bluuebunny/crossref_metadata_2025 huggingface dataset:
Floras: a model for biodiversity studies or a thing of the past?
Authors: Funk Victoria A.
Published: May 2010

Floras (and Faunas) have a rich history that involves examining questions on evolution and biogeography. However, in recent publications Floras have been viewed as an end unto themselves, separate from clade‐based monographs and evolutionary studies. Floras are not a separate entity but rather a part of a continuum that involves databases, checklists, floras, biodiversity studies, and conservation biology as well as monographs. As the importance of Floras and related studies has become more apparent, there have been comments about the lag time between when specimens are collected and when they are identified, the amount of time it takes to describe new taxa, and how long it takes to finish floras and other projects. Some have referred to this as the “Taxonomic Impediment”, and it is sometimes laid at the feet of taxonomists. Taxonomists can become more efficient by using various on‐line resources and this will continue to speed up as more literature, etc. become available but the impediments to taxonomy are many, not the least of which is a lack of funding and the dwindling number of taxonomists. Changes in how systematists work and interact with other branches of science must take place in order to speed up research and re‐establish the importance of Floras but only a substantial infusion of funds and personnel will really accelerate our progress.
On‐line keys: more than just paper on the web
Authors: Farr David F.
Published: May 2010

The internet has opened new opportunities for the distribution of systematic information. Advantages such as immediate worldwide distribution, affordable presentation of color illustrations, ease of updating the information, and low cost all suggest that the web is an ideal medium for the publication of taxonomic keys, descriptions, illustrations, and catalogues. Using examples from on‐line interactive keys published on the web and the interactive key projects developed at the USDA ARS Systematic Botany and Mycology Laboratory (SBML), this paper presents important points to be considered in developing online interactive keys. These include the use of standard internet protocols, emphasis on images, and easy maintenance by scientists without intervention of IT staff. An additional technical point is that morphological data should be external to the key program. As a result, when data are changed or replaced, the system will automatically be updated. In addition, these data can be used for applications outside of the key. While the potential usefulness of internet keys and other on‐line systematic information may be obvious, there are hurdles that must be overcome before there is any significant proliferation of on‐line keys. Systematists must embrace the internet as a desirable publishing option, peer review and institutional reward systems must recognize the significance of non‐paper publication, and systematists need to incorporate structured procedures for data collection.
First steps toward an electronic field guide for plants
Authors: Agarwal Gaurav , Belhumeur Peter , Feiner Steven , Jacobs David , Kress W. John , Ramamoorthi Ravi , Bourg Norman A. , Dixit Nandan , Ling Haibin , Mahajan Dhruv , Russell Rusty , Shirdhonkar Sameer , Sunkavalli Kalyan , White Sean
Published: May 2010

We describe an ongoing project to digitize information about plant specimens and make it available to botanists in the field. This first requires digital images and models, and then effective retrieval and mobile computing mechanisms for accessing this information. We have almost completed a digital archive of the collection of type specimens at the Smithsonian Institution Department of Botany. Using these and additional images, we have also constructed prototype electronic field guides for the flora of Plummers Island. Our guides use a novel computer vision algorithm to compute leaf similarity. This algorithm is integrated into image browsers that assist a user in navigating a large collection of images to identify the species of a new specimen. For example, our systems allow a user to photograph a leaf and use this image to retrieve a set of leaves with similar shapes. We measured the effectiveness of one of these systems with recognition experiments on a large dataset of images, and with user studies of the complete retrieval system. In addition, we describe future directions for acquiring models of more complex, 3D specimens, and for using new methods in wearable computing to interact with data in the 3D environment in which it is acquired.
Ledebouria, Resnova and Drimiopsis: a tale of three genera
Authors: Lebatha Pearl , Buys Matt H. , Stedje Brita
Published: May 2010

