36,738 research outputs found

    Ecological Genomics of Nematode Community Interactions: Model and Non-model Approaches

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    The effects of human-induced environmental change are evident at multiple levels of biological organization. To date, most environmental change studies have focused on effects at the ecosystem, community, and organismal levels. However, the ultimate controls of biological responses are located in the genome. Thus, genetic and genomic studies of organismal responses to environmental changes are necessary. Recent advances in genome analysis now make such analyses possible. In this chapter we describe a research approach and program that can begin to span this gap by using genome-enabled approaches to characterize organismal changes and then employing a genetically tractable model organism to identify genes involved in the response to environmental perturbations

    Intraspecific variability modulates interspecific variability in animal organismal stoichiometry.

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    Interspecific differences in organismal stoichiometry (OS) have been documented in a wide range of animal taxa and are of significant interest for understanding evolutionary patterns in OS. In contrast, intraspecific variation in animal OS has generally been treated as analytical noise or random variation, even though available data suggest intraspecific variability in OS is widespread. Here, we assess how intraspecific variation in OS affects inferences about interspecific OS differences using two co-occurring Neotropical fishes: Poecilia reticulata and Rivulus hartii. A wide range of OS has been observed within both species and has been attributed to environmental differences among stream systems. We assess the contributions of species identity, stream system, and the interactions between stream and species to variability in N:P, C:P, and C:N. Because predation pressure can impact the foraging ecology and life-history traits of fishes, we compare predictors of OS between communities that include predators, and communities where predators are absent. We find that species identity is the strongest predictor of N:P, while stream or the interaction of stream and species contribute more to the overall variation in C:P and C:N. Interspecific differences in N:P, C:P, and C:N are therefore not consistent among streams. The relative contribution of stream or species to OS qualitatively changes between the two predation communities, but these differences do not have appreciable effects in interspecific patterns. We conclude that although species identity is a significant predictor of OS, intraspecific OS is sometimes sufficient to overwhelm or obfuscate interspecific differences in OS

    The modern versus extended evolutionary synthesis : sketch of an intra-genomic gene's eye view for the evolutionary-genetic underpinning of epigenetic and developmental evolution

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    Studying the phenotypic evolution of organisms in terms of populations of genes and genotypes, the Modern Synthesis (MS) conceptualizes biological evolution in terms of 'inter-organismal' interactions among genes sitting in the different individual organisms that constitute a population. It 'black-boxes' the complex 'intra-organismic' molecular and developmental epigenetics mediating between genotypes and phenotypes. To conceptually integrate epigenetics and evo-devo into evolutionary theory, advocates of an Extended Evolutionary Synthesis (EES) argue that the MS's reductive gene-centrism should be abandoned in favor of a more inclusive organism-centered approach. To push the debate to a new level of understanding, we introduce the evolutionary biology of 'intra-genomic conflict' (IGC) to the controversy. This strategy is based on a twofold rationale. First, the field of IGC is both ‘gene-centered’ and 'intra-organismic' and, as such, could build a bridge between the gene-centered MS and the intra-organismic fields of epigenetics and evo-devo. And second, it is increasingly revealed that IGC plays a significant causal role in epigenetic and developmental evolution and even in speciation. Hence, to deal with the ‘discrepancy’ between the ‘gene-centered’ MS and the ‘intra-organismic’ fields of epigenetics and evo-devo, we sketch a conceptual solution in terms of ‘intra-genomic conflict and compromise’ – an ‘intra-genomic gene’s eye view’ that thinks in terms of intra-genomic ‘evolutionarily stable strategies’ (ESSs) among numerous and various DNA regions and elements – to evolutionary-genetically underwrite both epigenetic and developmental evolution, as such questioning the ‘gene-de-centered’ stance put forward by EES-advocates

