8 research outputs found
Germination Experience Microsatellite Data
Mothers, sporophytes and lab reared sporelings microsatellite data. Genome size of some samples was measured by flow cytometry. Haploid samples coded as haploid. Incomplete heterozygous diploid, triploid and tetraploid samples are coded accordingly to their microsatellite phenotype
Gametophytes_MsatData
Microsatellite data for gametophytes - mother, sterile and male plants. Haploids coded as homozygous diploids
Gene alignments
FASTA format alignments for 151 protein-coding using three assembly methods: consensus, ambiguity (iupac), and allele phasing. Alleles for each individual are annotated as _h1 or _h2; for SVDQuartets all SNPs are randomly assigned to _h1 or _h2. For the alleles dataset, alleles have been phased within the longest phaseable block. Outside this block, ambiguity codes are retained. Also contains partition files for RAxML, with each gene partitioned by codon position
scripts
Bash shell and python scripts used to prepare alignments for gene tree inference, phase alleles, and extract introns and exons for multiple-sequence alignment
Species Trees
Species phylogenies for the three assembly methods: consensus (default), ambiguity (iupac), and alleles. For the coalescent-based methods, two types of gene trees were used as input: one with fully bifurcating gene trees, and one where branches were collapsed if they had less than 33% gene tree bootstrap support
Phyparts Output
Output of Phyparts, a bipartition analysis method. Rooted gene trees were reconciled with the ASTRAL species tree produced for each of the assembly methods: consensus (default), ambiguity (IUPAC) and alleles
Gene_trees
Gene trees from three data assembly methods. The identity of each gene can be found in final_genelist.tx