evidence from silent sites

data and scripts from companion paper Bontrager et al. http://dx.doi.org/10.1101/03591

morphology data

Archive with all morphology data used in the publication, along with R script for analysi

molecular sequences from 54 primate genes

Molecular sequence data, used for the PTP tests, the tree-to-tree agreement test, and for the tests in companion papers (Bontrager et al. and Larget et al.). The archive contains aligned sequences for 54 primate genes, for a total of 178 species, originally from Perelman et al. 2011 (http://dx.doi.org/10.1371/journal.pgen.1001342)

<i>S</i>. <i>eubayanus</i> distribution and phylogeography.

<p>A) Geographic distribution of <i>S</i>. <i>eubayanus</i> isolates. B) Maximum-Likelihood (ML) phylogenetic tree reconstructed using the concatenated multi-locus Dataset A (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006155#pgen.1006155.s001" target="_blank">S1 Text</a>). Bar colors are defined in the legend in panel A. Asterisks highlight new isolates or strains not previously studied together [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006155#pgen.1006155.ref020" target="_blank">20</a>]. EU: Europe; QI: Qinghai (China); LA: Lanin (Argentina); NC: North Carolina (USA); NH: Nahuel Huapi (Argentina); NZ: New Zealand; SH: Shaanxi (China); SI: Sichuan (China); T: Tibet (China); VP: Villa Pehuenia (Argentina); WA: Washington (USA). C) ML phylogenetic tree reconstructed using the complete genome sequence data. Phylogenetic trees were rooted using <i>S</i>. <i>uvarum</i> (CBS7001) as the outgroup. The scale bars show the number of substitutions per site. The strain FM1318 is a monosporic derivative of CRUB1568^T (= CBS12357^T = PYCC6148^T). Bootstrap values above 50 are reported at their corresponding nodes. D) Neighbor-Net phylogenetic network reconstructed with the SNP dataset. In phylogenetic networks, incongruent data are represented by nodes subtended by multiple edges. Blue and red arrows indicate the fractional genomic contributions from PB-1 and PA-2, respectively. The scale bar represents the number of substitutions. Note that the admixed strains from Wisconsin [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006155#pgen.1006155.ref020" target="_blank">20</a>] and New Brunswick (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006155#pgen.1006155.g002" target="_blank">Fig 2</a>) are only shown in panel D to avoid implying a linear bifurcating ancestry.</p

Genome-wide analysis of admixed strains.

<p>A) Pairwise nucleotide sequence divergence of the admixed strain yHKS210 compared to strains from the Patagonia A and Patagonia B populations. Average pairwise divergence comparisons are represented with red and blue dots for Patagonia A and Patagonia B, respectively. Standard deviations of pairwise divergence among Patagonia A and Patagonia B are represented by shadows, with broader regions corresponding to higher genetic diversity within populations. B) To directly visualize which population is closest to each region of the genome, we calculated the log₂ ratio of the minimum PB-Admixed nucleotide sequence divergence (d_B-Ad) and the minimum PA-Admixed nucleotide sequence divergence (d_A-Ad) in 50-kbp windows. log₂ < 0 or >0 indicate that part of the genome is more closely related to Patagonia A or Patagonia B, respectively. Regions lacking values are due to filters imposed based on coverage, data quality, or their absence in some strains (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006155#pgen.1006155.s001" target="_blank">S1 Text</a>). C) Admixture ancestry assignment based on PCAdmix (i.e. an inference of which population is contributed that portion of the genome). Portions are defined by 20 SNPs. Blue indicates a chromosomal region inferred to share ancestry with PB-1, red indicates shared ancestry with PA-2, and white indicates that the method cannot make an inference. Roman numerals represent chromosomes. D) Unrooted ML phylogenetic tree reconstructed using SNPs. The scale bar shows the number of substitutions per site, corrected for invariant sites.</p

Genome-wide pairwise nucleotide sequence divergence to lager yeasts.

<p>A) and C) are pairwise nucleotide divergence comparisons to a Saaz and a Frohberg representative, respectively. Comparisons are made to the Patagonia A population, the Patagonia B strains, the two North Carolina strains, and the Tibetan representative. Dots represent average values, while standard deviations from the average are represented by the colored shadow area; red for Patagonia A, dark blue for Patagonia B, blue for Tibet (T), and light blue for North Carolina (NC). B) and D) are the log₂ ratios of the minimum NC-Lager divergence (d_NC-X) and the T-Lager nucleotide divergence (d_T-X) in 50-kbp windows, where X is B) Saaz (S) or D) Frohberg (F). log₂ < 0 or >0 indicate whether that part of the genome is more closely related to T or NC, respectively. Red lines in B) and D) are significance thresholds established by permutation tests (unbiased <i>P <</i> 0.019). Regions lacking values are due to filters imposed based on coverage, data quality, or their absence in some strains (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006155#pgen.1006155.s001" target="_blank">S1 Text</a>). Roman numerals represent chromosomes.</p