DOI: 10.5061/dryad.0674n
title: Data from: Ribosomal DNA sequence heterogeneity reflects intra-species phylogenies and predicts genome structure in two contrasting yeast species

description: The ribosomal RNA encapsulates a wealth of evolutionary information,
 including genetic variation that can be used to discriminate between
 organisms at a wide range of taxonomic levels. For example, the
 prokaryotic 16S rDNA sequence is very widely used both in phylogenetic
 studies and as a marker in metagenomic surveys and the ITS region,
 frequently used in plant phylogenetics, is now recognised as a fungal DNA
 barcode. However, this widespread use does not escape criticism,
 principally due to issues such as difficulties in classification of
 paralogous versus orthologous rDNA units and intragenomic variation, both
 of which may be significant barriers to accurate phylogenetic inference.
 We recently analysed datasets from the Saccharomyces Genome Resequencing
 Project, characterising rDNA sequence variation within multiple strains of
 the baker's yeast Saccharomyces cerevisiae and its nearest wild
 relative Saccharomyces paradoxus in unprecedented detail. Notably, both
 species possess single locus rDNA systems. Here, we use these new
 variation datasets to assess whether a more detailed characterisation of
 the rDNA locus can alleviate the second of these phylogenetic issues,
 sequence heterogeneity, while controlling for the first. We demonstrate
 that a strong phylogenetic signal exists within both datasets and
 illustrate how they can be used, with existing methodology, to estimate
 intra-species phylogenies of yeast strains consistent with those derived
 from whole-genome approaches. We also describe the use of partial Single
 Nucleotide Polymorphisms, a type of sequence variation found only in
 repetitive genomic regions, in identifying key evolutionary features such
 as genome hybridisation events and show their consistency with
 whole-genome Structure analyses. We conclude that our approach can
 transform rDNA sequence heterogeneity from a problem to a useful source of
 evolutionary information, enabling the estimation of highly accurate
 phylogenies of closely related organisms, and discuss how it could be
 extended to future studies of multi-locus rDNA systems.
description: Appendix 1 - S.
 paradoxus Variation TablepSNP and SNP frequencies
 for SGRP sequence reads of 26 S. paradoxus strains and the S288c S.
 cerevisiae strain compared with the rDNA consensus sequence of the CBS432
 S. paradoxus type strain.West_rDNA_Appendix_1.xlsxAppendix 2 - S. cerevisiae Variation TablepSNP and SNP frequencies for SGRP sequence reads of 34 S. cerevisiae strains and the Q32.3 S. paradoxus strain compared with the rDNA consensus sequence of the S288c S. cerevisiae type strain.West_rDNA_Appendix_2.xlsxAppendix 3 - Phylogenetic Networks of S. paradoxus and S. cerevisiae StrainsBoth a) and b) show an enlargement of the main population structure in the network, with the small boxed inset showing the whole network including the outgroup. a) The S. paradoxus network shows a clear separation of each geographic population. b) The S. cerevisiae network shows a more complex network structure, consistent with our knowledge of this population.West_rDNA_Appendix_3.pdfAppendix 4 - Bar Charts of the pSNP Percentage Occupancy in S. cerevisiae by Population Typea) Bar chart of the S. cerevisiae structured strains, with number of pSNPs against the pSNP occupancy. The boxed section highlights pSNPs with occupancies greater than 10% and less than 90%. The Malaysian, North American and West African strains have very few pSNPs within this boxed area, and these are denoted as structured clean strains. Those strains with a number of pSNPs within this boxed area show a degree of mosaicism, and we classify these strains as being structured mosaic strains. b) Bar chart of S. cerevisiae mosaic strains, where there are a large number of pSNPs within the 10% to 90% occupancy range.West_rDNA_Appendix_4.pdfS. paradoxus CE distance matrixCavalli-Sforza and Edwards rDNA-based distance matrix for 26 S. paradoxus strains plus S. cerevisiae strain S288cS_paradoxus_CE_Dist.nexS. cerevisiae CE distance matrixCavalli-Sforza and Edwards rDNA-based distance matrix for 34 S. cerevisiae strains plus S. paradoxus strain Q32.3S_cerevisiae_CE_Dist.nexS. paradoxus NJ treeNeighbor-Joining phylogenetic tree derived from the S. paradoxus CE distance matrixS_paradoxus_tree.nexS. cerevisiae NJ treeNeighbor-Joining phylogenetic tree derived from the S. cerevisiae CE distance matrixS_cerevisiae_tree.nexPerl script for coverage/copy number estimationPerl script to calculate the rDNA unit coverage from a sequence read dataset and to estimate the number of rDNA units (copy number) in an rDNA tandem array.coverage_v2.plUpdated Appendix 3 - Phylogenetic Networks of S. paradoxus and S. cerevisiae StrainsBoth a) and b) show an enlargement of the main population structure in the network, with the small grey inset showing the whole network including the outgroup. a) The S. paradoxus network shows a clear separation of each geographic population. b) The S. cerevisiae network shows a more complex network structure, consistent with our knowledge of this population.West_rDNA_Appendix_3.svgS. paradoxus CE distance matrixCavalli-Sforza and Edwards rDNA-based distance matrix for 26 S. paradoxus strains plus S. cerevisiae strain S288cS_paradoxus_CE_dist.nexUpdated S cerevisiae CE distance matrixCavalli-Sforza and Edwards rDNA-based distance matrix for 34 S. cerevisiae strains plus S. paradoxus strain Q32.3S_cerevisiae_CE_dist.nexUpdated S. paradoxus NJ treeNeighbor-Joining phylogenetic tree derived from the S. paradoxus CE distance matrixS_paradoxus_tree.nexUpdated S. cerevisiae NJ treeNeighbor-Joining phylogenetic tree derived from the S. cerevisiae CE distance matrixS_cerevisiae_tree.nex