A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.

School of Biological and Chemical Sciences Queen Mary University of London Mile End Road London E1 4NS UK; Jodrell Laboratory Royal Botanic Gardens Kew Richmond Surrey TW9 3DS UK; School of Plant Biology The University of Western Australia Crawley WA 6009 Australia; Institute of Plant Molecular Biology Biology Centre ASCR Branišovská 31 České Budějovice CZ 37005 Czech Republic; Systematic Botany and Mycology University of Munich Menzinger Straße 67 80638 München Germany; and Department of Systematic and Evolutionary Botany University of Vienna Rennweg 14 A 1030 Vienna Austria

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