Supplementary Data 2 - phylogenetic tree, presence-absence dendrogram, ancestral state reconstruction, and hybrid-parent alignment data

This datafile contains the phylogenetic tree, presence-absence dendrogram, ancestral state reconstruction, and hybrid-parent alignment data. The nuclear phylogenies made from the tefA and tubB nuclear genes are those with hybrids included using one copy of each gene (oc), with hybrids included using both copies of each gene found in the hybrids (bc), and with hybrids excluded (nh). Similarly, the phylogenies made from a concatenation of mitochondrial protein-coding genes have hybrids included and hybrids excluded (nh). Finally, there is a dendrogram using intron presence-absence as the phylogenetic character, again with hybrids included and hybrids excluded (nh). Therefore, these phylogenies have different numbers of tips, including some with more tips than the number of isolates used in this study because of the use of two copies of each gene present in hybrids.

For the presence-absence dendrograms, ancestral state reconstruction outputs from Mesquite and RASP are provided. The RASP tree include a legend file for the colours. The rootstrap tree used to determine the root position is also provided.

For the intron invasion phylogenetic analyses, the alignment and the rootstrap tree used to determine the root position are provided for each intron. For cox3_216, two separate analyses were performed for the long and short intron types as indicated.

For the alignment of the E. canadensis mitochondrial genome to those of its parental isolates, only the part of the mitochondrial genome containing the 14 protein-coding genes analysed in this study was included.

Note that older names are used for some isolates: E. typhina subspecies Holcus = E. clarkii; E. typhina subspecies poae = E. poae