The monophyletic status of Ledebouria, Resnova and Drimiopsis (Hyacinthaceae) was investigated using cladistic analyses of morphological characters as well as by combined trnL‐F and morphology dataset. Based on morphology alone, numerous synapomorphies support Ledebouria, Resnova and Drimiopsis as three separate clades. In contrast, trnL‐F data in a reduced taxon sample suggest that Resnova and Drimiopsis are imbedded within Ledebouria, while in combination with morphology again suggest them to be separate. The analysis of morphological data shows that the majority of morphological characters listed by Manning & al. (2004) to support Ledebouria s.l. are homoplasious or symplesiomorphies. A revised taxonomy of Ledebouria, Resnova and Drimiopsis is premature.
Adscription of Parafestuca albida (Lowe) E. B. Alexeev to Koeleria Pers.
Authors: Quintanar Alejandro , Catalán Pilar , Castroviejo Santiago
Published: May 2010

A new name, Koeleria loweana Quintanar, Catalán & Castrov. nom. nov., is provided for Parafestuca albida (Lowe) E. B. Alexeev, the single species of the endemic Madeiran genus created by Alexeev to accomodate Festuca albida Lowe. A lectotype is selected and a first chromosome number of 2n = ca. 175 is reported for this taxon. Careful re‐examination of morphological characters and new chromosome data support the inclusion of this relict Macaronesian lineage within the diploid‐to‐highly‐polyploid complex genus Koeleria Pers. Phylogenetic analyses based on both nuclear ribosomal ITS and chloroplast trnT‐F sequences further indicate that Parafestuca is neither related to Festuca nor to the festucoids (Loliinae, Poeae), but a member of a strong Koeleriinae core clade (Aveneae).
Morphological convergence or lineage sorting? The case of Cytisus purgans auct. (Leguminosae)
Authors: Cubas Paloma , Pardo Cristina , Tahiri Hikmat
Published: May 2010

Genetic distances among populations and phylogenetic hypothesis concerning origin and diversification of Cytisus purgans s.l. are inferred by analysis of the ITS and ETS regions (nrDNA) and the trnL‐trnF intergenic spacer (cpDNA). Cytisus purgans s.l., a shrub of western Mediterranean mountains, consists of two evolutionary units: C. balansae (Boiss.) Ball (Morocco, Algeria, southern Spain) and C. oromediterraneus Rivas Mart. & al. (France, Portugal, Andorra, central and northern Spain). The two units are related to different Cytisus groups, in Bayesian and Maximum Parsimony analyses, and may be genetically unrelated, their morphological similarities being the result of convergence. However, the incongruence in the position of both species in the ITS tree and the ETS and trnL‐trnF trees suggests an alternative explanation. Genetic differentiation could be due to lineage sorting of allelic polymorphism in the ITS region of the common ancestor, and the morphological similarities the result of morphological parallelism. Cytisus balansae conserves ITS sequences related to old Cytisus taxa; rapid radiation may have led to a western Mediterranean lineage in which C. oromediterraneus originated.
Roccella gracilis, the correct name for R. peruensis and R. humboldtiana (lichenized fungi, Roccellaceae)
Authors: Tehler Anders
Published: May 2010

The nomenclature and taxonomy of the American, sorediate Roccella species recently known as R. peruensis and R. humboldtiana is reassessed. The two taxa are conspecific and the first, oldest, legitimate name for the united taxon is Roccella gracilis Bory.
Lectotypification of Juncus kochii and Juncus supinus var. nigritellus (Juncaceae)
Authors: Procków Jarosław
Published: May 2010

The typifications of Juncus kochii F.W. Schultz and Juncus supinus Moench var. nigritellus W.D.J. Koch non (D. Don) F.W. Schultz are discussed. A specimen from the Koch Herbarium (at L) is designated lectotype for both names. The taxon to which they apply is at present best regarded as Juncus bulbosus L. subsp. kochii (F.W. Schultz) Reichg.
Acroscyphella N. Kitag. & Grolle, the correct substitute name for Acroscyphus N. Kitag. (Hepaticae: Balantiopsidaceae)
Authors: Zijlstra Gea
Published: May 2010

