whale hearing.

PubMed

Nummela, Sirpa; Thewissen, J G M; Bajpai, Sunil; Hussain, S Taseer; Kumar, Kishor

2004-08-12

The origin of whales (order Cetacea) is one of the best-documented examples of macroevolutionary change in vertebrates. As the earliest whales became obligately marine, all of their organ systems adapted to the new environment. The fossil record indicates that this evolutionary transition took less than 15 million years, and that different organ systems followed different evolutionary trajectories. Here we document the evolutionary changes that took place in the sound transmission mechanism of the outer and middle ear in early whales. Sound transmission mechanisms change early on in whale evolution and pass through a stage (in pakicetids) in which hearing in both air and water is unsophisticated. This intermediate stage is soon abandoned and is replaced (in remingtonocetids and protocetids) by a sound transmission mechanism similar to that in modern toothed whales. The mechanism of these fossil whales lacks sophistication, and still retains some of the key elements that land mammals use to hear airborne sound.

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

PubMed

Kisdi, Éva

2015-04-01

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

Determining Selection across Heterogeneous Landscapes: A Perturbation-Based Method and Its Application to Modeling Evolution in Space.

PubMed

Wickman, Jonas; Diehl, Sebastian; Blasius, Bernd; Klausmeier, Christopher A; Ryabov, Alexey B; Brännström, Åke

2017-04-01

Spatial structure can decisively influence the way evolutionary processes unfold. To date, several methods have been used to study evolution in spatial systems, including population genetics, quantitative genetics, moment-closure approximations, and individual-based models. Here we extend the study of spatial evolutionary dynamics to eco-evolutionary models based on reaction-diffusion equations and adaptive dynamics. Specifically, we derive expressions for the strength of directional and stabilizing/disruptive selection that apply both in continuous space and to metacommunities with symmetrical dispersal between patches. For directional selection on a quantitative trait, this yields a way to integrate local directional selection across space and determine whether the trait value will increase or decrease. The robustness of this prediction is validated against quantitative genetics. For stabilizing/disruptive selection, we show that spatial heterogeneity always contributes to disruptive selection and hence always promotes evolutionary branching. The expression for directional selection is numerically very efficient and hence lends itself to simulation studies of evolutionary community assembly. We illustrate the application and utility of the expressions for this purpose with two examples of the evolution of resource utilization. Finally, we outline the domain of applicability of reaction-diffusion equations as a modeling framework and discuss their limitations.

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

PubMed

Peña, Jorge; Rochat, Yannick

2012-01-01

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

Evolution of density-dependent movement during experimental range expansions.

PubMed

Fronhofer, E A; Gut, S; Altermatt, F

2017-12-01

Range expansions and biological invasions are prime examples of transient processes that are likely impacted by rapid evolutionary changes. As a spatial process, range expansions are driven by dispersal and movement behaviour. Although it is widely accepted that dispersal and movement may be context-dependent, for instance density-dependent, and best represented by reaction norms, the evolution of density-dependent movement during range expansions has received little experimental attention. We therefore tested current theory predicting the evolution of increased movement at low densities at range margins using highly replicated and controlled range expansion experiments across multiple genotypes of the protist model system Tetrahymena thermophila. Although rare, we found evolutionary changes during range expansions even in the absence of initial standing genetic variation. Range expansions led to the evolution of negatively density-dependent movement at range margins. In addition, we report the evolution of increased intrastrain competitive ability and concurrently decreased population growth rates in range cores. Our findings highlight the importance of understanding movement and dispersal as evolving reaction norms and plastic life-history traits of central relevance for range expansions, biological invasions and the dynamics of spatially structured systems in general. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Locus coeruleus and dopaminergic consolidation of everyday memory

PubMed Central

Takeuchi, Tomonori; Duszkiewicz, Adrian J.; Sonneborn, Alex; Spooner, Patrick A.; Yamasaki, Miwako; Watanabe, Masahiko; Smith, Caroline C.; Fernández, Guillén; Deisseroth, Karl; Greene, Robert W.; Morris, Richard G. M.

