An updated classification of Orchidaceae

Since the last classification of Orchidaceae in 2003, there has been major progress in the determination of relationships, and we present here a revised classification including a list of all 736 currently recognized genera. A number of generic changes have occurred in Orchideae (Orchidoideae), but the majority of changes have occurred in Epidendroideae. In the latter, almost all of the problematic placements recognized in the previous classification 11 years ago have now been resolved. In Epidendroideae, we have recognized three new tribes (relative to the last classification): Thaieae (monogeneric) for Thaia, which was previously considered to be the only taxon incertae sedis; Xerorchideae (monogeneric) for Xerorchis; and Wullschlaegelieae for achlorophyllous Wullschlaegelia, which had tentatively been placed in Calypsoeae. Another genus, Devogelia, takes the place of Thaia as incertae sedis in Epidendroideae. Gastrodieae are clearly placed among the tribes in the neottioid grade, with Neottieae sister to the remainder of Epidendroideae. Arethuseae are sister to the rest of the higher Epidendroideae, which is unsurprising given their mostly soft pollinia. Tribal relationships within Epidendroideae have been much clarified by analyses of multiple plastid DNA regions and the low‐copy nuclear gene Xdh. Four major clades within the remainder of Epidendroideae are recognized: Vandeae/Podochileae/Collabieae, Cymbidieae, Malaxideae and Epidendreae, the last now including Calypsoinae (previously recognized as a tribe on its own) and Agrostophyllinae s.s. Agrostophyllinae and Collabiinae were unplaced subtribes in the 2003 classification. The former are now split between two subtribes, Agrostophyllinae s.s. and Adrorhizinae, the first now included in Epidendreae and the second in Vandeae. Collabiinae, also probably related to Vandeae, are now elevated to a tribe along with Podochileae. Malaxis and relatives are placed in Malaxidinae and included with Dendrobiinae in Malaxideae. The increased resolution and content of larger clades, recognized here as tribes, do not support the ‘phylads’ in Epidendroideae proposed 22 years ago by Dressler. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 151–174.     

Molecular phylogenetics and taxonomic revision of Habenaria section Pentadactylae (Orchidaceae,Orchidinae)

As a step towards a revision of the sectional classification of Neotropical species of Habenaria, we focus here on section Pentadactylae. In its current delimitation, this is the largest of the 14 New World sections and embraces a group of 34 morphologically heterogeneous species. We expanded the sampling of Neotropical species currently placed in this section and performed Bayesian, maximum likelihood and parsimony analyses using nucleotide sequences from one nuclear (internal transcribed spacer, ITS) and three plastid (matK, trnK intron, rps16–trnK) DNA regions. In addition, morphological features of these species were reassessed. Based on our analyses, we propose that Habenaria section Pentadactylae should be recircumscribed to include only seven species: H. pentadactyla (the type species of the section), H. dutrae, H. ekmaniana, H. exaltata, H. henscheniana, H. megapotamensis and H. montevidensis. Thirty‐two species previously assigned to the section grouped within unrelated clades and are therefore excluded from the section. There are no unambiguous morphological synapomorphies for the section, but the group can be confidently recircumscribed and identified on the basis of a combination of diagnostic morphological vegetative and floral characters. Morphological floral features in Habenaria montevidensis are distinct from those of other species in the section, probably as a result of a shift to diurnal pollinators. Following a taxonomic revision of the group, H. crassipes is placed under the synonymy of H. exaltata and neotypes are designated for H. crassipes, H. montevidensis and H. recta (= H. ekmaniana). All species in the section live in marshes or wet grasslands from northern Argentina to central Brazil; most species are concentrated in southern Brazil. Most species are probably rare, and five may be threatened according to the World Conservation Union (IUCN) criteria. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 47–73.     

