Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
Quan Long,Fernando A. Rabanal,Dazhe Meng,Christian D. Huber,Ashley Farlow,Alexander Platzer,Qingrun Zhang,Bjarni J. Vilhjálmsson,Arthur Korte,Viktoria Nizhynska,Viktor Voronin,Pamela Korte,Laura Sedman,Terezie Mandáková,Martin A. Lysak,Ümit Seren,Ines Hellmann,Magnus Nordborg,Magnus Nordborg +18 more
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TLDR
The massive variation in genome size identified by flow cytometry seems largely to be due to 45S rDNA copy number variation, with lines from northern Sweden having particularly large numbers of copies.Abstract:
Despite advances in sequencing, the goal of obtaining a comprehensive view of genetic variation in populations is still far from reached. We sequenced 180 lines of A. thaliana from Sweden to obtain as complete a picture as possible of variation in a single region. Whereas simple polymorphisms in the unique portion of the genome are readily identified, other polymorphisms are not. The massive variation in genome size identified by flow cytometry seems largely to be due to 45S rDNA copy number variation, with lines from northern Sweden having particularly large numbers of copies. Strong selection is evident in the form of long-range linkage disequilibrium (LD), as well as in LD between nearby compensatory mutations. Many footprints of selective sweeps were found in lines from northern Sweden, and a massive global sweep was shown to have involved a 700-kb transposition.read more
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1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana
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TL;DR: Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.
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Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions.
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TL;DR: The promises and challenges of these genome scan methods are reviewed, including correcting for the confounding influence of a species’ demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations.
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Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
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