    Larval dispersal in a changing ocean with an emphasis on upwelling regions

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    Dispersal of benthic species in the sea is mediated primarily through small, vulnerable larvae that must survive minutes to months as members of the plankton community while being transported by strong, dynamic currents. As climate change alters ocean conditions, the dispersal of these larvae will be affected, with pervasive ecological and evolutionary consequences. We review the impacts of oceanic changes on larval transport, physiology, and behavior. We then discuss the implications for population connectivity and recruitment and evaluate life history strategies that will affect susceptibility to the effects of climate change on their dispersal patterns, with implications for understanding selective regimes in a future ocean. We find that physical oceanographic changes will impact dispersal by transporting larvae in different directions or inhibiting their movements while changing environmental factors, such as temperature, pH, salinity, oxygen, ultraviolet radiation, and turbidity, will affect the survival of larvae and alter their behavior. Reduced dispersal distance may make local adaptation more likely in well-connected populations with high genetic variation while reduced dispersal success will lower recruitment with implications for fishery stocks. Increased dispersal may spur adaptation by increasing genetic diversity among previously disconnected populations as well as increasing the likelihood of range expansions. We hypothesize that species with planktotrophic (feeding), calcifying, or weakly swimming larvae with specialized adult habitats will be most affected by climate change. We also propose that the adaptive value of retentive larval behaviors may decrease where transport trajectories follow changing climate envelopes and increase where transport trajectories drive larvae toward increasingly unsuitable conditions. Our holistic framework, combined with knowledge of regional ocean conditions and larval traits, can be used to produce powerful predictions of expected impacts on larval dispersal as well as the consequences for connectivity, range expansion, or recruitment. Based on our findings, we recommend that future studies take a holistic view of dispersal incorporating biological and oceanographic impacts of climate change rather than solely focusing on oceanography or physiology. Genetic and paleontological techniques can be used to examine evolutionary impacts of altered dispersal in a future ocean, while museum collections and expedition records can inform modern-day range shifts

    Not One, Not Two: Toward an Ontology of Pregnancy

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    Basic understandings of subjectivity are derived from the principles of masculine embodiment such as temporal stability and singularity. But pregnancy challenges such understandings because it represents a sort of splitting of the body. In the pregnant situation, a subject may experience herself as both herself and an other, as well as neither herself nor an other. This is logically untenable—an impossibility. If our discourse depends on singular, fixed referents, then what paradigms of identity are available to the pregnant subject? What could be the pregnant subject's ontology? Eric Bapteste and John Dupré offer the idea that organisms are processual beings. In their view, the ecological interrelationships between the objects of biology are defining, and render them dynamic processes, rather than stable things. Does Bapteste and Dupré’s processual ontological account accommodate pregnant organisms, including pregnant people? Here, I analyze the processual account and determine whether it can accommodate the phenomenon of pregnancy. I find that a processual ontology captures a great deal about pregnant embodiment and is a significant improvement over Cartesian and anti-metaphysical accounts. However, in order to accommodate pregnancy, what we still need from an ontology is the inclusion of subjectivity

    Lethal Mutagenesis in Viruses and Bacteria

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    Here we study how mutations which change physical properties of cell proteins (stability) impact population survival and growth. In our model the genotype is presented as a set of N numbers, folding free energies of cells N proteins. Mutations occur upon replications so that stabilities of some proteins in daughter cells differ from those in parent cell by random amounts drawn from experimental distribution of mutational effects on protein stability. The genotype-phenotype relationship posits that unstable proteins confer lethal phenotype to a cell and in addition the cells fitness (duplication rate) is proportional to the concentration of its folded proteins. Simulations reveal that lethal mutagenesis occurs at mutation rates close to 7 mutations per genome per replications for RNA viruses and about half of that for DNA based organisms, in accord with earlier predictions from analytical theory and experiment. This number appears somewhat dependent on the number of genes in the organisms and natural death rate. Further, our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. Our model predicts that species with high mutation rates, tend to have less stable proteins compared to species with low mutation rate

    Do cladistic and morphometric data capture common patterns of morphological disparity?

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    The distinctly non-random diversity of organismal form manifests itself in discrete clusters of taxa that share a common body plan. As a result, analyses of disparity require a scalable comparative framework. The difficulties of applying geometric morphometrics to disparity analyses of groups with vastly divergent body plans are overcome partly by the use of cladistic characters. Character-based disparity analyses have become increasingly popular, but it is not clear how they are affected by character coding strategies or revisions of primary homology statements. Indeed, whether cladistic and morphometric data capture similar patterns of morphological variation remains a moot point. To address this issue, we employ both cladistic and geometric morphometric data in an exploratory study of disparity focussing on caecilian amphibians. Our results show no impact on relative intertaxon distances when different coding strategies for cladistic characters were used or when revised concepts of homology were considered. In all instances, we found no statistically significant difference between pairwise Euclidean and Procrustes distances, although the strength of the correlation among distance matrices varied. This suggests that cladistic and geometric morphometric data appear to summarize morphological variation in comparable ways. Our results support the use of cladistic data for characterizing organismal disparity