nrITS Sequence Data Research Articles

Senecio imbaburensis, proposed name for Lasiocephalus sodiroi in the genus Senecio (Asteraceae)

Lasiocephalus Willd. ex Schlechtendal (1818: 308), as traditionally circumscribed (e.g., by Cuatrecasas 1978, Dušková et al. 2010), is a neotropical genus of ca 25 species confined to the Andes and distributed from Venezuela to Bolivia. Nevertheless, recent studies by Pelser et al. (2007, 2010) have shown that based on phylogenetic analyses of nrITS and plastid DNA sequence data, species of the genus Lasiocephalus are deeply embedded in Senecio Linnaeus (1753: 866), and, consequently, should be transferred into this latter genus. In fact, a number of species of Lasiocephalus were originally described as Senecio or had been, at some point, transferred into Senecio so only few transfers are necessary.

Generic status, circumscription, and allopolyploid origin of Faberia (Asteraceae: Cichorieae) as revealed by ITS and chloroplast DNA sequence data

AbstractThe Chinese endemic Faberia (Asteraceae: Cichorieae) is imperfectly understood: its generic status, circumscription, and subtribal affiliation have long been in dispute. Here we present a molecular analysis to address these problems. Nuclear (ITS) and plastid (matK, psbA–trnH, rbcL, and trnL–F) sequence data were analyzed by means of Bayesian inference, maximum likelihood and maximum parsimony methods. Our results support the independent generic status of Faberia but not that of Faberiopsis, which should be re–submerged in the former. Dubyaea glaucescens is revealed as a member of Faberia, resulting in a new combination, F. glaucescens. The recent addition of Youngia racemifera to Faberia is refuted but the transfer of Prenanthes faberi to Faberia as F. faberi is corroborated. Consequently, Faberia is circumscribed here to include eight species (F. cavaleriei, F. ceterach, F. faberi, F. glaucescens, F. lancifolia, F. nanchuanensis, F. sinensis, F. thibetica). Most notably, phylogenies based on nrITS and cpDNA sequence data are highly incongruent with respect to the subtribal relationship of Faberia. The ITS phylogeny locates the genus in Lactucinae, whereas the cpDNA phylogeny places it in Crepidinae. This incongruence, together with karyological (Faberia has x = 17, a very rare number in Cichorieae) and palynological (Faberia has larger, 4–porate pollen grains, which are associated with polyploidy in Cichorieae) data, strongly favors the hypothesis that Faberia may have originated via hybridization between a member of Lactucinae with x = 9 (paternal parent or pollen donor) and a member of Crepidinae with x = 8 (maternal parent or ovule donor) and subsequent polyploidization. This work greatly increases our knowledge of Faberia and provides a convincing example of allopolyploid origin at the generic level within Cichorieae.

<em>Thelomma ocellatum</em>, a range extension to the Yukon Territory and case study in the use of molecular data to recognize asexually reproducing crustose lichens

An unusual sterile, asexually reproducing crustose lichen was encountered during fieldwork in the Yukon Territory of Canada. Genus and family level placement of the taxon were precluded by a lack of both sexual characters and any non-sexual characters that would have suggested an unambiguous generic affiliation. Examination of mtSSU and nrITS sequence data of the taxon revealed it to be a member of the Caliciaceae, with a sister relationship to the genus Tholurna . Subsequent molecular phylogenetic analyses of mtSSU sequence data suggested conspecificity with Thelomma ocellatum , one of the few calicioid lichens that reproduce asexually via lichenized diaspores. Comparison of the material from the Yukon with reference specimens and descriptions of T. ocellatum confirmed the identification of these populations, which extend the known distribution of T. ocellatum considerably northward in North America.

