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The digitate-tubered clade (Dactylorhiza s.l. plus Gymnadenia s.l.) within subtribe Orchidinae is an important element of the North-temperate orchid flora and has become a model system for studying the genetic and epigenetic consequences of organism-wide ploidy change. Here, we integrate morphological phylogenetics with Sanger sequencing of nrITS and the plastid region trnL-F in order to explore phylogenetic relationships and phenotypic character evolution within the clade. The resulting morphological phylogenies are strongly incongruent with the molecular phylogenies, instead reconstructing through parsimony the genus-level boundaries recognised by traditional 20th Century taxonomy. They raise fresh doubts concerning whether Pseudorchis is sister to Platanthera or to Dactylorhiza plus Gymnadenia. Constraining the morphological matrix to the topology derived from ITS sequences increased tree length by 20%, adding considerably to the already exceptional level of phenotypic homoplasy. Both molecular and morphological trees agree that D. viridis and D. iberica are the earliest-diverging species within Dactylorhiza (emphasising the redundancy of the former genus Coeloglossum). Morphology and ITS both suggest that the former genus Nigritella is nested within (and thus part of) Gymnadenia, the Pyrenean endemic 'N.' gabasiana apparently forming a molecular bridge between the two radically contrasting core phenotypes. Comparatively short subtending molecular branches plus widespread (though sporadic) hybridisation indicate that Dactylorhiza and Gymnadenia approximate the minimum level of molecular divergence acceptable in sister genera. They share similar tuber morphologies and base chromosome numbers, and both genera are unusually prone to polyploid speciation. Another prominent feature of multiple speciation events within Gymnadenia is floral paedomorphosis. The 'traditional' morphological and candidate-gene approaches to phylogeny reconstruction are critically appraised.

Molecular and morphological phylogenetics of the digitate-tubered clade within subtribe Orchidinae s.s. (Orchidaceae: Orchideae)