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Data from: Data management, archiving and sharing for biologists and the role of research institutions in the technology-oriented age
Renaut, Sebastien; Budden, Amber E.; Gravel, Dominique; Poisot, Timothée; Peres-Neto, Pedro — 2018-03-20 Data are one of the primary outputs of science. Although certain sub-disciplines of biology have pioneered efforts to ensure their long-term preservation and facilitate collaborations, data continue to disappear, owing mostly to technological, regulatory and ideological hurdles. In this review, we describe the important steps towards proper data management and archiving, and provide a critical discussion on the importance of long term data conservation. We then illustrate the rise in data archiving through the Joint Data Archiving Policy and the Dryad Digital Repository. In particular, we discuss data integration and how the limited availability of large scale datasets can hinder new discoveries. Finally, we propose solutions to increase the rate of data preservation. For example, by generating mechanisms insuring proper data management and archiving, by providing training in data management, and by transforming the traditional role of research institutions and libraries as data generators towards managers and archivers.
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Data from: Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers
Dryad
Renaut, Sebastien; Owens, Gregory L.; Rieseberg, Loren H. — 2013-11-26 The repeated evolution of traits in organisms facing similar environmental conditions is considered to be fundamental evidence for the role of natural selection in moulding phenotypes. Yet, aside from case studies of parallel evolution and its genetic basis, the repeatability of evolution at the level of the whole genome remains poorly characterized. Here, through the use of transcriptome sequencing, we examined genomic divergence for three pairs of sister species of sunflowers. Two of the pairs (Helianthus petiolaris – H. debilis and H. annuus – H. argophyllus) have diverged along a similar latitudinal gradient and presumably experienced similar selective pressure. In contrast, a third species pair (H. exilis – H. bolanderi) diverged along a longitudinal gradient. Analyses of divergence, as measured in terms of FST, indicated little repeatability across the three pairs of species for individual genetic markers (SNPs), modest repeatability at the level of individual genes and the highest repeatability when large regions of the genome were compared. As expected, higher repeatability was observed for the two species pairs that have diverged along a similar latitudinal gradient, with genes involved in flowering time among the most divergent genes. Genes showing extreme low or high differentiation were more similar than genes showing medium levels of divergence, implying that both purifying and divergent selection contributed to repeatable patterns of divergence. The location of a gene along the chromosome also predicted divergence levels, presumably because of shared heterogeneity in both recombination and mutation rates. In conclusion, repeated genome evolution appeared to result from both similar selective pressures and shared local genomic landscapes.
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Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops
Dryad
Renaut, Sebastien; Rieseberg, Loren H. — 2016-04-29 For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. Although we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased toward nonsynonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Finally, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. Although the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.

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(auteur : Renaut, Sebastien)

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