Acroscyphus N. Kitag. (1984) is a later homonym of Acroscyphus Lév. 1846. The first substitute name published for it is Acroscyphella N. Kitag. & Grolle, which antedates Austroscyphus R.M. Schust. by just over two weeks.
Are mitochondrial genes useful for the analysis of monocot relationships?
Authors: Davis Jerrold I. , Petersen Gitte , Seberg Ole , Stevenson Dennis W. , Hardy Christopher R. , Simmons Mark P. , Michelangeli Fabian A. , Goldman Douglas H. , Campbell Lisa M. , Specht Chelsea D. , Cohen James I.
Published: May 2010

A phylogenetic analysis of monocots and related dicots was conducted, using a four‐gene matrix consisting of two genes from the plastid genome (matK and rbcL) and two from the mitochondrial genome (atpA/atp1 and cob). The taxon sample includes 101 monocots and 36 dicots, and all four genes were sampled for all 137 taxa. Jackknife support was assessed for clades resolved by the four‐gene analysis, and compared to support for the same clades by each of the four three‐gene subset matrices, in order to quantify the degree to which each gene contributed to or detracted from support for each clade. Instances of positively and negatively correlated support for clades by genes of the same and different genomes were observed. In particular, the placement of Acorus within a clade that also includes Tofieldiaceae, Araceae, and Alismatales s.s., as opposed to its frequent placement as sister of all other monocots, is supported by atpA and matK. The results indicate that genes from the mitochondrial genome provide a unique test of relationships that have been inferred with plastid‐encoded genes.
Molecular phylogeny, morphology and taxonomic re‐circumscription of the generic complex Nonea/Elizaldia/Pulmonaria/Paraskevia (Boraginaceae‐Boragineae)
Authors: Selvi Federico , Bigazzi Massimo , Hilger Hartmut H. , Papini Alessio
Published: May 2010

We performed a molecular phylogenetic analysis of the generic complex Nonea/Elizaldia/Paraskevia/Pulmonaria (Boraginaceae‐Boragineae), using trnLUAA and ITS1 sequences from non‐coding plastid and nuclear DNA, respectively. In the strict consensus of most parsimonious trees from combined ITS1/trnL sequences the ingroup forms a monophyletic group with two sister clades of Nonea/Elizaldia and Paraskevia/Pulmonaria. The eastern Mediterranean Nonea obtusifolia is sister to the rest of the ingroup and more distant to Nonea taxa than to those of Pulmonaria. Elizaldia is firmly nested in Nonea and forms a clade that includes the southern Mediterranean species N. vesicaria. Nonea as currently circumscribed is therefore paraphyletic. The molecular results are congruent with morphological, karyological and chorological features and suggest a redefinition of Nonea s.l. based on monophyletic groups. We propose: (i) the institution of the new monotypic genus Melanortocarya gen. nov. for N. obtusifolia, (ii) the inclusion of Elizaldia within Nonea, and (iii) the transfer of Paraskevia (Nonea) cesatiana to Pulmonaria. Nonea embergeri, previously treated at the infraspecific level, is recognized at species rank and E. calycina subsp. multicolor is placed in synonymy of N. calycina.
Serpocaulon (Polypodiaceae), a new genus segregated from Polypodium
Authors: Smith Alan R. , Kreier Hans-Peter , Haufler Christopher H. , Ranker Tom A. , Schneider Harald
Published: May 2010