Two New Sterile Species of Loxospora (Sarrameanaceae: Lichenized Ascomycetes) from the Mid-Atlantic Coastal Plain

Abstract Molecular phylogenetic analyses of mtSSU and nrITS sequence data show that two new crustose species belong to the genus Loxospora. Both species are sterile asexually reproducing crustose lichens from the Mid-Atlantic Coastal Plain of eastern North America, and are chemically similar to L. lecanoriformis in producing 2-0-methylperlatolic acid. Loxosopora assateaguensis is a sorediate species that is described from a single locality on Assateague Island in Maryland. Loxospora confusa is a granulose-isidiate species that is widespread in the Mid-Atlantic with a disjunct population in the Joccassee Gorges of the southern Appalachian Mountains.

The rediscovery of Passiflora kwangtungensis Merr. (subgenus Decaloba supersection Disemma): acriticallyendangered Chinese endemic.

Passiflora kwangtungensis is a critically endangered Chinese species known from Guangxi, Guangdong, and Jiangxi Provinces. The species belongs to Passiflora subgenus Decaloba, supersection Disemma, section Octandranthus. Field observations decreased rapidly during the 1970s to 1980s, and it was suspected that this species might have been extirpated due to repeated deforestation events throughout southern China. In recent years, however, small isolated populations of this species have been rediscovered in Hunan Province, representing new locality records for Passiflora kwangtungensis. New herbarium collections, color photographs, and silica gel collections have provided an unexpected opportunity to examine the evolutionary significance of this species. The current study presents a revised morphological description of Passiflora kwangtungensis based on fresh material, along with an updated distribution map. Using nrITS sequence data, preliminary insights into the phylogenetic position of Passiflora kwangtungensis are presented. Molecular data support the placement of Passiflora kwangtungensis within supersection Disemma section Octandranthus. However, the exact placement of Passiflora kwangtungensis within this lineage is unclear. The nrITS data suggest that Passiflora kwangtungensis may be sister to a clade containing Passiflora from China, Nepal, India, and Southeast Asia. Morphologically, Passiflora kwangtungensis displays the most similarity Passiflora geminiflora (Nepal, India) and Passiflora henryi (China). Lastly, conservation status and recommendations are made for Passiflora kwangtungensis following the IUCN Red List Criteria, where this species is classified as CR C1+C2a(i); D.

Lepiota (Agaricales) in northern Thailand – 1. L. section Stenosporae

Eleven species of Lepiota section Stenosporae, reported as new for Thailand, are fully described and illustrated. Five are compared with European and North American collections based on nrITS sequence data. Two species possess a cutis-like pileipellis (L. aureofulvella, L. sp. 2) and nine are characterized by a trichodermium (L. alopochroa, L. castanea, L. citrophylla, L. erythrosticta, L. griseovirens, L. infelix, L. papillata, L. poliochloodes , L. sp. 1). New to science are Lepiota aureofulvella (close to L. boudieri) and L. papillata, which is characterized by small basidiomata covered with gray-brown to olive brown squamules, an orange-white to brownishorange context, spurred basidiospores with straight or outgrown base, clavate to cylindrical cheilocystidia, and a trichodermal pileus covering. A key to Lepiota sect. Stenosporae in northern Thailand is provided.

English

The water-lily genus Nymphaea exhibits a worldwide distribution with an estimated number of more than 50 extant species. Recent phylogenetic analyses resolved three major lineages, a subg. Brachyceras–subg. Anecphya clade, also including Nymphaea ondinea, a subg. Hydrocallis-subg. Lotos clade, and the temperate subg. Nymphaea as a third clade. This study extends the taxon sampling for Brachyceras, previously the least understood subgenus. Maximum Parsimony and Bayesian analysis of nrITS sequence data depict a monophyletic subg. Brachyceras-clade and show a New World clade to be nested within African taxa. Plastid trnT-trnF sequence data are less conclusive. A middle Miocene origin is inferred for the New World Brachyceras lineage that must have dispersed out of Africa either via a Beringian migrational route or through immediate long distance dispersal. Within subg. Brachyceras, the West African individuals of Nymphaea guineensis form a distinct clade in both nuclear and plastid trees to which the Madagascan Nymphaea minuta is sister. Central and East African Brachyceras species appear well separated, suggesting a separating effect of the Dahomey gap to the evolution of these species. ITS sequences are more powerful in identifying Nymphaea species than trnT–trnF sequences. Nevertheless, about 15% of the known species remain to be sampled for a complete molecular tree of water-lilies. This also requires sampling of multiple populations in order to discover entities with a common evolutionary history and distinct molecular and morphological characters.

