Phylogenetic relationships amongst the African genera of subtribe Orchidinae s.l. (Orchidaceae; Orchideae): Implications for subtribal and generic delimitations.

Phylogenetic relationships within the Orchideae sensu Pridgeon et al, remain one of the biggest unresolved issues in our understanding of the taxonomy of the orchids. Members of the Orchideae are numerous and widespread in Africa but remain poorly represented in phylogenetic research. In this study we included a broad sampling of African taxa for which we sequenced three plastid (rbcl, matK and trnL + trnL-F) and two nuclear regions (ITS and 18S). We used 368 sequences representing 278 species and 49 genera to infer relationships using the Bayesian Inference and Maximum Likelihood method. Our results show strong support for three clades, two of which almost entirely match the historical circumscription of Orchidinae and Habenariinae, and the third, Bartholininae, sister to the former two, includes the genera Holothrix and Bartholina. Stenoglottis should be assigned to Orchidinae and not to Habenariinae. Several genera such as Habenaria, Cynorkis and Benthamia are shown to be para- or polyphyletic: Bonatea, Centrostigma, Platycoryne and Roeperocharis are all embedded in Habenaria; Physoceras, Arnottia and part of Benthamia are embedded in Cynorkis. We propose a subdivision of Orchideae sensu lato into nine subtribes, but refrain from making generic re-arrangements until more extensive or more in-depth studies have been done.

Using a multilocus phylogeny to test morphology-based classifications of Polystichum (Dryopteridaceae), one of the largest fern genera.

BACKGROUND: Polystichum (Dryopteridaceae) is probably the third largest fern genus in the world and contains ca. 500 species. Species of Polystichum occur on all continents except Antarctica, but its highest diversity is found in East Asia, especially Southwest China and adjacent regions. Previous studies typically had sparse taxon sampling and used limited DNA sequence data. Consequently, the majority of morphological hypotheses/classifications have never been tested using molecular data. RESULTS: In this study, DNA sequences of five plastid loci of 177 accessions representing ca. 140 species of Polystichum and 13 species of the closely related genera were used to infer a phylogeny using maximum likelihood, Bayesian inference, and maximum parsimony. Our analyses show that (1) Polystichum is monophyletic, this being supported by not only molecular data but also morphological features and distribution information; (2) Polystichum is resolved into two strongly supported monophyletic clades, corresponding to the two subgenera, P. subg. Polystichum and P. subg. Haplopolystichum; (3) Accessions of P. subg. Polystichum are resolved into three major clades: clade K (P. sect. Xiphophyllum), clade L (P. sect. Polystichum), and the HYMASO superclade dominated by accessions of P. sect. Hypopeltis, P. sect. Macropolystichum, and P. sect. Sorolepidium, while those of P. subg. Haplopolystichum are resolved into eight major clades; and (4) The monophyly of the Afra clade (weakly supported), the Australasian clade (weakly supported), and the North American clade (strongly supported) is confirmed. CONCLUSIONS: Of the 23 sections of Polystichum recognized in a recent classification of the genus, four (P. sect. Hypopeltis, P. sect. Neopolystichum, P. sect. Sorolepidium, P. sect. Sphaenopolystichum) are resolved as non-monophyletic, 16 are recovered as monophyletic, and three are monospecific. Of the 16 monophyletic sections, two (P. sect. Adenolepia, P. sect. Cyrtogonellum) are weakly supported and 14 are strongly supported as monophyletic. The relationships of 11 sections (five in P. subg. Haplopolystichum; six in P. subg. Polystichum) are well resolved.

On the relevance of molecular tools for taxonomic revision in Malvales, Malvaceae s.l., and Dombeyoideae.