2016-01-01

Summary The retention of episodic-like memory is enhanced, in humans and animals, when something novel happens shortly before or after encoding. Using an everyday memory task in mice, we sought the neurons mediating this dopamine-dependent novelty effect, previously thought to originate exclusively from the tyrosine hydroxylase-expressing (TH+) neurons in the ventral tegmental area (VTA). We report that neuronal firing in the locus coeruleus (LC) is especially sensitive to environmental novelty, LC-TH+ neurons project more profusely than VTA-TH+ neurons to the hippocampus, optogenetic activation of LC-TH+ neurons mimics the novelty effect, and this novelty-associated memory enhancement is unaffected by VTA inactivation. Surprisingly, two effects of LC-TH+ photoactivation are sensitive to hippocampal D1/D5 receptor blockade and resistant to adrenoceptors blockade – memory enhancement and long lasting potentiation of synaptic transmission in CA1 ex vivo. Thus, LC-TH+ neurons can mediate post-encoding memory enhancement in a manner consistent with possible co-release of dopamine in hippocampus. PMID:27602521

Differential Hemodynamic Response in Affective Circuitry with Aging: An fMRI Study of Novelty, Valence, and Arousal

PubMed Central

Moriguchi, Yoshiya; Negreira, Alyson; Weierich, Mariann; Dautoff, Rebecca; Dickerson, Bradford C.; Wright, Christopher I.; Barrett, Lisa Feldman

2011-01-01

Emerging evidence indicates that stimulus novelty is affectively potent and reliably engages the amygdala and other portions of the affective workspace in the brain. Using fMRI, we examined whether novel stimuli remain affectively salient across the lifespan, and therefore, whether novelty processing—a potentially survival-relevant function—is preserved with aging. Nineteen young and 22 older healthy adults were scanned during observing novel and familiar affective pictures while estimating their own subjectively experienced aroused levels. We investigated age-related difference of magnitude of activation, hemodynamic time course, and functional connectivity of BOLD responses in the amygdala. Although there were no age-related differences in the peak response of the amygdala to novelty, older individuals showed a narrower, sharper (i.e., “peakier”) hemodynamic time course in response to novel stimuli, as well as decreased connectivity between the left amygdala and the affective areas including orbito-frontal regions. These findings have relevance for understanding age-related differences in memory and affect regulation. PMID:20521849

HORMONAL AND PHYSICAL MARKERS OF PUBERTY AND THEIR RELATIONSHIP TO ADOLESCENT-TYPICAL NOVELTY-DIRECTED BEHAVIOR

PubMed Central

Vetter-O’Hagen, Courtney S.; Spear, Linda P.

2011-01-01

The extent to which characteristic adolescent behaviors are associated with pubertal changes or driven by more general, puberty-independent developmental alterations is largely unknown. Using physiological and hormonal markers of puberty, this experiment characterized pubertal timing across adolescence and examined the relationships among these variables and novelty-directed behaviors. Males and females were tested for response to novelty at P28, P32, P36, P40, P44, P48 and P75, and examined for balano-preputial skinfold separation and sperm presence (males) or vaginal opening (females), followed by blood collection for hormonal assessments. Despite earlier pubertal maturation in females, with maturation generally completed by P36 in females and P44 in males, novelty-directed behavior peaked at P32 and P36 in both sexes, and was unrelated to pubertal measures. These data support the suggestion that the ontogenetic peak in this behavior during adolescence is not notably puberty-dependent. PMID:21953609

Locus coeruleus and dopaminergic consolidation of everyday memory.

PubMed

Takeuchi, Tomonori; Duszkiewicz, Adrian J; Sonneborn, Alex; Spooner, Patrick A; Yamasaki, Miwako; Watanabe, Masahiko; Smith, Caroline C; Fernández, Guillén; Deisseroth, Karl; Greene, Robert W; Morris, Richard G M

