Phylogenomics and intergenomic conflict in a challenging orchid clade (Calypsoinae): monophyly of <i>Corallorhiza</i> , paraphyly of <i>Oreorchis</i> , and resurrection of <i>Kitigorchis</i>

Abstract Heterotrophic plants are among the most recalcitrant from a systematics perspective because of reduced morphological and genomic features, and often extreme substitution rate heterogeneity. The orchid subtribe Calypsoinae exemplifies this, containing several lineages that have lost leaves and photosynthesis. In particular, relationships of the leafy Asian Oreorchis and the leafless American Corallorhiza have been contentious. Here we used nuclear sequence capture to resolve relationships within Calypsoinae and addressed the monophyly of Corallorhiza and Oreorchis, for which previous studies have highlighted conflicting patterns of monophyly or paraphyly, depending on the data analysed. Nuclear analyses provided strong support for a monophyletic Corallorhiza and paraphyletic Oreorchis, the latter with two strongly supported clades. As in previous studies, plastid analyses recovered strongly supported paraphyletic assemblages for both genera. Topology tests using plastid and nuclear relationships and data rejected the constrained topologies, further revealing strong cytonuclear conflict. Network-based analyses revealed a lack of evidence for hybridization, suggesting incomplete lineage sorting associated with biological and historical factors have driven intergenomic conflict. Additionally, we found that loci identified as putatively lost in holomycotrophic Corallorhiza species are functionally enriched for organellar functions. The study provides a strong case for the resurrection of Kitigorchis as the sister of Corallorhiza, with two species, Kitigorchis erythrochrysea and Kitigorchis indica, and highlights the challenges associated with phylogenetics of lineages containing mycoheterotrophs.