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      The rate and potential relevance of new mutations in a colonizing plant lineage

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          Abstract

          By following the evolution of populations that are initially genetically homogeneous, much can be learned about core biological principles. For example, it allows for detailed studies of the rate of emergence of de novo mutations and their change in frequency due to drift and selection. Unfortunately, in multicellular organisms with generation times of months or years, it is difficult to set up and carry out such experiments over many generations. An alternative is provided by “natural evolution experiments” that started from colonizations or invasions of new habitats by selfing lineages. With limited or missing gene flow from other lineages, new mutations and their effects can be easily detected. North America has been colonized in historic times by the plant Arabidopsis thaliana, and although multiple intercrossing lineages are found today, many of the individuals belong to a single lineage, HPG1. To determine in this lineage the rate of substitutions—the subset of mutations that survived natural selection and drift–, we have sequenced genomes from plants collected between 1863 and 2006. We identified 73 modern and 27 herbarium specimens that belonged to HPG1. Using the estimated substitution rate, we infer that the last common HPG1 ancestor lived in the early 17 th century, when it was most likely introduced by chance from Europe. Mutations in coding regions are depleted in frequency compared to those in other portions of the genome, consistent with purifying selection. Nevertheless, a handful of mutations is found at high frequency in present-day populations. We link these to detectable phenotypic variance in traits of known ecological importance, life history and growth, which could reflect their adaptive value. Our work showcases how, by applying genomics methods to a combination of modern and historic samples from colonizing lineages, we can directly study new mutations and their potential evolutionary relevance.

          Author summary

          A consequence of an increasingly interconnected world is the spread of species outside their native range—a phenomenon with potentially dramatic impacts on ecosystem services. Using population genomics, we can robustly infer dynamics of colonization and successful population establishment. We have compared hundred genomes of a single Arabidopsis thaliana lineage in North America, including genomes of contemporary individuals as well as 19 th century herbarium specimens. These differ by an average of about 200 mutations, and calculation of the nuclear evolutionary rate enabled the dating of the initial colonization event to about 400 years ago. We also found mutations associated with differences in traits among modern individuals, suggesting a role of new mutations in recent adaptive evolution.

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          The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana.

          To take complete advantage of information on within-species polymorphism and divergence from close relatives, one needs to know the rate and the molecular spectrum of spontaneous mutations. To this end, we have searched for de novo spontaneous mutations in the complete nuclear genomes of five Arabidopsis thaliana mutation accumulation lines that had been maintained by single-seed descent for 30 generations. We identified and validated 99 base substitutions and 17 small and large insertions and deletions. Our results imply a spontaneous mutation rate of 7 x 10(-9) base substitutions per site per generation, the majority of which are G:C-->A:T transitions. We explain this very biased spectrum of base substitution mutations as a result of two main processes: deamination of methylated cytosines and ultraviolet light-induced mutagenesis.
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            Whole-genome sequencing of multiple Arabidopsis thaliana populations.

            The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations.
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              Chapter 11: Genome-Wide Association Studies

              Genome-wide association studies (GWAS) have evolved over the last ten years into a powerful tool for investigating the genetic architecture of human disease. In this work, we review the key concepts underlying GWAS, including the architecture of common diseases, the structure of common human genetic variation, technologies for capturing genetic information, study designs, and the statistical methods used for data analysis. We also look forward to the future beyond GWAS.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: InvestigationRole: Methodology
                Role: InvestigationRole: Methodology
                Role: InvestigationRole: Methodology
                Role: InvestigationRole: Methodology
                Role: InvestigationRole: Methodology
                Role: Formal analysisRole: InvestigationRole: Methodology
                Role: Formal analysisRole: InvestigationRole: Methodology
                Role: InvestigationRole: Methodology
                Role: Funding acquisitionRole: Supervision
                Role: ConceptualizationRole: Funding acquisitionRole: SupervisionRole: Writing – review & editing
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Genet
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, CA USA )
                1553-7390
                1553-7404
                12 February 2018
                February 2018
                : 14
                : 2
                : e1007155
                Affiliations
                [1 ] Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
                [2 ] Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
                [3 ] Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany
                [4 ] Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany
                [5 ] Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
                [6 ] Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
                [7 ] Institute of Tibet Plateau Research, Chinese Academy of Sciences, Beijing, China
                [8 ] Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
                [9 ] Department of Archeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
                University of California Davis, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                [¤a]

                Current address: INRA, UMR 1202 Biodiversité Gènes & Communautés, Cestas, Bordeaux, France

                [¤b]

                Current address: Computomics, Tübingen, Germany

                [¤c]

                Current address: Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland

                [¤d]

                Current address: Salk Institute for Biological Studies, La Jolla, California, United States of America

                ‡ MEA and CB share co-first authorship of this work.

                Author information
                http://orcid.org/0000-0001-5711-0700
                http://orcid.org/0000-0003-3406-4670
                http://orcid.org/0000-0003-2042-7290
                http://orcid.org/0000-0001-7893-7387
                http://orcid.org/0000-0001-9144-3920
                http://orcid.org/0000-0003-3433-719X
                http://orcid.org/0000-0002-2114-7963
                Article
                PGENETICS-D-17-01896
                10.1371/journal.pgen.1007155
                5825158
                29432421
                4c2f9796-921a-4ab2-b99d-5aec5ffc01bd
                © 2018 Exposito-Alonso et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 24 September 2017
                : 13 December 2017
                Page count
                Figures: 4, Tables: 1, Pages: 21
                Funding
                Funded by: Max-Planck-Gesellschaft (DE)
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100004189, Max-Planck-Gesellschaft;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100004189, Max-Planck-Gesellschaft;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000781, European Research Council;
                Award Recipient :
                This study was supported by the President’s Fund of the Max Planck Society (project “Darwin”) to HAB and by an ERC grant (AdG IMMUNEMESIS) and core funds of the Max Planck Society to DW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Research and Analysis Methods
                Experimental Organism Systems
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                Arabidopsis Thaliana
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                Model Organisms
                Arabidopsis Thaliana
                Biology and Life Sciences
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                Plants
                Brassica
                Arabidopsis Thaliana
                Research and Analysis Methods
                Experimental Organism Systems
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                Mutation
                Substitution Mutation
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                Physical Sciences
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                Methylation
                Custom metadata
                vor-update-to-uncorrected-proof
                2018-02-23
                Short reads have been deposited in the European Nucleotide Archive under the accession number PRJEB24619 and are available at https://www.ebi.ac.uk/ena/data/view/PRJEB24619.

                Genetics
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