2016-09-15

The retention of episodic-like memory is enhanced, in humans and animals, when something novel happens shortly before or after encoding. Using an everyday memory task in mice, we sought the neurons mediating this dopamine-dependent novelty effect, previously thought to originate exclusively from the tyrosine-hydroxylase-expressing (TH + ) neurons in the ventral tegmental area. Here we report that neuronal firing in the locus coeruleus is especially sensitive to environmental novelty, locus coeruleus TH + neurons project more profusely than ventral tegmental area TH + neurons to the hippocampus, optogenetic activation of locus coeruleus TH + neurons mimics the novelty effect, and this novelty-associated memory enhancement is unaffected by ventral tegmental area inactivation. Surprisingly, two effects of locus coeruleus TH + photoactivation are sensitive to hippocampal D 1 /D 5 receptor blockade and resistant to adrenoceptor blockade: memory enhancement and long-lasting potentiation of synaptic transmission in CA1 ex vivo. Thus, locus coeruleus TH + neurons can mediate post-encoding memory enhancement in a manner consistent with possible co-release of dopamine in the hippocampus.

Blunted ventral striatal responses to anticipated rewards foreshadow problematic drug use in novelty-seeking adolescents

PubMed Central

Büchel, Christian; Peters, Jan; Banaschewski, Tobias; Bokde, Arun L. W.; Bromberg, Uli; Conrod, Patricia J.; Flor, Herta; Papadopoulos, Dimitri; Garavan, Hugh; Gowland, Penny; Heinz, Andreas; Walter, Henrik; Ittermann, Bernd; Mann, Karl; Martinot, Jean-Luc; Paillère-Martinot, Marie-Laure; Nees, Frauke; Paus, Tomas; Pausova, Zdenka; Poustka, Luise; Rietschel, Marcella; Robbins, Trevor W.; Smolka, Michael N.; Gallinat, Juergen; Schumann, Gunter; Knutson, Brian; Arroyo, Mercedes; Artiges, Eric; Aydin, Semiha; Bach, Christine; Barbot, Alexis; Barker, Gareth; Bruehl, Ruediger; Cattrell, Anna; Constant, Patrick; Crombag, Hans; Czech, Katharina; Dalley, Jeffrey; Decideur, Benjamin; Desrivieres, Sylvane; Fadai, Tahmine; Fauth-Buhler, Mira; Feng, Jianfeng; Filippi, Irinia; Frouin, Vincent; Fuchs, Birgit; Gemmeke, Isabel; Genauck, Alexander; Hanratty, Eanna; Heinrichs, Bert; Heym, Nadja; Hubner, Thomas; Ihlenfeld, Albrecht; Ing, Alex; Ireland, James; Jia, Tianye; Jones, Jennifer; Jurk, Sarah; Kaviani, Mehri; Klaassen, Arno; Kruschwitz, Johann; Lalanne, Christophe; Lanzerath, Dirk; Lathrop, Mark; Lawrence, Claire; Lemaitre, Hervé; Macare, Christine; Mallik, Catherine; Mar, Adam; Martinez-Medina, Lourdes; Mennigen, Eva; de Carvahlo, Fabiana Mesquita; Mignon, Xavier; Millenet, Sabina; Miranda, Ruben; Müller, Kathrin; Nymberg, Charlotte; Parchetka, Caroline; Pena-Oliver, Yolanda; Pentilla, Jani; Poline, Jean-Baptiste; Quinlan, Erin Burke; Rapp, Michael; Ripke, Stephan; Ripley, Tamzin; Robert, Gabriel; Rogers, John; Romanowski, Alexander; Ruggeri, Barbara; Schmäl, Christine; Schmidt, Dirk; Schneider, Sophia; Schubert, Florian; Schwartz, Yannick; Sommer, Wolfgang; Spanagel, Rainer; Speiser, Claudia; Spranger, Tade; Stedman, Alicia; Stephens, Dai; Strache, Nicole; Ströhle, Andreas; Struve, Maren; Subramaniam, Naresh; Theobald, David; Vetter, Nora; Vulser, Helene; Weiss, Katharina; Whelan, Robert; Williams, Steve; Xu, Bing; Yacubian, Juliana; Yu, Tao; Ziesch, Veronika