Further support for the phylogenetic relationships within Euphorbia L. (Euphorbiaceae) from nrITS and trnL–trnF IGS sequence data

The cosmopolitan genus Euphorbia is one of the largest plant genera with an extreme phenotypic plasticity ranging from globose succulents to large shrubs and trees adapted to very divergent habitats like forests or deserts. We compiled the current knowledge about the evolution of Euphorbia by reconstructing a molecular phylogeny based on nearly all available internal transcribed spacer (nrITS) sequence data from previous investigations and sequences of newly sampled species. We compared the results with phylogenetic analyses based on a combined data set of nrITS and trnL–trnF intergenic spacer sequences of a subset of taxa. Apart from a few exceptions, the results correspond well to recently published studies based on different molecular markers. The genus Euphorbia is divided into four major clades, of which the clade comprising subgen. Rhizanthium is restricted to Africa and Madagascar, whereas the remaining three clades are distributed over several continents. Our results support the hypothesis that Euphorbia evolved in Africa from progenitors of subgen. Esula.

Are Lotus creticus and Lotus cytisoides (Leguminosae) closely related species? Evidence from nuclear ribosomal ITS sequence data

Lotus creticus is a potentially important perennial legume for soil management in the Mediterranean climate. This plant is in focus of experimental research in different countries. The so-called Lotus creticus group is taxonomically problematic. Although some authors consider all members of the group as a single variable species, others segregate several species distinct from L. creticus, especially L. cytisoides. Recent morphological studies suggested that L. creticus and L. cytisoides are taxonomically distinct at specific level and not even closely related to each other. Two molecular phylogenetic studies published so far and based on one accession of L. creticus each gave conflicting results on relationships of this species. In this paper, sequences of nuclear ribosomal ITS (nrITS) are produced from multiple accessions of both L. creticus and L. cytisoides. Taxonomic identity of each accession has been tested using morphology. The new nrITS sequences are inserted in a data matrix containing a representative set of Lotus species covering all the geographical range and all major taxonomic groups of Lotus. Phylogenetic analysis of nrITS sequence data showed that L. creticus is related to L. assakensis and other species of the section Pedrosia while L. cytisoides is related to L. longisiliquosus and other species of the section Lotea. These results are important for establishing future germplasm collection, breeding and selection programs of perennial Lotus species.

Molecular and morphological studies on the Didymodon tophaceus complex

Recently two Mediterranean species closely related to Didymodon tophaceus (Brid.) Lisa have been described in the genus Didymodon Hedw.: Didymodon sicculus M. J. Cano et al. and Didymodon erosus J. A. Jiménez & J. Guerra. The former has been proved to be widespread around the Mediterranean basin in recent years, and this study points to a considerable extension of its distribution area towards north, since it has also been discovered in the Netherlands. D. erosus, with its narrow morphological characterization, was only described four years ago and has hitherto only been known from the original localities in Spain. The molecular study based on nrITS sequence data of some selected specimens of all the three species suggests that D. erosus is much more frequent and widespread in Europe than supposed and, furthermore, is morphologically much more variable than previously described. A key for the identification of the three species, an amended description of D. erosus and a map showing the known distribution area are presented.