We describe the neotropical fern genus Serpocaulon (Polypodiaceae), segregated from Polypodium, and make new combinations for the forty known species. Serpocaulon has been recognized previously as a putatively natural group by several authors, based on morphological evidence, but never accorded generic rank. The monophyly of Serpocaulon is strongly supported in chloroplast DNA‐based phylogenetic analyses, using the genes rbcL, rps4, rps4‐trnS intergenic spacer, and trnL‐F intergenic spacer on 29 samples from 22 species. Serpocaulon is readily separated from other subclades within Polypodiaceae, and especially from Polypodium, which is less closely related to Serpocaulon than are several other genera. Serpocaulon differs from other New World polypods in the combination of usually long‐creeping, sparingly branched rhizomes with clathrate (sometimes strongly so), usually peltately attached scales; regularly anastomosing (goniophlebioid) veins with individual areoles chevron‐shaped and each with a single, free, included excurrent veinlet; and non‐paraphysate sori in one to 10 rows between costae and pinna margins. In Polypodium, the rhizome scales are not clathrate, ± concolorous, and invaginated at the base, with somewhat overlapping basal lobes, and rhizomes are generally shorter‐creeping and more frequently branched, the veins are free or forming a single row of areoles, and the sori uniseriate on each side of the costae. Most species of true Polypodium are north‐temperate, Mexican, or Mesoamerican in distribution, while Serpocaulon is entirely neotropical or subtropical, with the greatest number of species in South America. There appears to be no convenient infrageneric division of the species within Serpocaulon, although the most widespread species, S. triseriale, is somewhat isolated at the base of the clade. Species with the thinnest rhizomes also have the fewest scales, and generally grow at high elevations. Species having the scaliest rhizomes, with scales spreading and strongly overlapping, form a weakly supported subclade, as do species with multiseriate rows of areoles between costae and pinna margins.
Evolutionary relationships and diversification of Stachyuraceae based on sequences of four chloroplast markers and the nuclear ribosomal ITS region
Authors: Zhu Yu-Ping , Wen Jun , Zhang Zhi-Yun , Chen Zhi-Duan
Published: May 2010

Stachyuraceae consist of a single genus Stachyurus with about ten species endemic to eastern Asia. The family was recently shown to be sister to the western North American Crossosomataceae. The phylogeny of Stachyuraceae and its relatives was reconstructed based on sequences of four chloroplast DNA regions (trnL intron and adjacent trnL‐trnF spacer, rps16 intron, ndhF gene, trnS‐trnG‐trnG region) and the nuclear ribosomal ITS region. The monophyly of Stachyurus was strongly supported. The divergence time between Stachyuraceae and Crossosomataceae was estimated to be 68.25 ± 10.36 million years ago (MYA) using the penalized likelihood method based on rbcL sequences data with fossil calibration. Stachyurus sigeyosii was previously synonymized as S. himalaicus, but our analysis shows that it is sister to the morphologically highly distinct S. praecox from Japan and does not form a clade with S. himalaicus.
The systematic significance of seed morphology in Stenocereus (Cactaceae)
Authors: Arroyo-Cosultchi Gabriel , Terrazas Teresa , Arias Salvador , Arreola-Nava Hilda J.
Published: May 2010

Seed morphology of 24 species of Stenocereus was examined by scanning electron microscopy. Quantitative and qualitative features were evaluated to identify groups of species using a phenetic analysis. Two groups were distinguished based on morphological variations of seed size, luster, multicellular sculpture, keeling, cell‐size, periclinal wall sculpture, microrelief and HM complex shape and position relative to rim. All species studied were keeled, with isodiametric cells in the lateral region. Stenocereus alamosensis, S. kerberi and S. beneckei are unique among Stenocereus species in that their seeds are flat but lack micro‐relief. Stenocereus aragonii and S. eichlamii have large, glossy seeds lacking micro‐relief unlike other Stenocereus species, but like most Pachycereus, are unique in that cells in the lateral region display partly convex, low domes. Quantitative and qualitative congruence and discordance among characters that determine species groups in stenocereus are discussed.
A new combination in Senegalia and typification of six New World Acacia names
Authors: Glass Catherine E. , Seigler David S.
Published: May 2010

Recent and past morphological and genetic studies suggest that the genus Acacia s.l. is better treated as a number of segregate genera. The generic segregates more or less follow the boundaries of the former Acacia subgenera. It is thus an appropriate time to transfer Acacia kelloggiana A.M. Carter & Rudd from Acacia subgenus Aculeiferum to Senegalia Rafinesque. Studies of New World members of Acacia subgenus Aculeiferum have also revealed the necessity to select neotypes or lectotypes for some names of species now placed in the genus Senegalia.
Typification of names of lichen taxa described by W. Nylander from Angola and São Tomé e Príncipe
Authors: Paz-Bermúdez Graciela
Published: May 2010

