Abstract
Many present-day organisms are descendants of ancient polyploids. While recently generated polyploids are easily detected due to the presence of a complete set of duplicated chromosomes, the footprint of ancient polyploidy may be more subtle. After many generations of gene deletion, divergence of paralogous genes, and chromosomal rearrangements, an ancient polyploid comes to resemble a nonpolyploid genome that has experienced multiple local duplication events. Here we simulate genomes evolving under these conditions and monitor the resultant distances between paralogous pairs of genes, as measured by the number of intervening genes in each genome. Some measures of this nearest neighbor distribution decay very slowly following polyploidy and thus may offer a means of experimentally testing alternative hypothesis concerning ancestral ploidy. The nearest neighbor distribution for yeast appears consistent with the proposed ancient tetraploidy of this genome. We briefly review empirical data relevant to these processes and suggest areas for future research.
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Vision, T.J., Brown, D.G. (2000). Genome Archaeology: Detecting Ancient Polyploidy in Contemporary Genomes. In: Sankoff, D., Nadeau, J.H. (eds) Comparative Genomics. Computational Biology, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-4309-7_41
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DOI: https://doi.org/10.1007/978-94-011-4309-7_41
Publisher Name: Springer, Dordrecht
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