Support for an expanded family concept of Malvaceae within a recircumscribed order Mai vales: a combined analysis of plastid atpB and rbcL DNA sequences

Sequence analyses of the plastid genes atpB and rbcL support an expanded order Malvales. Within this alliance, core Malvales are clearly supported and comprise most genera that have previously been included in Sterculiaceae, Tiliaceae, Bombacaceae, and Malvaceae. Additional well supported malvalean alliances include the bixalean clade (Bixaceae, Diego-dendraceae, and Cochlospermaceae), the cistalean clade (Cistaceae, Dipterocarpaceae, and Sarcolaenaceae) and Thymelaeaceae (including Gonystyloideae and Aquilarioideae). Our results indicate sister-group relationships between (1) Neuradaceae and the cistalean clade; (2) Sphaerosepalaceae and Thymelaeaceae; (3) these two clades (1 and 2); and (4) all these and an alliance comprising the bixalean clade and core Malvales, but this pattern is weakly supported by the bootstrap. The affinities of Muntingiaceae and Petenaea are especially ambiguous, although almost certainly they are Malvales s.l. The traditional delimitation of families within core Malvales is untenable. Instead, we propose to merge Sterculiaceae, Tiliaceae and Bombacaceae with Malvaceae and subdivide this enlarged family Malvaceae into nine subfamilies based on molecular, morphological, and biogeographical data: (1) Byttnerioideae, including tribes Byttnerieae, Lasiopetaleae and Theobromeae (all of which have cucullate petals) and Hermannieae; (2) Grewioideae, including most genera of former Tiliaceae; (3) Tilioideae, monogeneric in our analysis; (4) Helicteroideae, comprising most of the taxa previously included in Helictereae, plus Mansonia, Triplochiton (indicating that apocarpy evolved at least twice within Malvaceae) and possibly Durioneae; (5) Sterculioideae, defined by apetalous, apocarpous, usually unisexual flowers with androgynophores; (6) Brownlowioideae, circumscribed as in previous classifications; (7) Dombeyoideae, expanded to include Burretiodendron, Eriolaena, Pterospermum, and Schoutmia; (8) Bombacoideae, corresponding to former Bombacaceae (without Durioneae) but including Fremontodendreae     

Comparative floral structure and systematics of the clade of Lophopyxidaceae and Putranjivaceae (Malpighiales)

In molecular phylogenetic studies, Lophopyxidaceae and Putranjivaceae are well supported as sisters in the large rosid order Malpighiales. As the floral structure of both families is poorly known and the two families have never been compared, the present comparative study was carried out, as part of a larger project on the comparative floral structure of Malpighiales, using microtome section series and scanning electron microscopy (SEM) studies. Similar to other angiosperm clades, it appears that the structure of the ovules is a strong marker for suprafamilial relationships in Malpighiales. Both families have two collateral pendant antitropous ovules per carpel associated with obturators (as in some Euphorbiaceae s.l., to which Putranjivaceae belonged in earlier classifications). However, in contrast with Euphorbiaceae s.l., the ovules are not crassinucellar, but either incompletely tenuinucellar or only weakly crassinucellar with a long and conspicuously slender nucellus and an endothelium, and do not have a nucellar beak, but a normal micropyle, features they share with families other than Euphorbiaceae s.l. among Malpighiales. Other shared features of the two families include the following. The outer sepals tend to be smaller than the inner ones and the sepals do not protect the gynoecium in older buds. Sepals of some taxa have a single vascular trace. A short zone of synsepaly tends to be present. Stamens tend to be antesepalous in haplostemonous flowers. A short gynophore is present. The synascidiate zone extends up to above the placenta, but is restricted to the ovary in taxa with more than one carpel. The micropyle is formed by the inner integument. The ventral carpel slits extend down into the synascidiate zone as postgenitally fused furrows. The carpels have a broad dorsal band of vascular bundles in the style. The overall floral structure of the two families corroborates their sister position well and does not support the earlier association of Putranjivaceae with Euphorbiaceae s.l. or of Lophopyxidaceae with Geraniales–Sapindales–Celastrales, which rely on shared superficial floral similarities. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 404–448.     