William Nylander described two new lichen taxa from Angola and 24 from São Tomé and Príncipe based on material gathered by various Portuguese collectors, mainly Francisco Newton and Adolpho Moller. This material is deposited in the herbaria of Porto (PO), Coimbra (COI) and Helsinki (H‐NYL). A list of these specimens and information on the types, including 12 new lectotypifications, is presented here.
Typification of the accepted names in the Jacobaea maritima group (Asteraceae)
Authors: Peruzzi Lorenzo , Passalacqua Nicodemo G. , Jarvis Charlie E.
Published: May 2010

All the seven accepted names for species of the Jacobaea maritima group are discussed and typified. Lectotypes are selected for Cineraria bicolor Willd. from the Willdenow Herbarium (B); C. gibbosa Guss. and C. nebrodensis Guss. from the Gussone Herbarium (NAP); Othonna maritima L. from the Clifford Herbarium (BM); Senecio gnaphalodes Sieber from the Brno Herbarium (BRNM) and S. taygeteus Boiss & Heldr. from the Boissier Herbarium (G). A neotype, conserved in the Herbarium of the University of Calabria (CLU), is proposed for Cineraria ambigua Biv. Four needed combinations under Jacobaea Mill. are here proposed for the first time: J. maritima subsp. bicolor (Willd.) Peruzzi & al., J. maritima subsp. gibbosa (Guss.) Peruzzi & al., Jacobaea ambigua subsp. nebrodensis (Guss.) Peruzzi & al. and J. ambigua subsp. taygetea (Boiss. & Heldr.) Peruzzi & al.
Typification of some of Hudson’s plant names in Carex L.
Authors: Molina Ana , Acedo Carmen , Jarvis Charlie , Llamas Félix
Published: May 2010

The types of seven names of Carex species described by Hudson in the first and second editions of Flora anglica are designated here. Four lectotypes are chosen; two are plates, from Morison and Plukenet, a third is from original material conserved at BM‐SL (all of them fixed by epitypes) and a fourth is from original material conserved at K. For the remaining three names, we have designed neotypes, selecting among appropriate material from the same regions and habitats indicated by Hudson.
The typification and identity of Cyperus hirtus Thunb. (1803)
Authors: Lye Kåre Arnstein
Published: May 2010

Cyperus hirtus Thunb. from South Africa is lectotypified and shown to belong to Fimbristylis squarrosa Vahl. Misidentification of this plant and misapplication of its name by Kükenthal in 1936 has resulted in American botanists using Bulbostylis hirta (Thunb.) Svenson (e.g., in Flora Mesoamericana) for the pantropical taxon Bulbostylis hispidula (Vahl) R. Haines.
Pollination drops, pollen, and insect pollination of Mesozoic gymnosperms
Authors: Labandeira Conrad C. , Kvaček Jiří , Mostovski Mikhail B.
Published: May 2010

Recent focus on plant‐insect associations during the angiosperm radiation from the last 30 million years of the Early Cretaceous has inadvertently de‐emphasized a similar but earlier diversification that occurred among gymnosperms. The existence of gymnosperm‐insect associations during the preangiospermous Mesozoic is evidenced by mouthparts capable of reaching and imbibing pollination drops or similar fluids, availability of pollen types consistent with entomophily, and opportunities for related consumption of pollen, seeds, and reproductively associated tissues in major seed‐plant groups, namely seed ferns, conifers, cycads, bennettitaleans, and gnetaleans. Based on stereotypical plant damage, head‐adherent pollen, gut contents, wing structure, mouthpart morphology and insect damage to plant reproductive organs, the likely nectarivores, pollinivores and pollinators were orthopterans, phasmatodeans, webspinners, sawflies and wasps, moths, beetles, mecopteroids, and true flies. These associations are ranked from possible to probable although the last three insect clades provide the strongest evidence for pollinator activity. We document two mid Cretaceous examples of these associations—cycadeoideaceous bennettitaleans and beetles and a cheirolepidiaceous conifer and flies—for which there are multiple lines of evidence for insect consumption of plant reproductive tissues but also pollination mutualisms. These data highlight the independent origin of a major phase of plant‐insect pollinator‐related associations during the mid Mesozoic that served as a prelude for the separate, iterative and later colonization of angiosperms.
The problem of generalized flowers: morphological aspects
Authors: Weberling Focko
Published: May 2010

