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Audio versions of bioRxiv paper abstracts

    The Genetic Variation Landscape of African Swine Fever Virus Reveals Frequent Positive Selection on Amino Acid Replacements

    The Genetic Variation Landscape of African Swine Fever Virus Reveals Frequent Positive Selection on Amino Acid Replacements

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.08.12.249045v1?rss=1

    Authors: Bao, Y.-J., Qiu, J., Rodriguez, F., Qiu, H.-J.

    Abstract:
    African swine fever virus (ASFV) is a lethal disease agent that causes high mortality in swine population and devastating loss in swine industries. The development of efficacious vaccines has been hindered by the knowledge gap in genetic properties of ASFV and the interface of virus-host interactions. In this study, we performed a genetic study of ASFV aiming to profile the variation landscape and identify genetic factors with signatures of positive selection and relevance to virus-host interactions. To achieve this goal, we developed a new tool "SweepCluster" for systematic identification of selective sweep. Our data reveals a high level of genetic variability of ASFV shaped by both diversifying selection and selective sweep. The selection signatures are widely distributed across the genome with the diversifying selection falling within 29 genes and selection sweep within 25 genes. Further examination of the structure properties reveals the link of the selection signatures with virus-host interactions. Specifically, we discovered a site at 157th of the antigen protein EP402R under diversifying selection located in the cytotoxic T-cell epitope involved in the serotype-specific T-cell response. Moreover, we reported 24 novel candidate genes with relevance to virus-host interactions. By integrating the candidate genes with selection signatures into a unified framework of interactions between ASFV and hosts, we showed that those genes are involved in multiple processes of host immune evasion and virus life cycles, and may play crucial roles in circumventing host defense systems and enhancing adaptive fitness.

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    Evolution of Chi motifs in Proteobacteria

    Evolution of Chi motifs in Proteobacteria

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.08.13.249359v1?rss=1

    Authors: Bobay, L.-M., Buton, A. J.

    Abstract:
    Homologous recombination is a key pathway found in nearly all bacterial taxa. The recombination complex allows bacteria to repair DNA double strand breaks but also promotes adaption through the exchange of DNA between cells. In Proteobacteria, this process is mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi to initiate recombination. The Chi motif has been characterized in Escherichia coli and analogous sequences have been found in several other species from diverse families, suggesting that this mode of action is widespread across bacteria. However, the sequences of Chi-like motifs are known for only five bacterial species: E. coli, Haemophilus influenzae, Bacillus subtilis, Lactococcus lactis and Staphylococcus aureus. In this study we detected putative Chi motifs in a large dataset of Proteobacteria and we identified four additional motifs sharing high sequence similarity and similar properties to the Chi motif of E. coli in 85 species of Proteobacteria. Most Chi motifs were detected in Enterobacteriaceae and this motif appears well conserved in this family. However, we did not detect Chi motifs for the majority of Proteobacteria, suggesting that different motifs are used in these species. Altogether these results substantially expand our knowledge on the evolution of Chi motifs and on the recombination process in bacteria.

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    Temporal instability of lake charr phenotypes: synchronicity of growth rates and morphology linked to environmental variables?

    Temporal instability of lake charr phenotypes: synchronicity of growth rates and morphology linked to environmental variables?

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.08.13.249557v1?rss=1

    Authors: Chavarie, L., Voelker, S., Hansen, M., Bronte, C., Muir, A., Zimmerman, M., Krueger, c.

    Abstract:
    Pathways through which phenotypic variation arises among individuals arise can be complex. One assumption often made in relation to intraspecific diversity is that the stability or predictability of the environment will interact with expression of the underlying phenotypic variation. To address biological complexity below the species level, we investigated variability across years in morphology and annual growth increments between and within two sympatric lake charr ecotypes in Rush Lake, USA. We found a rapid phenotypic shift in body and head shape within a decade. The magnitude and direction of the observed phenotypic change was consistent in both ecotypes, which suggests similar pathways caused the temporal variation over time. Over the same time period, annual growth increments declined for both lake charr ecotypes and corresponded with a consistent phenotypic shift of each ecotype. Despite ecotype-specific annual growth changes in response to winter conditions, the observed annual growth shift for both ecotypes was linked, to some degree, with variation in the environment. Particularly, a declining trend in regional cloud cover was associated with an increase of early stage (age 1-3) annual growth for lake charr of Rush Lake. Underlying mechanisms causing reduced growth rates and constrained morphological modulation are not fully understood. An improved knowledge of the biology hidden within the expression of phenotypic variation promises to clarify our understanding of temporal morphological diversity and instability.

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    Culture volume influences the dynamics of adaptation under long-term stationary phase

    Culture volume influences the dynamics of adaptation under long-term stationary phase

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.08.13.249599v1?rss=1

    Authors: Gross, J., Avrani, S., Katz, S., Hershberg, R.

    Abstract:
    Escherichia coli and many other bacterial species, which are incapable of sporulation, can nevertheless survive within resource exhausted media by entering a state termed long-term stationary phase (LTSP). We have previously shown that E. coli populations adapt genetically under LTSP in an extremely convergent manner. Here we examine how the dynamics of LTSP genetic adaptation are influenced by varying a single parameter of the experiment - culture volume. We find that culture volume affects survival under LTSP, with viable counts decreasing as volumes increase. Across all volumes, mutations accumulate with time, and the majority of mutations accumulated demonstrate signals of being adaptive. However, positive selection appears to affect mutation accumulation more strongly at higher, compared to lower volumes. Finally, we find that several similar genes are likely involved in adaptation across volumes. However, the specific mutations within these genes that contribute to adaptation can vary in a consistent manner. Combined, our results demonstrate how varying a single parameter of an evolutionary experiment can substantially influence the dynamics of observed adaptation.

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    Differing effects of size and lifestyle on bone structure in mammals

    Differing effects of size and lifestyle on bone structure in mammals

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.08.13.249128v1?rss=1

    Authors: Amson, E., Bibi, F.

    Abstract:
    The skeleton is involved in most aspects of vertebrate life history. Previous macroevolutionary analyses have shown that structural, historical, and functional factors influence the gross morphology of bone. The inner structure of bone has, however, received comparatively little attention. Here we address this gap in our understanding of vertebrate evolution by quantifying bone structure in appendicular and axial elements (humerus and mid-lumbar vertebra) across therian mammals (placentals + marsupials). Our sampling captures all transitions to aerial, fully aquatic, and subterranean lifestyles in extant mammal clades. We found that mammalian inner bone structure is highly disparate. We show that vertebral structure mostly correlates with body size, but not lifestyle, while the opposite is true for humeral structure. The latter also shows a high degree of convergence among the clades that have acquired specialised lifestyles. Our results suggest that radically different extrinsic constraints can apply to bone structure in different skeletal elements.

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    Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution

    Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.08.12.248328v1?rss=1

    Authors: PAPADOPULOS, A. S. T., Helmstetter, A. J., Osborne, O. G., Comeault, A. A., Wood, D. P., Straw, E. A., Mason, L. D., Fay, M. F., Parker, J., Dunning, L. T., Foote, A. D., Smith, R. J., Lighten, J.

    Abstract:
    The impact of human mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, species' capacity to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonised isolated, disused mines with phytotoxic, zinc-contaminated soils. Here, we found that rapid parallel adaptation to anthropogenic pollution has taken place without geneflow spreading adaptive alleles between populations of the mine ecotype. Across replicate ecotype pairs, we identified shared targets of selection with functions linked to physiological differences between the ecotypes, although the genetic response is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.

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