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

Sporophytes_MsatData

Microsatellite data for triploid and tetraploid sporophytes

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