Shared single copy genes are generally reliable for inferring phylogenetic relationships among polyploid taxa

Polyploidy, or whole-genome duplication, is expected to confound the inference of species trees with phylogenetic methods for two reasons. First, the presence of retained duplicated genes requires the reconciliation of the inferred gene trees to a proposed species tree. Second, even if the analyses are restricted to shared single copy genes, the occurrence of reciprocal gene loss, where the surviving genes in different species are paralogs from the polyploidy rather than orthologs, will mean that such genes will not have evolved under the corresponding species tree and may not have gene trees that allow inference of the species tree. Here we analyze three different ancient polyploidy events, using synteny-based inferences of orthology and paralogy to infer gene trees from more than 17,000 sets of homologous genes. We find that the simple use of single copy genes from polyploid organisms provides reasonably robust phylogenetic signals, despite the presence of reciprocal gene losses. Such..., Data on syntentic orthologs were obtained from the POInT browse webs server (wgd.statgen.ncsu.edu) and derived from the papers cited there and in the manuscript., , # Shared single copy genes are generally reliable for inferring phylogenetic relationships among polyploid taxa

[https://doi.org/10.5061/dryad.7d7wm3821](https://doi.org/10.5061/dryad.7d7wm3821)

## Description of the data and file structure

These data allow for the replication of the phylogenetic analyses presented in the associated manuscript. We proved data for three different polyploidy events: the At-Alpha, TGD and YeastWGD events.

For each event, we provide six (6) types of file:

1\) Codon-preserving nucleotide alignments for all sets of WGD-derived homologous genes for each event (aka \"Pillars\"), in NEXUS format. Phylogenetic trees can be produced from each files using PAUP* with parameters noted in the manuscript. Pillar numbers are 7243 for AtAlpha (AtAlpha_nexus.tar.gz), 5589 for TGD ( TGD_nexus.tar.gz) and 4065 for the yeast WGD (YeastWGD_nexus.tar.gz). Format: GZIPed TAR files.

2\) Coding region sequences for the same pillars as #1. If these are translated and aligned w...