| Summary: | <p>Abstract</p> <p>Background</p> <p>The fern genus <it>Dryopteris</it> (Dryopteridaceae) is among the most common and species rich fern genera in temperate forests in the northern hemisphere containing 225–300 species worldwide. The circumscription of <it>Dryopteris</it> has been controversial and various related genera have, over the time, been included in and excluded from <it>Dryopteris</it>. The infrageneric phylogeny has largely remained unclear, and the placement of the majority of the supraspecific taxa of <it>Dryopteris</it> has never been tested using molecular data.</p> <p>Results</p> <p>In this study, DNA sequences of four plastid loci (<it>rbcL</it> gene, <it>rps4-trnS</it> spacer, <it>trnL</it> intron, <it>trnL-F</it> spacer) were used to reconstruct the phylogeny of <it>Dryopteris</it>. A total of 122 accessions are sampled in our analysis and they represent 100 species of the expanded <it>Dryopteris</it> including <it>Acrophorus</it>, <it>Acrorumohra</it>, <it>Diacalpe</it>, <it>Dryopsis</it>, <it>Nothoperanema</it>, and <it>Peranema</it>. All four subgenera and 19 sections currently recognized in <it>Dryopteris</it> s.s. are included. One species each of <it>Arachniodes</it>, <it>Leptorumohra</it>, and <it>Lithostegia</it> of Dryopteridaceae are used as outgroups. Our study confirms the paraphyly of <it>Dryopteris</it> and provides the first strong molecular evidence on the monophyly of <it>Acrophorus</it>, <it>Diacalpe</it>, <it>Dryopsis</it>, <it>Nothoperanema</it>, and <it>Peranema</it>. However, all these monophyletic groups together with the paraphyletic <it>Acrorumohra</it> are suggested to be merged into <it>Dryopteris</it> based on both molecular and morphological evidence. Our analysis identified 13 well-supported monophyletic groups. Each of the 13 clades is additionally supported by morphological synapomophies and is inferred to represent a major evolutionary lineage in <it>Dryopteris</it>. In contrast, monophyly of the four subgenera and 15 out of 19 sections currently recognized in <it>Dryopteris</it> s.s is not supported by plastid data.</p> <p>Conclusions</p> <p>The genera, <it>Acrophorus</it>, <it>Acrorumohra</it>, <it>Diacalpe</it>, <it>Dryopsis</it>, <it>Nothoperanema</it>, and <it>Peranema</it>, should all be merged into <it>Dryopteris</it>. Most species of these genera share a short rhizome and catadromic arrangement of frond segments, unlike the sister genus of <it>Dryopteris</it> s.l., <it>Arachniodes</it>, which has anadromic arrangement of frond segments. The non-monophyly of the 19 out of the 21 supraspecific taxa (sections, subgenera) in <it>Dryopteris</it> strongly suggests that the current taxonomy of this genus is in need of revision. The disagreement between the previous taxonomy and molecular results in <it>Dryopteris</it> may be due partly to interspecific hybridization and polyplodization. More morphological studies and molecular data, especially from the nuclear genome, are needed to thoroughly elucidate the evolutionary history of <it>Dryopteris</it>. The 13 well-supported clades identified based on our data represent 13 major evolutionary lineages in <it>Dryopteris</it> that are also supported by morphological synapomophies.</p>
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