http://precedings.nature.com/subjects/evolutionary-biology/ Recently posted documents in Evolutionary Biology Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3955/version/1 The drones of dwarf honeybees assemble at the drone congregation areas close to small trees with dense leafage at the heights between 2 to 4 meters. http://precedings.nature.com/documents/3955/version/1 Fri, 06 Nov 2009 14:21:06 UTC Drone congregation areas of red dwarf honeybee, Apis florea hdl:10101/npre.2009.3955.1 2009-11-06 Narayanappa Nagaraja Nature Precedings 2009-11-06T14:21:06Z Manuscript Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3892/version/1 Serial endosymbiosis theory provides a unifying paradigm for examining the interaction of cognitive modules at vastly different scales of biological, social, and cultural organization. A trivial but not unimportant model associates a dual information source with a broad class of cognitive processes, and punctuated phenomena akin to phase transitions in physical systems, and associated coevolutionary processes, emerge as consequences of the homology between information source uncertainty and free energy density. The dynamics, including patterns of punctuation similar to ecosystem resilience transitions, are largely dominated by the availability of ‘Roman roads’ constituting channels for the transmission of information between modules. http://precedings.nature.com/documents/3892/version/1 Mon, 02 Nov 2009 09:47:58 UTC Roman roads: The hierarchical endosymbiosis of cognitive modules hdl:10101/npre.2009.3892.1 2009-11-02 Rodrick Wallace Nature Precedings 2009-11-02T09:47:58Z Manuscript Ecology Neuroscience Earth & Environment Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3839.1 In order to detailed study of Echinoids, some samples are collected from Brown limestone member of Seimare from Gurpi Formation with 213 meter thickness which located in the vicinity of Ilam province; settling over Ilam Formation continuously. Paleontological results indicated Campanian – maastrichtian age at this section. Detailed analyse of the 300 samples led to recognition of Bivalve especially Bivalve of Lofa, Brachiopods and five species of Echinoids such as: Salenia nutrix, Globator bleicheri، Orthopsis miliarisi, Goniopygus superbus, Conulus douville http://dx.doi.org/10.1038/npre.2009.3839.1 Mon, 02 Nov 2009 09:42:00 UTC Study of Echinoids of Gurpi formation, Iran doi:10.1038/npre.2009.3839.1 2009-11-02 Behnaz Balmaki Nature Precedings 2009-11-02T09:42:00Z Manuscript Earth & Environment Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3922/version/1 Perfect behaviours that are optimal to the environment an agent operates within rarely exist in real animals or in robotic systems. The costs (be they biological or economic) of building sensors and processing the information they capture become excessive compared to the small advantages that occur from the modifications of behaviour. Many self-organised systems are thought to change their properties as a result of changes in individual behaviour. Here, using both natural systems and computer simulations, we demonstrate that intertidal snail aggregations slightly decrease in size when individuals forage for shorter periods due to hotter and more desiccating conditions – a non-optimal behaviour for the snails since aggregation reduces desiccation stress. However, this decrease only occurs in simple experimental systems (and simulations of these systems). When studied in their more complex natural environment, and when simulated in such an environment, using the same information-processing behaviours, no difference in aggregation behaviour was found between hot and cool days. These results give an indication of the robustness of self-organised systems to changes in individual-level behaviour. They demonstrate that information processing capabilities of self-organised groups may not need to be as great as for agents that perform solitary tasks, and also that oversimplified tests of swarm intelligence may not give a true indication of how tasks may be performed in a more complex environment. http://precedings.nature.com/documents/3922/version/1 Fri, 30 Oct 2009 20:30:29 UTC Robustness of self-organised systems to changes in individual level behaviour: an example from real and simulated self-organised snail aggregations hdl:10101/npre.2009.3922.1 2009-10-30 Richard Stafford Nature Precedings 2009-10-30T20:30:29Z Manuscript Biotechnology Ecology Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3915/version/1 Much literature invokes natural selection to explain the pervasive deficit in the average lifespan of men compared to women.1 The explanation assumes that mothers, not fathers, provisioned children over much of human existence, and that women who lived long enough to help their