Revisiting the phylogeny of papilionoid legumes: New insights from comprehensively sampled early-branching lineages

• Premise of study: Phylogenetic relationships of the papilionoid legumes (Papilionoideae) reveal that the early branches are more highly diverse in floral morphology than are other clades of Papilionoideae. This study attempts for the first time to comprehensively sample the early-branching clades of this economically and ecologically important legume subfamily and thus to resolve relationships among them. • Methods: Parsimony and Bayesian phylogenetic analyses of the plastid matK and trnL intron sequences included 29 genera not yet sampled in matK phylogenies of the Papilionoideae, 11 of which were sampled for DNA sequence data for the first time. • Key results: The comprehensively sampled matK phylogeny better resolved the deep-branching relationships and increased support for many clades within Papilionoideae. The potentially earliest-branching papilionoid clade does not include any genus traditionally assigned to tribe Swartzieae. Dipterygeae is monophyletic with the inclusion of Monopteryx. The genera Aldina and Amphimas represent two of the nine main but as yet unresolved lineages comprising the large 50-kb inversion clade within papilionoids. The quinolizidine-alkaloid-accumulating genistoid clade is expanded to include a strongly supported subclade containing Ormosia and the previously unplaced Clathrotropis s.s., Panurea, and Spirotropis. Camoensia is the first-branching genus of the core genistoids. • Conclusions: The well-resolved phylogeny of the earliest-branching papilionoids generated in this study will greatly facilitate the efforts to redefine and stabilize the classification of this legume subfamily. Many key floral traits did not often predict phylogenetic relationships, so comparative studies on floral evolution and plant–animal interactions, for example, should also benefit from this study.     

Phylogenetic analysis of the genus Hexachlamys (Myrtaceae) based on plastid and nuclear DNA sequences and their taxonomic implications

Myrtaceae are one of the most species‐rich families of flowering plants in the Neotropics. They include several complex genera and species; Hexachlamys is one of the complex genera. It has not been recognized as a distinct genus and has been included in Eugenia, based on morphological grounds. Therefore, molecular systematic studies may be useful to understand and to help to solve these relationships. Here, we performed a molecular phylogenetic analysis using plastid and nuclear data in order to check the inclusion of Hexachlamys in Eugenia. Plastid (accD, rpoB, rpoC1, trnH‐psbA) and nuclear (ITS2) sequence data were analysed using Bayesian and maximum parsimony methods. The trees constructed using ITS2 and trnH‐psbA were the best able to resolve the relationships between species and genera, revealing the non‐monophyly of Hexachlamys. The molecular phylogenetic analyses were in agreement with previous morphological revisions that have included Hexachlamys in Eugenia. These results reinforce the importance of uniting knowledge and strategies to understand better issues of delimitation of genera and species in groups of plants with taxonomic problems. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 532–543.     

Relationships of the haematophagous marine snail Colubraria (Rachiglossa: Colubrariidae), within the neogastropod phylogenetic framework

The gastropod genus Colubraria includes marine shallow‐water species from tropical, subtropical, and temperate rocky coral environments. At least six species are known to feed on fish blood. Although there is general consensus in placing Colubraria in the Neogastropoda, the actual relationships and the systematic position of Colubraria and related genera are unknown. This is partly the consequence of the lack of a clear phylogenetic framework for the Neogastropoda. This study attempts to propose a phylogenetic framework for the Neogastropoda, by testing: (1) a preliminary phylogenetic arrangement for a large number of recognized neogastropod families; (2) the position of Colubraria within the neogastropods; and (3) the relationships of Colubraria within one of the major neogastropod lineages. We used two different molecular data sets. The first set included representatives of at least 14 neogastropod families, for points (1) and (2), and was based on mitochondrial (16S, 12S, and cytochrome oxidase subunit I, COI) and nuclear (28S) DNA sequences, giving a total of 3443 aligned positions. The second data set, for point (3), included 30 buccinoid sequences from mitochondrial 16S, giving a total of 1029 aligned positions. We also studied the anatomy of the type species of Colubraria and compared it with other neogastropods within the new phylogenetic framework. The results included the first phylogeny of the neogastropod based on 50% of the recognized families. This clearly indicated that the nematoglossan Cancellariidae represent a basal offshoot of the monophyletic Neogastropoda, and that the toxoglossan Conoidea are the sister group to the Rachiglossa. Within the Rachiglossa, a colubrariid clade, worthy of family ranking, showed clear buccinoid affinities. Most of the anatomy of Colubraria is congruent with a buccinoid model. The peculiar anatomical features that do not conform to the buccinoid model seem to be related to the evolution of haematophagous feeding. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 779–800.     