2017-01-01

Novelty-seeking tendencies in adolescents may promote innovation as well as problematic impulsive behaviour, including drug abuse. Previous research has not clarified whether neural hyper- or hypo-responsiveness to anticipated rewards promotes vulnerability in these individuals. Here we use a longitudinal design to track 144 novelty-seeking adolescents at age 14 and 16 to determine whether neural activity in response to anticipated rewards predicts problematic drug use. We find that diminished BOLD activity in mesolimbic (ventral striatal and midbrain) and prefrontal cortical (dorsolateral prefrontal cortex) regions during reward anticipation at age 14 predicts problematic drug use at age 16. Lower psychometric conscientiousness and steeper discounting of future rewards at age 14 also predicts problematic drug use at age 16, but the neural responses independently predict more variance than psychometric measures. Together, these findings suggest that diminished neural responses to anticipated rewards in novelty-seeking adolescents may increase vulnerability to future problematic drug use. PMID:28221370

NodePM: A Remote Monitoring Alert System for Energy Consumption Using Probabilistic Techniques

PubMed Central

Filho, Geraldo P. R.; Ueyama, Jó; Villas, Leandro A.; Pinto, Alex R.; Gonçalves, Vinícius P.; Pessin, Gustavo; Pazzi, Richard W.; Braun, Torsten

2014-01-01

In this paper, we propose an intelligent method, named the Novelty Detection Power Meter (NodePM), to detect novelties in electronic equipment monitored by a smart grid. Considering the entropy of each device monitored, which is calculated based on a Markov chain model, the proposed method identifies novelties through a machine learning algorithm. To this end, the NodePM is integrated into a platform for the remote monitoring of energy consumption, which consists of a wireless sensors network (WSN). It thus should be stressed that the experiments were conducted in real environments different from many related works, which are evaluated in simulated environments. In this sense, the results show that the NodePM reduces by 13.7% the power consumption of the equipment we monitored. In addition, the NodePM provides better efficiency to detect novelties when compared to an approach from the literature, surpassing it in different scenarios in all evaluations that were carried out. PMID:24399157

Group-level traits can be studied with standard evolutionary theory.

PubMed

Scott-Phillips, Thomas C; Dickins, Thomas E

2014-06-01

Smaldino's target article draws on and seeks to add to a literature that has partially rejected orthodox, gene-centric evolutionary theory. However, orthodox theory has much to say about group-level traits. The target article does not reference or refute these views, and provides no explicit arguments for this narrow approach. In this commentary we: (i) give two examples of topics that the target article might and probably should have discussed (cultural epidemiology and the psychology of individual differences); and (ii) argue that the orthodox approach has much more to say about the emergence of group-level traits than the target article recognises, or gives credit for.

Evolutionary turnover of kinetochore proteins: a ship of Theseus?

PubMed Central

Drinnenberg, Ines A.; Henikoff, Steven; Malik, Harmit S.

2016-01-01

Summary The kinetochore is a multi-protein complex that mediates the attachment of a eukaryotic chromosome to the mitotic spindle. The protein composition of kinetochores is similar across species as divergent as yeast and human. However, recent findings have revealed an unexpected degree of compositional diversity in kinetochores. For example, kinetochore proteins that are essential in some species have been lost in others, whereas new kinetochore proteins have emerged in other lineages. Even in lineages with similar kinetochore composition, individual kinetochore proteins have functionally diverged to acquire either essential or redundant roles. Thus, despite functional conservation, the repertoire of kinetochore proteins has undergone recurrent evolutionary turnover. PMID:26877204

An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology.

PubMed

Pennell, Matthew W; Harmon, Luke J

2013-06-01

Recent innovations in phylogenetic comparative methods (PCMs) have spurred a renaissance of research into the causes and consequences of large-scale patterns of biodiversity. In this paper, we review these advances. We also highlight the potential of comparative methods to integrate across fields and focus on three examples where such integration might be particularly valuable: quantitative genetics, community ecology, and paleobiology. We argue that PCMs will continue to be a key set of tools in evolutionary biology, shedding new light on how evolutionary processes have shaped patterns of biodiversity through deep time. © 2013 New York Academy of Sciences.

Adaptive evolution of body size subject to indirect effect in trophic cascade system.