children and grand children survive to reproductive age had more grandchildren and great-grandchildren than did shorter-lived women.2 Although this argument implies that natural selection would conserve mutations that conferred longevity on mothers but not fathers,3,4 it offers no explanation of the considerable changes over historic time in the male longevity deficit thereby implying that these arise solely from culture.5 I show, however, that natural selection in utero empirically predicts variability over time in the deficit. This mechanism spontaneously aborts less fit fetuses during stressful times and reportedly selects more against males than females. My finding suggests that natural selection interacts with culture to predictably affect both the life span and sex ratio of contemporary human populations. http://precedings.nature.com/documents/3915/version/1 Thu, 29 Oct 2009 13:30:34 UTC Natural Selection In Utero Contributes to the Male Longevity Deficit in Contemporary Human Populations hdl:10101/npre.2009.3915.1 2009-10-29 Ralph Catalano Nature Precedings 2009-10-29T13:30:34Z Manuscript Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3913.1 A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The effectiveness of the approach is demonstrated on a series of benchmark tests. http://dx.doi.org/10.1038/npre.2009.3913.1 Thu, 29 Oct 2009 10:09:24 UTC Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico doi:10.1038/npre.2009.3913.1 2009-10-29 Nature Precedings 2009-10-29T10:09:24Z Manuscript Biotechnology Developmental Biology Genetics & Genomics Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3902/version/1 Generalizing Landau’s spontaneous symmetry breaking arguments using the standard groupoid approach to stereochemistry allows reconsideration of the origin of biological homochirality. On Earth, limited metabolic free energy density may have served as a low temperature analog to ‘freeze’ the system into the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process licked in this initial condition. Astrobiological outcomes, in the presence of higher initial metabolic free energy densities, could well be considerably richer, perhaps of mixed chirality. One result would be a complicated distribution of biological chirality across a statistically large sample of extraterrestrial stereochemistry, in contrast with a recent prediction of a racemic average. http://precedings.nature.com/documents/3902/version/1 Mon, 26 Oct 2009 17:52:17 UTC On biological homochirality hdl:10101/npre.2009.3902.1 2009-10-26 Rodrick Wallace Nature Precedings 2009-10-26T17:52:17Z Manuscript Chemistry Earth & Environment Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3901/version/1 Although the natural history of the Caribbean is better understood now than ever before, a general biogeographic explanation for the peculiar faunal composition of the islands remains elusive. New molecular phylogenetic and divergence analyses presented here show that dispersal and diversification in Caribbean bats are synchronous with sea level drops during inter-stage transitions in the Miocene. The phylogenies indicate that several continental bat species descended from West Indian ancestors, as the exceptionally low sea level of the Miocene transitions allowed for two-way biotic exchange between the islands and the continent. These results suggest a common mechanism underlies colonization and subsequent speciation in the Caribbean, and underscore the importance of geological history in all biogeographic scenarios, including dispersal. http://precedings.nature.com/documents/3901/version/1 Mon, 26 Oct 2009 14:04:29 UTC Earth History and the Evolution of Caribbean Bats hdl:10101/npre.2009.3901.1 2009-10-26 Liliana Dávalos Nature Precedings 2009-10-26T14:04:29Z Manuscript Earth & Environment Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3886/version/1 Viruses are the most abundant life forms and the repertoire of viral genes is greater than that of cellular genes. It is also evident that viruses have played a major role in driving cellular evolution, and yet, viruses are not part of mainstream biology, nor are they included in the Tree of Life. A reason for this major paradox in biology is the misleading dogma of viruses as viral particles and their enigmatic evolutionary origin. This article presents an alternative view about the nature of viruses based on their properties during the intracellular stage of their life cycle, when viruses express features comparable to those of many parasitic cellular species. Supporting this view about the nature of viruses is a novel hypothetical evolutionary model for their origin from parasitic cellular species that fused with their host cells. By losing their membrane and cellular structure within the host cell, these new types of