A model of bulb evolution in the eudicot genus Oxalis (Oxalidaceae)

The origins and monophyly of the bulbous habit in the eudicot genus Oxalis are uncertain, but key character state transitions in the evolution of true bulbs are currently thought to be reflected in extant pseudobulbous and other geophytic taxa. We test the relationships between the two major groups of bulbous Oxalis taxa, namely the southern African lineage which is centered in the speciose Cape Floristic Region (CFR), and the New World section Ionoxalis, by including the rhizomatous geophyte Oxalis acetosella, the caudiciform stem succulent Oxalis articulata, and the rhizomiform pseudobulbous Oxalis triangularis, in combined phylogenetic analyses of nrITS and trnL-F sequence data. We optimize several key bulbous characters in ancestral state reconstructions on produced phylogenies. Results of our analyses indicate that the evolution of bulbous characters in the genus is more complex than previously thought. Although the two major bulb types are homologous, the rhizomiform pseudobulbous habit arises from within true bulbs, and in most reconstructions the caudiciform stem succulent O. articulata is inferred to have secondarily lost several distinctive bulbous characters. O. acetosella is not as closely related to the bulbous lineage as previously thought. More sampling from other key taxa are needed before the order in which key bulbous characters were acquired can be verified. We discuss these results in terms of the taxonomic and ecological implications for the CFR Oxalis taxa.

Ezosciadium (Apiaceae): a taxonomic revision of yet another early diverging South African apioid genus

The hitherto poorly known Cape endemic genus Ezosciadium (Apiaceae) is revised. This genus is highly distinctive and can be distinguished from other annual genera of the region by its pilose vegetative and reproductive organs, the sessile compound umbels with conspicuously unequal rays, the non-inflexed petal tips, the relatively small, highly-inflexed stamens which appear almost sessile, and the prominent carpophores which persist on the plant. The fruit are unusual in the presence of druse crystals around the carpophore and tanniniferous substances in the epidermal cells of the ribs. The phylogenetic position of the genus within the subfamily Apioideae was assessed using rbcL, rps16 intron (2 new accessions) and nrITS (1 new accession) sequence data. Ezosciadiumcapense was found to form part of an early diverging lineage within the subfamily, sister group to the Annesorhiza clade and possibly also closely related to the genera Molopospermum and Astydamia. A comprehensive taxonomic revision, including typification, detailed descriptions, geographical range and illustrations, is presented.

Preliminary Molecular Phylogenetic Studies in Pachyanthus (Miconieae, Melastomataceae)

Pachyanthus (Melastomataceae: Miconieae) is traditionally circumscribed as a group of 20 species of Caribbean shrubs, mostly local Cuban endemics. However, the exact number of species is unknown because generic delimitations are still unclear for most genera of Miconieae. To test the monophyly of Pachyanthus, we produced a molecular phylogeny using nrITS and plastid trnS-G sequence data for 38 taxa of Miconieae in the genera Pachyanthus, Calycogonium, Tetrazygia, and Miconia. A species of Graffenrieda, a member of the sister group, Merianieae, was used as an outgroup. In the single-gene and combined analyses Pachyanthus is never recovered as a monophyletic group in any of its traditional circumscriptions. However, it is possible to distinguish a clade, Pachyanthus s.s., which is characterized by ovate to obovate petals that are conspicuously unguiculate; calyx lobes connate before anthesis, that separate into sepal-like segments; straight, ovate to oblong, yellow anthers without connective appendages or, if present, then inconspicuous, anthers dehiscing by small apical pores, and fruits with numerous seeds, 1–2 mm long, obpyramidal, with a smooth testa. The remaining species traditionally included in Pachyanthus do not have any of these features. They do not form a single monophyletic group, but instead are scattered across several clades, which also contain species of Calycogonium, Miconia, and Tetrazygia. Additional detailed molecular and morphological studies are needed in the Miconieae to ascertain whether these clades should be treated as new genera or recircumscribed as part of currently recognized genera in the Caribbean region, such as Calycogonium and Tetrazygia.

An ITS phylogeny of tribe Senecioneae (Asteraceae) and a new delimitation of Senecio L.

