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  1. ; ; ; ; ; ; ; ; ; ; et al ( , Nature Communications)
    null (Ed.)
    Abstract Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken ( Gallus gallus ), pig ( Sus scrofa ), and cattle ( Bos taurus ). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources. 
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  2. ; ; ; ( , Journal of Ecology)
    Abstract

    By causing phenological shifts that vary among species, climate change is altering time envelopes for species interactions, often with unexpected demographic consequences. Indirect interactions, like apparent competition and apparent facilitation, are especially likely to change in duration because they involve multiple interactors, increasing the likelihood of asynchronous phenological shifts by at least one interactor. Thus, we might observe ecological surprises if intermediaries of indirectly interacting species change their mediating behaviour.

    We explored this possibility in a plant–pollinator community that is likely to experience asynchronous phenological shifts. We advanced and delayed the flowering phenology of two ubiquitous exotic plants of western Washington prairies,Hypochaeris radicataandCytisus scoparius, relative to seven native perennial forb species whose phenologies remained unmanipulated. These species interact indirectly through shared pollinators, whose foraging behaviour influences plant reproductive success. We quantified impacts of experimental phenological shifts on seedset, pollinator visitation rates and visiting pollinator composition relative to an unmanipulated control. We first verified that unmanipulated indirect interactions between native and exotic plants were strong, ranging from facilitative to competitive.

    Seedset of native plants was strongly affected by changes in exotic flowering phenology, but the magnitude and direction of effects were not predicted by the nature of the original indirect interaction (facilitative vs. neutral vs. competitive) or the change in interaction duration. The relationship between pollinator visitation and seedset changed for most species, though changes in pollinator visitation rate and pollinator composition were not as widespread as effects on native seedset.

    Synthesis. Changes in pollinator foraging behaviour in response to changes in available floral resources are probably responsible for the unexpected effects we observed. Asynchronous phenological shifts have the potential to produce large and unexpected effects on reproductive success via indirect interactions.

     
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