Discordance Down Under: Combining phylogenomics & fungal symbioses to detangle difficult nodes in a diverse tribe of Australian terrestrial orchids

Orchid mycorrhizal fungi (OMF) associations in the Orchidaceae are thought to have been a major driver of diversification in the family. In the terrestrial orchid tribe Diurideae, it has long been hypothesised that OMF symbiont associations may reflect evolutionary relationships among orchid hosts. Given that recent phylogenomic efforts have been unable to fully resolve relationships among subtribes in the Diurideae, we sought to ascertain whether orchid OMF preferences may lend support to certain phylogenetic hypotheses. First, we used phylogenomic methods and Bayesian divergence time estimation to produce a genus-level tree for the Diurideae. Next, we synthesised decades of published fungal sequences and morphological/germination data to identify dominant fungal partners at the genus scale and perform ancestral state reconstruction to estimate the evolutionary trajectory of fungal symbiont shifts. Across the tribe, we found phylogenomic discordance stemming from incomplete lineage sor..., , , # *Discordance Down Under*: Combining phylogenomics & fungal symbioses to detangle difficult nodes in a diverse tribe of Australian terrestrial orchids

[https://doi.org/10.5061/dryad.b2rbnzsqp](https://doi.org/10.5061/dryad.b2rbnzsqp)

## Supporting Material

Supporting material for this study has been uploaded as a zip file containing several folders and files matching the relevant supporting data captions below. 

**Data S1** Custom RefSeq Fungal ITS BLAST Database with additional ex-type sequences of Ceratobasidiaceae, Tulasnellaceae, Serendipitaceae, and Sebacinaceae. This folder contains the original raw RefSeq database (fungi.ITS.raw.fna), our modified RefSeq fasta set containing additional ex-type sequences (fungi.ITS.mod.fna), and all database files produced by blastn using the fungi.ITS.mod.fna file as the query set.  

**Data S2** Raw, unpruned cpDNA tree with reference plastome tips displayed and associated input alignments and *IQ-TREE *output. This folder contains two ...