A new genus of African Acrometopini (Tettigoniidae: Phaneropterinae) based on morphology,chromosomes, acoustics,distribution, and molecular data,and the description of a new species

A new genus, Altihoratosphaga, is erected for species formerly assigned to Horatosphaga Schaum, 1853, and a new species is described. Four species are included in Altihoratosphaga: Altihoratosphaga nomima (Karsch, 1896), Altihoratosphaga montivaga ( Sjöstedt, 1909 ), Altihoratosphaga nou (Hemp, 2007) and Altihoratosphaga hanangensis sp. nov. All four species are restricted to Tanzanian localities, and, except for A. nomima, for which no ecological data are available, are confined to montane forest habitats. Data on ecology, acoustics, chromosomes, and molecular relationships are provided, as well as a key to Altihoratosphaga species. The present‐day distribution of Altihoratosphaga species suggests former migration events at times when wetter and colder climatic fluctuations favoured connections between montane forest communities, which today are isolated, enabling flightless taxa such as Altihoratosphaga and Monticolaria to spread. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 66–82.     

A review of the phylogeny and biology of the Diaporthales

The ascomycete order Diaporthales is reviewed based on recent phylogenetic data that outline the families and integrate related asexual fungi. The order now consists of nine families, one of which is newly recognized as Schizoparmeaceae fam. nov., and two families are recircumscribed. Schizoparmeaceae fam. nov., based on the genus Schizoparme with its anamorphic state Pilidella and including the related Coniella, is distinguished by the three-layered ascomatal wall and the basal pad from which the conidiogenous cells originate. Pseudovalsaceae is recognized in a restricted sense, and Sydowiellaceae is circumscribed more broadly than originally conceived. Many species in the Diaporthales are saprobes, although some are pathogenic on woody plants such as Cryphonectria parasitica, the cause of chestnut blight, and agricultural crops such as canker diseases of soybean and sunflower caused by species of Diaporthe-Phomopsis in both temperate and tropical regions. Members of the Diaporthales such as Apiognomonia-Discula and Diaporthe-Phomopsis are commonly encountered as endophytes of woody plants.     

Phylogenetic position and delimitation of the moss family Plagiotheciaceae in the order Hypnales

The phylogenetic position and generic composition of the moss family Plagiotheciaceae were explored using DNA sequence data from three genomes: plastid trnL‐F and rps4, mitochondrial nad5 intron and nuclear ITS1‐5.8S‐ITS2. Our phylogenetic analyses included 35 terminals from Plagiotheciaceae and 71 outgroup taxa from a representative set of hypnalean moss families. The family Plagiotheciaceae is resolved in the early‐diverging Hypnales grade, together with Fontinalaceae, Habrodontaceae and several genera which are mainly distributed in the area of the former Gondwanan supercontinent. However, monophyly of the family can only be attained if the three Southern Hemisphere genera, Acrocladium, Catagonium and Rhizofabronia, are excluded. Ancestral state reconstruction for eight morphological characters reveals that many characters used to delimit the family, such as a lack of pseudoparaphyllia and rhizoids inserted in the leaf axils, were already present in the ancestor of Hypnales. Dispersal–vicariance analysis suggests that Plagiotheciaceae and Fontinalaceae have their ancestral distributions in the area of the former Laurasian supercontinent. As the analyses also reveal a Gondwanan distribution for the ancestor of Hypnales in general, Plagiotheciaceae and Fontinalaceae represent the first diverging Laurasian lineages in the order. © 2013 The Linnean Society of London     

