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Summary  The first study of the taxonomically critical European orchid genus  Dactylorhiza  to use next-generation DNA sequencing generated the statistically best-supported reconstruction of its phylogeny to date. However, the two competing topologies obtained within the monophyletic Section  Maculatae  differed radically in the placement of the  D. maculata  s.s.– D. foliosa  clade. Both topologies showed  D. foliosa  to be nested deeply within  D. maculata  s.s., and suggested that  D. saccifera  s.l. is paraphyletic,  D. saccifera  s.s. from south-eastern Europe and Asia Minor diverging before  D. gervasiana  from south-central Europe (a taxon typically viewed as a subspecies of  D. saccifera  or, more often, ignored completely). The poorly-sampled but character-rich morphometric comparison presented here suggests that  D. saccifera  s.s. and  D. gervasiana  cannot be distinguished with confidence using morphological characters and that, if  D. gervasiana  is accepted as a species, it is effectively cryptic. The diploid  D. foliosa  is accepted as an island endemic species, despite rendering paraphyletic the autotetraploid  D. maculata  s.s.; all other named taxa within the  D. maculata  s.s. clade are considered infraspecific.  Dactylorhiza fuchsii  is indisputably a  bona fide  species rather than a subspecies but it does not merit becoming the basis of a taxonomic section separate from  D. maculata  s.s. The strongly contrasting degrees of molecular vs morphological disparity reported here are representative of a more general trend evident in groups that have experienced comparatively recent speciation, as is the need to recognise occasional paraphyletic species when circumscribing species by integrating genotypic and phenotypic data categories. Explicit taxonomic criteria combined with a comparative, monographic approach are needed to achieve consistency of ranking. Disproving hypotheses of species status is judged a criminally underrated activity, actually being as important to outcomes as much-vaunted species "discovery".

Challenges of applying monophyly in the phylogenetic shallows: taxonomic reappraisal of the Dactylorhiza maculata group