Data from: 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 sorting.
However, our results also revealed unprecedented phylogenetic niche
conservatism of fungal symbionts within the tribe: entire genera,
subtribes, and even groups of related subtribes associate with only a
single fungal family, suggesting that fungal symbiont preferences in the
Diurideae do indeed reflect phylogenetic relationships among orchid hosts.
Moreover, we show that these relationships have evolved directionally from
generalist associations with multiple fungal families towards more
specific partnerships with only one fungal family. Orchid symbiont
preferences here provide new insights into the placement of several groups
with longstanding phylogenetic uncertainty. In spite of complex
evolutionary histories, host-symbiont relationships can be used to help
detangle alternative phylogenetic hypotheses.