Senecioneae is the largest tribe of Asteraceae, comprised of ca. 150 genera and 3,000 species. Approximately one‐third of its species are placed in Senecio, making it one of the largest genera of flowering plants. Despite considerable efforts to classify and understand the striking morphological diversity in Senecioneae, little is known about its intergeneric relationships. This lack of phylogenetic understanding is predominantly caused by conflicting clues from morphological characters, the large size of the tribe, and the absence of a good delimitation of Senecio. Phylogenetic analyses of nrITS and plastid DNA sequence data were used to produce a hypothesis of evolutionary relationships in Senecioneae and a new, monophyletic, delimitation of Senecio. The results of separate and combined phylogenetic analyses of the two datasets were compared to previous taxonomic treatments, morphological and karyological data, and biogeographic patterns. These studies indicate that the subtribal delimitation of Senecioneae needs to be revised to reflect exclusively monophyletic subtribes. This would involve abolishing subtribes Adenostylinae, Blennospermatinae, and Tephroseridinae and recognizing subtribes Abrotanellinae, Othonninae, and Senecioninae. Moreover, Tussilagininae may need to be split into three or four subtribes: Brachyglottidinae, Chersodominae, Tussilagininae, and perhaps Doronicinae. On the intergeneric level, these phylogenies provide new insights into evolutionary relationships, resulting in a first approximation of a comprehensive phylogeny for the tribe. Most species currently assigned to Senecio form a well supported clade. Thus, a new delimitation of Senecio is proposed, which involves transferring the species of Aetheolaena, Culcitium, Hasteola, Iocenes, Lasiocephalus, and Robinsonia to Senecio and removing several Senecio groups that are only distantly related to the core of Senecio. Area optimization analyses indicate a strong African influence throughout the evolutionary history of Senecioneae, predominantly in subtribes Senecioninae and Othonninae.

A phylogenetic evaluation of Leandra (Miconieae, Melastomataceae): a polyphyletic genus where the seeds tell the story, not the petals

AbstractMelastomataceae is a tropical family of 4500–5000 species divided into nine tribes. The largest tribe, Miconieae, is composed of approximately 2200 species in 30 genera and is found exclusively in the Neotropics. Previous phylogenetic analyses of the Miconieae have suggested that many of the genera are derived from a paraphyletic Miconia. However, these analyses only included six species of the large genus Leandra, so its phylogenetic affinities remained unclear. As currently defined Leandra is characterized by acute petals and terminal inflorescences, but some species of Miconia, Clidemia and Ossaea also have these characters. In this study, we present an analysis of nrITS sequence data for a sample of 63 species of Leandra. The genus is clearly resolved as polyphyletic, but some distinct and well‐supported clades exist. Some of these partially correspond to sections recognized in the nineteenth century by Cogniaux, or to geographic distribution. The distribution of seed structure characters is better correlated with the phylogeny than traditional characters, such as petal morphology. Seed appendages in Leandra have evolved independently at least four times.© The Willi Hennig Society 2007.

A phylogenetic study of Echidnopsis Hook. f. (Apocynaceae-Asclepiadoideae) - taxonomic implications and the colonization of the Socotran archipelago

We investigated the phylogeny, taxonomy and biogeography of the Eritreo-Arabian genus Echidnopsis Hook. f. (Apocynaceae-Asclepiadoideae). Phylogenetic reconstructions based on nrITS sequence data were obtained using maximum likelihood and parsimony analyses. The results reveal two weakly supported clades, each with a mix of African and Arabian taxa, including the genus Rhytidocaulon, and with four Socotran species forming a subclade of their own. Rather than a vicariance origin of these island elements, our data suggest a single dispersal event from eastern Africa. Echidnopsis thus parallels biogeographic patterns found for other Socotran endemic plants. Our revised taxonomy recognizes 28 species and 4 subspecies in the genus. Two new combinations, E. planiflora subsp. chrysantha and E. sharpei subsp. bavazzani are proposed.

