### README file for Dryad data package David Peris, Kayla Sylvester, Diego Libkind, Paula Gonçalves, José Paulo Sampaio, William G Alexander, Chris Todd Hittinger Correspondence email: perisnavarro@wisc.edu, cthittinger@wisc.edu ------------------------------------------------------- Arlequin folder: >Normal.arp: input file used in Arlequin analysis >Normal.htm, Normal.js, Normal_main.html, Normal_tree: output files from Arlequin analysis. They include the ANOVA result shown as Table 3 in the paper. ------------------------------------------------------- Calibrated tree folder: >Concatenated_4fold.nex: the recombinant-free concatenated alignment for the four-fold degenerate codon positions. >Coding_seq_concat_fourfold.xml: the file with priors and parameters generated by BEAUTI that were used in BEAST as an input for obtaining the calibrated tree. >Calibrated_tree: calibrated phylogenetic tree obtained by the combination of the 3 independent runs in BEAST. ------------------------------------------------------- eBSP folder: >PA.nex and PB(L).nex: alignments used for the reconstruction of extended Bayesian Skyline Plots for the Patagonia A and Patagonia B (Lager) populations, respectively. >PA.xml and PB(L).xml: the file with priors and parameters generated by BEAUTI that were used in BEAST as an input for obtaining the eBSPs for Patagonia A and Patagonia B (Lager), respectively. >*.csv files: BEAST output results from the three independent runs for each population, Patagonia A and Patagonia B (Lager). >PA.png and PB(L).png: extended Bayesian Skyline Plots for Patagonia A and Patagonia B (Lager) populations, respectively. Time is represented by kya. ------------------------------------------------------- IBD folder: >Number correspondence.txt: as the next programs use numbers instead of strain names, this document translate the numbers in yeast names. >Seub_input_txt_OUT1.txt: output result from IBD Web Service v3.23 >*_matrix.txt: dissimilarity matrix for altitude and geographic distance obtained using ecodist package in R. ------------------------------------------------------- IBE folder: >Number correspondence.txt: as the next programs use numbers instead of strain names, this document translate the numbers in yeast names. >*.jpg: scatter plots correlating genetic distance and ecological factors obtained in STRUCTURE. >PCA_Ecological_traits.pptx: Principal Component Analysis using all ecological traits, only climatic traits, or only isolation substrate as the input. PCA were obtained using rgl package in R. >*_matrix.txt: ecological dissimilarity matrix for each ecological factors: climatic, isolation substrate,temperature and genetic distance; obtained using ecodist package in R. >Seub_ecological_traits.txt: ecological traits used as an input for ecodist. The presence or absence of a strain in a host, substrate, etc. is encoded by 1 or 0, respectively. ------------------------------------------------------- Individual Alignments folder: >*.meg: individual alignments for the nuclear and the mitochondrial genes. ------------------------------------------------------- ML Trees folder: >*.nwk: Maximum Likelihood individual gene trees for the nuclear and the mitochondrial genes obtained in MEGA 5. ------------------------------------------------------- MrBayes&Bucky folder: with_NA: folder with data including the North American strains in the analysis. >*.in: input files obtained in MrBayes to be used in BUCKy. >*.input: *.in file list used in the analysis in BUCKy >*.cluster, *.concordance, *.gene, *.joint, *.out, *.pairs, *.single: BUCKy output files for runs involving different alpha values. without_NA: folder with data not including the North American strains in the analysis. >*.in: input files previously obtained in MrBayes to be used in BUCKy. >*.input: *.in file list used in the analysis in BUCKy >*.cluster, *.concordance, *.gene, *.joint, *.out, *.pairs, *.single: BUCKy output files for runs involving different alpha values. ------------------------------------------------------- Phylonet folder: >COX2_NN.nex: Neighbor-Net phylogenetic network reconstructed for the partial COX2 gene. Can be opened by SPLITSTREE. ------------------------------------------------------- Structure folder: >Concatenated.nex: concatenated alignment that will be phased by SeqPHASE. >Concatenated_str: SeqPHASE file, input for STRUCTURE program. >names.names: as the next programs use numbers instead of strain names, this document translate the numbers in yeast names. >pop.languages: as the next programs use numbers instead of population names, this document translate the numbers in population names. CLUMPP folder: files used in CLUMPP software, obtained previously in STRUCTURE, and the output files. Distruct folder: input and output files used in DISTRUCT software to represent the STRUCTURE HARVESTER results in a graphical view. Harvester folder: input and output files from the STRUCTURE HARVESTER software. ------------------------------------------------------- Supernetwork folder: >supernet_trees_w_bay_w_HTZ.nex: file containing the Maximum Likelihood individual gene trees and the supernetwork reconstructed using them. The file can be opened by SPLITSTREE.