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      Polyploidy can drive rapid adaptation in yeast

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          Abstract

          Polyploidy is observed across the tree of life, yet its influence on evolution remains incompletely understood 14 . Polyploidy, usually whole genome duplication (WGD), is proposed to alter the rate of evolutionary adaptation. This could occur through complex effects on the frequency or fitness of beneficial mutations 2, 57 . For example, in diverse cell types and organisms, immediately after a WGD, newly formed polyploids missegregate chromosomes and undergo genetic instability 813 . The instability following WGDs is thought to provide adaptive mutations in microorganisms 13, 14 and can promote tumorigenesis in mammalian cells 11, 15 . Polyploidy may also affect adaptation independent of beneficial mutations through ploidy-specific changes in cell physiology 16 . Here, we performed in vitro evolution experiments to directly test whether polyploidy can accelerate evolutionary adaptation. Compared to haploids and diploids, tetraploids underwent significantly faster adaptation. Mathematical modeling suggested that rapid adaptation of tetraploids was driven by higher rates of beneficial mutations with stronger fitness effects, which was supported by whole-genome sequencing and phenotypic analyses of evolved clones. Chromosome aneuploidy, concerted chromosome loss, and point mutations all provided large fitness gains. We identified several mutations whose beneficial effects were manifest specifically in the tetraploid strains. Together, these results provide direct quantitative evidence that in some environments polyploidy can accelerate evolutionary adaptation.

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          Most cited references76

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          Is Open Access

          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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              Is Open Access

              BEDTools: a flexible suite of utilities for comparing genomic features

              Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools Contact: aaronquinlan@gmail.com; imh4y@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                27 June 2015
                02 March 2015
                19 March 2015
                19 September 2015
                : 519
                : 7543
                : 349-352
                Affiliations
                [1 ]Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Cell Biology Harvard Medical School, and Howard Hughes Medical Institute
                [3 ]Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Department of Biostatistics, Harvard School of Public Health
                [4 ]BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder
                [5 ]Broad Institute
                [6 ]Department of Medicine, University of Colorado School of Medicine, Department of Biostatistics and Informatics, Colorado School of Public Health, and Molecular Oncology Program, University of Colorado Cancer Center
                [7 ]Department of Systems Biology, Harvard Medical School, and Department of Biology, Israel Institute of Technology
                [8 ]Department of Pediatric Hematology/Oncology, Children’s Hospital
                Author notes
                Correspondence and request for materials should be addressed to: Anna Selmecki ( anna_selmecki@ 123456dfci.harvard.edu ) or David Pellman ( david_pellman@ 123456dfci.harvard.edu )
                [2]

                Current address: Department of Medical Microbiology and Immunology, Creighton University School of Medicine.

                Article
                NIHMS652288
                10.1038/nature14187
                4497379
                25731168
                2b230617-7665-4b62-8e6f-bd9e130fcfca

                Reprints and permissions information is available at www.nature.com/reprints

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