PubMed

Wang, Xin; Fan, Meng; Hao, Lina

2017-09-01

Trophic cascades represent a classic example of indirect effect and are wide-spread in nature. Their ecological impact are well established, but the evolutionary consequences have received even less theoretical attention. We theoretically and numerically investigate the trait (i.e., body size of consumer) evolution in response to indirect effect in a trophic cascade system. By applying the quantitative trait evolutionary theory and the adaptive dynamic theory, we formulate and explore two different types of eco-evolutionary resource-consumer-predator trophic cascade model. First, an eco-evolutionary model incorporating the rapid evolution is formulated to investigate the effect of rapid evolution of the consumer's body size, and to explore the impact of density-mediate indirect effect on the population dynamics and trait dynamics. Next, by employing the adaptive dynamic theory, a long-term evolutionary model of consumer body size is formulated to evaluate the effect of long-term evolution on the population dynamics and the effect of trait-mediate indirect effect. Those models admit rich dynamics that has not been observed yet in empirical studies. It is found that, both in the trait-mediated and density-mediated system, the body size of consumer in predator-consumer-resource interaction (indirect effect) evolves smaller than that in consumer-resource and predator-consumer interaction (direct effect). Moreover, in the density-mediated system, we found that the evolution of consumer body size contributes to avoiding consumer extinction (i.e., evolutionary rescue). The trait-mediate and density-mediate effects may produce opposite evolutionary response. This study suggests that the trophic cascade indirect effect affects consumer evolution, highlights a more comprehensive mechanistic understanding of the intricate interplay between ecological and evolutionary force. The modeling approaches provide avenue for study on indirect effects from an evolutionary perspective. Copyright © 2017 Elsevier B.V. All rights reserved.

Curiosity Search: Producing Generalists by Encouraging Individuals to Continually Explore and Acquire Skills throughout Their Lifetime.

PubMed

Stanton, Christopher; Clune, Jeff

2016-01-01

Natural animals are renowned for their ability to acquire a diverse and general skill set over the course of their lifetime. However, research in artificial intelligence has yet to produce agents that acquire all or even most of the available skills in non-trivial environments. One candidate algorithm for encouraging the production of such individuals is Novelty Search, which pressures organisms to exhibit different behaviors from other individuals. However, we hypothesized that Novelty Search would produce sub-populations of specialists, in which each individual possesses a subset of skills, but no one organism acquires all or most of the skills. In this paper, we propose a new algorithm called Curiosity Search, which is designed to produce individuals that acquire as many skills as possible during their lifetime. We show that in a multiple-skill maze environment, Curiosity Search does produce individuals that explore their entire domain, while a traditional implementation of Novelty Search produces specialists. However, we reveal that when modified to encourage intra-life behavioral diversity, Novelty Search can produce organisms that explore almost as much of their environment as Curiosity Search, although Curiosity Search retains a significant performance edge. Finally, we show that Curiosity Search is a useful helper objective when combined with Novelty Search, producing individuals that acquire significantly more skills than either algorithm alone.

Infants prefer the faces of strangers or mothers to morphed faces: an uncanny valley between social novelty and familiarity.

PubMed

Matsuda, Yoshi-Taka; Okamoto, Yoko; Ida, Misako; Okanoya, Kazuo; Myowa-Yamakoshi, Masako

2012-10-23

The 'uncanny valley' response is a phenomenon involving the elicitation of a negative feeling and subsequent avoidant behaviour in human adults and infants as a result of viewing very realistic human-like robots or computer avatars. It is hypothesized that this uncanny feeling occurs because the realistic synthetic characters elicit the concept of 'human' but fail to satisfy it. Such violations of our normal expectations regarding social signals generate a feeling of unease. This conflict-induced uncanny valley between mutually exclusive categories (human and synthetic agent) raises a new question: could an uncanny feeling be elicited by other mutually exclusive categories, such as familiarity and novelty? Given that infants prefer both familiarity and novelty in social objects, we address this question as well as the associated developmental profile. Using the morphing technique and a preferential-looking paradigm, we demonstrated uncanny valley responses of infants to faces of mothers (i.e. familiarity) and strangers (i.e. novelty). Furthermore, this effect strengthened with the infant's age. We excluded the possibility that infants detect and avoid traces of morphing. This conclusion follows from our finding that the infants equally preferred strangers' faces and the morphed faces of two strangers. These results indicate that an uncanny valley between familiarity and novelty may accentuate the categorical perception of familiar and novel objects.