parasitic species gained full access to precursors for the synthesis of their specific molecules and to the host’s information processing machineries, such as translation, which created unique parasitic and evolutionary opportunities. To identify viruses during their intracellular stage of their life cycle, in which their specific molecules are free or dispersed within the host cell, this paper introduces the concept of “molecular structure” and labels viruses as “molecular organisms.” Among the extant viruses, the life cycle of poxviruses and other complex viruses that fuse with their host cells provides compelling evidence for the fusion model. One of the most remarkable implications of fusion model is that new viral lineages originated from parasitic cellular species throughout the history of life, and that this process might still be active. Surprisingly, it appears that several parasitic cellular species are currently evolving into molecular organisms. More remarkably though, according to this model, several parasites that are currently classified as cellular organisms are in fact genuine molecular organisms. The current evidence for the fusion hypothesis is strong and it is fully testable using both experimental and phylogenetic approaches. The academic and research implications of this model, which supports the inclusion of viruses in the Tree of Life, are highly significant. Some of these implications are discussed in more detail in two other articles of this series, which presents a unifying model for the origin and evolution of cellular and viral domains, including the origin of life. http://precedings.nature.com/documents/3886/version/1 Fri, 23 Oct 2009 11:33:49 UTC The Origin and Evolution of Viruses as Molecular Organisms hdl:10101/npre.2009.3886.1 2009-10-23 Claudiu I. Bandea Nature Precedings 2009-10-23T11:33:49Z Manuscript Genetics & Genomics Microbiology Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3887/version/1 Transmissible spongiform encephalopathies (TSEs), or prion diseases, are a group of incurable neurodegenerative disorders, including Kuru and Creutzfeldt-Jakob disease in humans, “mad cow” disease in cattle, and scrapie in sheep. This paper presents structural, genetic, and evolutionary evidence supporting an endogenous TSE virus model that integrates the three major traditional views on the nature of TSE pathogens, the conventional virus view, the prion hypothesis, and the virino concept, into a novel conceptual and evolutionary framework. According to this model, the TSE pathogens are symbiotic endogenous viruses that inadvertently produce transmissible viral particles that lack the viral genome and are composed primarily of the viral prion protein (PrP). Production of defective viral particles that contain a partial genome or lack the viral genome entirely is a relatively common event in the life cycle of many viruses. Similar to the normal viral particles, which contain a genome, these defective viral particles can be transmitted to new host cells. Obviously, in the absence of viral genome, these protein-only viral particles cannot establish a productive infection. However, if these viral particles enter a host cell that carries the parental or a related virus and induce the production of similar protein-only particles, then they would appear as self-replicating, protein-only infectious pathogens if mistakenly taken out from the context of the viral life cycle. This misconception, which is rooted into the current dogma of viruses as viral particles, led to the development of the prion theory. The endogenous TSE virus model is consistent with the TSE data and offers solutions to many enigmatic features associated with TSE, including the function of PrP that, despite more than two decades of TSE research conducted primarily within the framework of the prion hypothesis, is still not known. According to the TSE endogenous virus model, PrP is the protein of an endogenous virus that has co-evolved with their vertebrate hosts by providing a protective function against pathogenic viruses. The evidence for the endogenous TSE virus model and for the antiviral protective function of PrP is strong, and they are fully open to additional experimental testing. The endogenous virus model opens the TSE research field to new interpretations and directions, both in basic research and in associated biomedical and public health fields, and could lead to development of new diagnostic and therapeutic approaches. http://precedings.nature.com/documents/3887/version/1 Fri, 23 Oct 2009 11:27:57 UTC Endogenous Viral Etiology of Prion Diseases hdl:10101/npre.2009.3887.1 2009-10-23 Claudiu I. Bandea Nature Precedings 2009-10-23T11:27:57Z Manuscript Microbiology Neuroscience Evolutionary Biology http://creativecommons.org/licenses/by/3.0/