Phylogenetic hypotheses: Cladoniaceae,Stereocaulaceae, Baeomycetaceae,and Icmadophilaceae revisited

Parsimony analyses of SSU rDNA sequences were conducted to examine phylogenetic relationships of selected genera within the families Cladoniaceae, Stereocaulaceae, Icmadophilaceae and Baeomycetaceae (lichen-forming ascomycetes). The analyses included 93 taxa (84 species) representing various groups of ascomycetous fungi. Analyses of the matrix with pre-aligned sequences were performed using heuristic and parsimony ratchet searches, and support values for the same matrix were calculated using parsimony jackknifing. The results support the recognition of the four families. Cladoniaceae are recircumscribed to accommodate Cladia, Cladonia, Heterodea, Metus, Pilophorus, Pycnothelia, Ramalea, Thysanothecium and the newly erected genus Carassea. Myelorrhiza is excluded from the family, while the status of other potential members, Calathaspis, Gymnoderma s.str. and Squamella, remains unresolved. Baeomycetaceae include Baeomyces and Phyllobaeis. Stereocaulaceae include Stereocaulon only, although the status of Muhria is still unclear. Finally, Icmadophilaceae include Dibaeis, Endocena, Knightiella, Icmadophila, Siphula and Thamnolia, while the status of Pseudobaeomyces and Siphulella requires further elucidation. The genus Cladonia appeared to be a polyphyletic assemblage, and accordingly, a new genus Carassea S. Stenroos, gen. nov., represented by C. connexa (Vain.) S. Stenroos, comb. nov., is described. Carassea is most closely related to Pycnothelia and Metus in the Cladoniaceae. Siphula, represented in the present analysis by six species, is not monophyletic, and is in need of reclassification.     

An evolutional special case in the lower Orthorrhapha: some attractive fossil flies from the Middle Jurassic of China (Insecta: Diptera: Brachycera)

More than ten extinct Lower Brachycera families have been discovered throughout the world. These fossil records are of great significance in piecing together jigsaw puzzles of evolution for the Order Diptera. However, the distinct systematic relationships of the Diptera, one of the four largest orders, remain obscure. Herein, we erect a new family to enhance our systematic understanding of the Diptera. The Uranorhagionidae fam. nov. is a bewildering new extinct family comprising two new genera, Uranorhagio gen. nov. and Strenorhagio gen. nov. , and five new species, Uranorhagio daohugouensis sp. nov. , Strenorhagio deviatus sp. nov. , Strenorhagio grimaldi sp. nov. , Strenorhagio asymmetricus sp. nov. , and Strenorhagio conjugovenius sp. nov. , from the Middle Jurassic of China. Members of the new family are moderate to large in size and robust in shape. This family possesses a peculiar shape of vein R₂₊₃, the basal part of which is strongly fornical and nearly geniculate, and has the crossvein r–m at variable position. Furthermore, the Uranorhagionidae fam. nov. exhibits a mixture of distinct characters of two families in two disparate superfamilies, i.e. Rhagionemestriidae (Nemestrinoidea) and Rhagionidae (Tabanoidea), thus suggesting that this family might be in an inclusive position in dipteran phylogeny. We tentatively place this new family as a member of Tabanoidea, pending the discovery of more fossil specimens and further study. The comparison between the new family and other relative families will be discussed. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 563–572.     

The Linear Angiosperm Phylogeny Group (LAPG) III: a linear sequence of the families in APG III

The publication of the third Angiosperm Phylogeny Group (APG) classification (APG III. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 161: 128–131) has resulted in the need for a revised systematic listing of the accepted families. This linear APG III (LAPG III) sequence of families is presented here. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161 , 128–131.     