Curiosity Search: Producing Generalists by Encouraging Individuals to Continually Explore and Acquire Skills throughout Their Lifetime

PubMed Central

Clune, Jeff

2016-01-01

Natural animals are renowned for their ability to acquire a diverse and general skill set over the course of their lifetime. However, research in artificial intelligence has yet to produce agents that acquire all or even most of the available skills in non-trivial environments. One candidate algorithm for encouraging the production of such individuals is Novelty Search, which pressures organisms to exhibit different behaviors from other individuals. However, we hypothesized that Novelty Search would produce sub-populations of specialists, in which each individual possesses a subset of skills, but no one organism acquires all or most of the skills. In this paper, we propose a new algorithm called Curiosity Search, which is designed to produce individuals that acquire as many skills as possible during their lifetime. We show that in a multiple-skill maze environment, Curiosity Search does produce individuals that explore their entire domain, while a traditional implementation of Novelty Search produces specialists. However, we reveal that when modified to encourage intra-life behavioral diversity, Novelty Search can produce organisms that explore almost as much of their environment as Curiosity Search, although Curiosity Search retains a significant performance edge. Finally, we show that Curiosity Search is a useful helper objective when combined with Novelty Search, producing individuals that acquire significantly more skills than either algorithm alone. PMID:27589267

Evolutionary history of the recruitment of conserved developmental genes in association to the formation and diversification of a novel trait.

PubMed

Shirai, Leila T; Saenko, Suzanne V; Keller, Roberto A; Jerónimo, Maria A; Brakefield, Paul M; Descimon, Henri; Wahlberg, Niklas; Beldade, Patrícia

2012-02-15

The origin and modification of novel traits are important aspects of biological diversification. Studies combining concepts and approaches of developmental genetics and evolutionary biology have uncovered many examples of the recruitment, or co-option, of genes conserved across lineages for the formation of novel, lineage-restricted traits. However, little is known about the evolutionary history of the recruitment of those genes, and of the relationship between them -for example, whether the co-option involves whole or parts of existing networks, or whether it occurs by redeployment of individual genes with de novo rewiring. We use a model novel trait, color pattern elements on butterfly wings called eyespots, to explore these questions. Eyespots have greatly diversified under natural and sexual selection, and their formation involves genetic circuitries shared across insects. We investigated the evolutionary history of the recruitment and co-recruitment of four conserved transcription regulators to the larval wing disc region where circular pattern elements develop. The co-localization of Antennapedia, Notch, Distal-less, and Spalt with presumptive (eye)spot organizers was examined in 13 butterfly species, providing the largest comparative dataset available for the system. We found variation between families, between subfamilies, and between tribes. Phylogenetic reconstructions by parsimony and maximum likelihood methods revealed an unambiguous evolutionary history only for Antennapedia, with a resolved single origin of eyespot-associated expression, and many homoplastic events for Notch, Distal-less, and Spalt. The flexibility in the (co-)recruitment of the targeted genes includes cases where different gene combinations are associated with morphologically similar eyespots, as well as cases where identical protein combinations are associated with very different phenotypes. The evolutionary history of gene (co-)recruitment is consistent with both divergence from a recruited putative ancestral network, and with independent co-option of individual genes. The diversity in the combinations of genes expressed in association with eyespot formation does not parallel diversity in characteristics of the adult phenotype. We discuss these results in the context of inferring homology. Our study underscores the importance of widening the representation of phylogenetic, morphological, and genetic diversity in order to establish general principles about the mechanisms behind the evolution of novel traits.

phyloXML: XML for evolutionary biology and comparative genomics

PubMed Central

Han, Mira V; Zmasek, Christian M

2009-01-01

Background 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. Results 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. Conclusion 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 . PMID:19860910

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-12-01

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

Indexing the Comics: A Librarian's Perspective on Comics Research.

ERIC Educational Resources Information Center

Scott, Randall W.

The potential for computers in indexing popular fiction study materials is discussed, and specific examples of comic book indexing are provided through descriptions of projects and a bibliography. The 4-stage evolutionary development of popular fiction studies includes: (1) discovery and reading; (2) bibliography and collecting; (3) cataloging and…