title: Prevalence and Dynamics of Ribosomal DNA Micro-heterogeneity Are Linked to Population History in Two Contrasting Yeast Species.
abstract: Despite the considerable number and taxonomic breadth of past and current genome sequencing projects, many of which necessarily encompass the ribosomal DNA, detailed information on the prevalence and evolutionary significance of sequence variation in this ubiquitous genomic region are severely lacking. Here, we attempt to address this issue in two closely related yet contrasting yeast species, the baker's yeast Saccharomyces cerevisiae and the wild yeast Saccharomyces paradoxus. By drawing on existing datasets from the Saccharomyces Genome Resequencing Project, we identify a rich seam of ribosomal DNA sequence variation, characterising 1,068 and 970 polymorphisms in 34 S. cerevisiae and 26 S. paradoxus strains respectively. We discover the two species sets exhibit distinct mutational profiles. Furthermore, we show for the first time that unresolved rDNA sequence variation resulting from imperfect concerted evolution of the ribosomal DNA region follows a U-shaped allele frequency distribution in each species, similar to loci that evolve under non-concerted mechanisms but arising through rather different evolutionary processes. Finally, we link differences between the shapes of these allele frequency distributions to the two species' contrasting population histories.
authors.affiliation: National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: James
authors.affiliation: National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK.
authors.forename: Claire
authors.initials: C
authors.lastname: West
authors.affiliation: Digital Biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK.
authors.forename: Robert P
authors.initials: RP
authors.lastname: Davey
authors.affiliation: National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK.
authors.forename: Jo
authors.initials: J
authors.lastname: Dicks
authors.affiliation: National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK.
authors.forename: Ian N
authors.initials: IN
authors.lastname: Roberts
mesh_terms: D004275:DNA, Ribosomal / Q000235:genetics*; D019143:Evolution, Molecular; D005787:Gene Frequency / Q000235:genetics; D016681:Genome, Fungal / Q000235:genetics*; D023281:Genomics / Q000379:methods; D009154:Mutation / Q000235:genetics; D011110:Polymorphism, Genetic / Q000235:genetics; D015995:Prevalence; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004275:DNA, Ribosomal