In this article, we present an overview of changes to the taxonomy of Malvales. In traditional classifications, this order was variously circumscribed as including four main families (i.e., Malvaceae, Bombacaceae, Sterculiaceae, and Tiliaceae, also known now as "Core Malvales"), but major disagreements existed between different taxonomic treatments. Contributions from molecular data, new morpho-anatomical data, and progress in methodological approaches have recently led to a new broader concept of this order (namely, "expanded Malvales"). Now, expanded Malvales includes ten families (Neuradaceae, Thymelaeaceae, Sphaerosepalaceae, Bixaceae, Cistaceae, Sarcolaenaceae, Dipterocarpaceae, Cytinaceae, Muntingiaceae, Malvaceae s.l.) distributed among seven monophyletic lineages. All these families were previously considered to have malvalean affinities in some traditional treatments, except the holoparasitic and highly modified Cytinaceae. Although molecular evidence has clarified the Malvales taxonomy, the phylogenetic positions of Sarcolaenaceae, Thymelaeaceae, and Sphaerosepalaceae are still controversial and need new analyses focusing specifically on these families to assess their phylogenetic placement and their morphological evolution.In a phylogenetic context, molecular data combined with recent examination of morphological characters supported the hypothesis of a common origin of "core Malvales." However, these analyses also showed that the former families but Malvaceae s.s. were paraphyletic or polyphyletic. As a consequence, recent taxonomic treatments grouped taxa formerly included in "Core Malvales" in a broader concept of Malvaceae s.l. Additionally, the intrafamilial taxonomy has been deeply modified, and in its present circumscription, Malvaceae includes nine subfamilies (Grewioideae, Byttnerioideae, Sterculioideae, Dombeyoideae, Brownlowioideae, Tilioideae, Bombacoideae, Malvoideae, Helicteroideae) in two main lineages. Phylogenetic studies on subfamilial rearrangements have focused on the relationships between emblematic taxa such as Bombacoideae and Malvoideae (which form together the /Malvatheca lineage). However, our understanding of the phylogenetic relationships among and within taxa of the other subfamilies (e.g., Dombeyoideae, Tilioideae, and Sterculioideae) has not followed at the same pace. Despite recent investigations, the relationships between the subfamilies of Malvaceae s.l. remain controversial. As an example of these taxonomic issues, we review the systematic studies on Dombeyoideae, with special emphasis on taxa endemic to the Mascarene archipelago (Indian Ocean). Recent investigations have shown that several island endemic genera such as Trochetia, Ruizia, and Astiria (endemic to the Mascarenes) are nested within the mega-genus Dombeya. Consequently, the current taxonomy of this genus does not match the phylogeny and should be modified. Therefore, we propose three possible taxonomic schemes as part of an ongoing revision of the Mascarene Dombeyoideae. However, these taxonomic rearrangements should only be made after a broader study of the diversity in Madagascar and adjacent areas. This broader approach shall avoid possibly multiple and contradictory taxonomic revisions of restricted regions if they were each studied in isolation.

Multiple colonizations from Madagascar and converged acquisition of dioecy in the Mascarene Dombeyoideae (Malvaceae) as inferred from chloroplast and nuclear DNA sequence analyses.

BACKGROUND AND AIMS: In the Mascarenes, a young oceanic archipelago composed of three main islands, the Dombeyoideae (Malvaceae) have diversified extensively with a high endemism rate. With the exception of the genus Trochetia, Mascarene Dombeyoideae are described as dioecious whereas Malagasy and African species are considered to be monocline, species with individuals bearing hermaphrodite/perfect flowers. In this study, the phylogenetic relationships were reconstructed to clarify the taxonomy, understand the phylogeographic pattern of relationships and infer the evolution of the breeding systems for the Mascarenes Dombeyoideae. METHODS: Parsimony and Bayesian analysis of four DNA markers (ITS, rpl16 intron and two intergenic spacers trnQ-rsp16 and psbM-trnD) was used. The molecular matrix comprised 2985 characters and 48 taxa. The Bayesian phylogeny was used to infer phylogeographical hypotheses and the evolution of breeding systems. KEY RESULTS: Parsimony and Bayesian trees produced similar results. The Dombeyoideae from the Mascarenes are polyphyletic and distributed among four clades. Species of Dombeya, Trochetia and Ruizia are nested in the same clade, which implies the paraphyly of Dombeya. Additionally, it is shown that each of the four clades has an independent Malagasy origin. Two adaptive radiation events have occurred within two endemic lineages of the Mascarenes. The polyphyly of the Mascarene Dombeyoideae suggests at least three independent acquisitions of dioecy. CONCLUSIONS: This molecular phylogeny highlights the taxonomic issues within the Dombeyoideae. Indeed, the limits and distinctions of the genera Dombeya, Trochetia and Ruizia should be reconsidered. The close phylogeographic relationships between the flora of the Mascarenes and Madagascar are confirmed. Despite their independent origins and a distinct evolutionary history, each endemic clade has developed a different breeding systems (dioecy) compared with the Malagasy Dombeyoideae. Sex separation appears as an evolutionary convergence and may be the consequence of selective pressures particular to insular environments.