A new family of lithophoran Proseriata (Platyhelminthes), with the description of seven new species from the Indo‐Pacific and South America,and the proposal of three new genera

In this contribution a new representative of the taxon Meidiama Marcus, 1946, Meidiama uruguayensis sp. nov. , from Uruguay, is described, as are six more new species, for which three new genera are proposed: Dreuxiola philippi gen. nov. sp. nov. , from the French subantarctic archipelago Kerguelen; Yorknia aprostatica gen. nov. sp. nov. ; Serrula byronensis gen. nov. sp. nov. ; Serrula maxillaria sp. nov. ; Serrula concharum sp. nov. ; and Serrula acuta sp. nov. , from eastern Australia and Tasmania. Arguments are presented to propose a new taxon to contain these new species, rather than include them in the Archimonocelididae Meixner, 1938 (of which Meidiama has been considered a member so far), as well as to remove the Calviriinae Martens & Curini‐Galletti from the Archimonocelididae to become a separate taxon Calviriidae. Possible autapomorphies for the three families are discussed. It is also concluded that, with the present state of our knowledge, no sound indications can be given about close relationships. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 759–773.     

Cyanogenic glycosides of the Turneraceae

Eighty species of Turneraceae were tested and found to be cyanogenic. Analysis by HPLC and NMR and comparisons of R_t values from paper chromatograms showed all to possess tetraphyllin A and B and epitetraphyllin B and deidaclin as their cyanogens. These data confirm the close relationship of this family with other families which produce structurally related cyanogens: the Passifloraceae, Malesherbiaceae and Flacourtiaceae.     

Foliar anatomy of neotropical Salicaceae: potentially useful characters for taxonomy

The taxonomy of neotropical Salicaceae, a family that now includes the majority of the former Flacourtiaceae, has been problematic, especially because they display very diverse morphology and have several characteristics in common with many other families. Recent phylogenetic studies have proposed substantial changes at both family and generic levels. Considering the importance of anatomy as an aid for taxonomy, the gathering of anatomical data for the family is fundamental to help clarify the taxonomic problems. Leaves belonging to Abatia americana (four samples), Banara brasiliensis (2), Casearia arborea (4), C. decandra (5), C. gossypiosperma (2), C. obliqua (1), C. sylvestris (3), C. ulmifolia (3), Prockia crucis (3), and Xylosma prockia (4) and the closely related Carpotroche brasiliensis (3) from Achariaceae, were studied by standard microscopy techniques. The leaves were anatomically described, emphasizing their differences and similarities. Similar characters for the neotropical Salicaceae (former Flacourtiaceae) and Salicaceae strictu sensu were recognized, such as the presence of salicoid leaf teeth, brachyparacytic stomata, secondary growth of the petiole, abundance of crystals, collateral and arch-shaped vascular system at the midrib, and sclerenchyma accompanying the bundles. These data demonstrate that leaf anatomy can provide evidence to assist with the taxonomy of Salicaceae, at family, generic, and specific levels.     

A revised classification of subtribe Helianthinae (Asteraceae: Heliantheae) II. Derived lineages

Sequence data for internal transcribed spacer (ITS) and partial external transcribed spacer (ETS) regions were combined in a phylogenetic analysis with previously obtained plastid DNA restriction site data to provide a comprehensive molecular phylogenetic hypothesis for derived members of subtribe Helianthinae. Analyses of the two molecular datasets provided conflicting evidence on relationships among some groups, supporting the hypothesis that hybridization has played a significant role in the divergence of the subtribe. A revised generic‐level classification is presented that divides the approximately 350 species of the subtribe among 21 genera. The paraphyletic Viguiera is narrowed to embrace only the type species, V. dentata. Four newly described genera, Dendroviguiera, Gonzalezia, Heiseria and Sidneya, are composed of species formerly included in Viguiera. Aldama is expanded to include 118 species extending from southwestern North America and Mexico to South America. This requires 116 new combinations, including 58 that were recently transferred into Rhysolepis, which is a synonym of Aldama, based on molecular phylogenetic results. One species of Viguiera is transferred to Tithonia, and two combinations in Hymenostephium are validated. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167 , 311–331.