A preliminary phylogeny of the tribe Miconieae (Melastomataceae) based on nrITS sequence data and its implications on inflorescence position

Miconieae is the most diverse tribe of Melastomataceae, with 30 genera and over 2200 species. The tribe is characterized by fleshy fruits and partially to totally inferior ovaries. To test monophyly of the tribe and assess phylogenetic relationships within it, sequence data from nrITS were gathered and analyzed for 110 taxa in Miconieae and 32 putative outgroups. The tribe Miconieae is not resolved as monophyletic, but rather composed of two distinct clades: one composed of the cauliflorous genera Henriettea, Henriettella, Loreya and Bellucia, and a second clade with all other taxa in Miconieae, sister to a polytomy that includes representatives from tribes Merianieae and Blakeeae. Terminal inflorescences are optimized as basal within Miconieae, with lateral inflorescences evolving in at least four different instances. Cauliflory does not appear to be derived from truly axillary inflorescences; instead it seems to have evolved independently. The terminal–flowered genera Tococa, Conostegia, Tetrazygia, Anaectocalyx, Charianthus, Calycogonium, and Leandra pro parte seem to be derived from within the large genus Miconia, as is Clidemia, a genus with both axillary inflorescences and terminal inflorescences that are deflexed to a lateral position by an axillary branch. Maieta and Necranium, both with axillary inflorescences, are resolved as derived from within Clidemia.

Phylogeny of subsect. Meleuphorbia (A. Berger) Pax & Hoffm. ( Euphorbia L.) reflects the climatic regime in South Africa

The nuclear ITS region and four noncoding cpDNA regions were directly sequenced to reconstruct the phylogeny of subsect. Meleuphorbia (Euphorbia L.), which is endemic to South Africa. Sequence polymorphism within cpDNA regions was too low to permit phylogenetic analyses. Large deletions including the ctp2-atpB proximal promoter in the atpB-rbcL IGS were found in two individuals. Phylogeny of subsect. Meleuphorbia was reconstructed using nrITS sequence data. The two resulting major clades are consistent with the geographic distribution of the investigated taxa. Plants distributed in the winter rainfall area in the Little Karoo form one clade, plants growing in the Great Karoo with predominant summer rainfall form the other. Subsect. Meleuphorbia is not monophyletic, because members of subsect. Anthacantha are clustered within the meleuphorbias. Both share functional unisexuality, form angled stems and the key character of Anthacantha (inflorescence spines) occurs as a transitional stage in form of persistent peduncles in Meleuphorbia.

Fine-level mycorrhizal specificity in the Monotropoideae (Ericaceae): specificity for fungal species groups.

The Monotropoideae (Ericaceae) are non-photosynthetic angiosperms that obtain fixed carbon from basidiomycete ectomycorrhizal fungi. In previous work, we showed that each plant species is associated with a single genus or a set of closely related genera of ectomycorrhizal fungi. Here we show that the level of specificity is much higher. We used a molecular phylogenetic approach to contrast specificity patterns among eight plant lineages and three fungal genera. We relied on fungal nuclear internal transcribed spacer (nrITS) sequence data obtained from 161 basidiocarps and 85 monotropoid roots representing 286 sampled plants screened using restriction length polymorphisms. From the phylogenetic placement of fungal symbionts in fungal phylograms, we found that three basal (Sarcodes, Pterospora, Pleuricospora) and one derived lineage (Allotropa) of plants target narrow clades of closely related species groups of fungi, and four derived lineages (Monotropa hypopithys species group, Pityopus) target more distant species groups. Within most plant lineages, geography and photobiont association constrain specificity. Specificity extended further in Pterospora andromedea, in which sequence haplotypes at the plastid trn L-F region of 73 plants were significantly associated with different fungal species groups even in sympatry. These results indicate that both the macro- and microevolution of the Monotropoideae are tightly coupled to their mycorrhizal symbionts.