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Supplementary Data 3 - ancestral state reconstructions of intron presence/absence and their associated phylogenies

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posted on 2024-07-04, 00:53 authored by Austen GanleyAusten Ganley

Supplementary Data 3 Readme

This datafile contains the ancestral state reconstruction data. There are six different sets of phylogenies/dendrograms used for the ancestral state reconstructions. These are phylogenies made from the tefA and tubB nuclear genes with hybrids included using one copy of each gene, with hybrids included using both copies of each gene found in the hybrids are included, and with hybrids excluded. Similarly, they are from a concatenation of mitochondrial protein-coding genes with hybrids included and with hybrids excluded. Finally, there is a dendrogram using intron presence-absence as the phylogenetic character. 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 each phylogeny/dendrogram, ancestral state reconstruction outputs from Mesquite and RASP are provided, as are the tables of intron gains/losses inferred from the Mesquite analyses.

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

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