Since Delpino (1868–74) recognized that flowers sharing similar physiognomies are preferentially visited by certain groups of animals, it has been commonly inferred that these biological groups (flowers and pollinators) have passed a more or less complicated evolutionary process of mutual specialization. The question, however, as to what were the initial angiosperm floral forms remains unanswered. Whatever the form, a broad spectrum of visitors was likely. Each organism needs to be adapted to its environment, for which reason the term “generalized” instead of “non‐specialized” is to be preferred. Generalized flowers occur even in otherwise highly evolved families, suggesting that these representatives have developed secondarily from a somewhat specialized pollination type; this points to the fact that “generalized” and “specialized” are relative terms. It also means that a generalized flower is not synonymous with a “primitive flower”! In terms of morphology, the original “primitive flower” form is a subject of debate. Neither in the fossil records nor among extant, archaic angiosperms is there a model organism bearing a flower with a broad spectrum of visitors, and which exhibits all organs in their plesiomorphic state. Nor is it likely that such a plant will ever be discovered. Thus, we must be content with a relative solution; there is one—hitherto only one—magnolioid family, the Winteraceae, some members of which approach the idealized model. Representatives of this family are characterized by many plesiomorphic features and have open flowers visited by a broad spectrum of pollen vectors. An explanation of how these plants could have remained in this generalized condition over long time periods is offered.
Multiple meanings and modes: on the many ways to be a generalist flower
Authors: Ollerton Jeff , Killick Ant , Lamborn Ellen , Watts Stella , Whiston Margaret
Published: May 2010

The concept of a generalist flower appears to mean different things to different people, depending upon their background and training. We assess the different meanings of generalist flowers with respect to the ecological “set and setting” of pollination, and then we discuss notions of ecological, functional and phenotypic generalization. These ideas are explored in more detail using examples from our own published and unpublished studies on the pollination ecology of Daucus carota, Hedera helix, and Chamerion angustifolium, and from the published work of other researchers. Finally we relate these ideas and clarified definitions of “generalist” and “specialist” flowers to the pollination syndrome concept.
Polyphyly of Polycarpon (Caryophyllaceae) inferred from DNA sequence data
Authors: Kool Anneleen , Bengtson Annika , Thulin Mats
Published: May 2010

A phylogenetic study of the genus Polycarpon was made using DNA sequence data from the chloroplast rps16 intron and nuclear RPB2 regions. Polycarpon as currently recognised is shown to be polyphyletic. The South American species P. coquimbense and P. suffruticosum are more closely related to Haya obovata (Socotra) and Polycarpaea spicata (paleotropical) than to the remaining species of Polycarpon, and the widespread tropical species P. prostratum is nested with Macaronesian species of Polycarpaea. All three should therefore be excluded from Polycarpon. The remaining species, the P. tetraphyllum group, has its main diversity in the Mediterranean region. It is a polyploid complex with morphologically very similar taxa mostly separated only by partially overlapping characters. The members of this group form a strongly supported, but largely unresolved clade. It is proposed that they are all included in a widely circumscribed P. tetraphyllum. The dehiscence of the capsules in P. tetraphyllum, by valves that elastically roll inwards and finally throw out the seeds, is unique in Caryophyllaceae and provides a strong synapomorphy for Polycarpon in this new restricted sense.
Phylogeny and biogeography of Craspedia (Asteraceae: Gnaphalieae) based on ITS, ETS and psbA-trnH sequence data
Authors: Ford Kerry A. , Ward Josephine M. , Smissen Rob D. , Wagstaff Steven J. , Breitwieser Ilse
Published: May 2010

Craspedia (Asteraceae: Gnaphalieae) is a genus of 23 species found only in Australia and New Zealand. Maximum parsimony and maximum likelihood analyses of ITS and ETS intergenic spacers from the nuclear genome recovered three main lineages. The first lineage consists solely of the Australian species C. haplorrhiza, the relationships of which are unresolved, and the second includes species that are also exclusively Australian in distribution. The third lineage comprises two monophyletic groups; one including all the remaining Australian species sampled and the other, all New Zealand entities sampled. Monophyly of New Zealand Craspedia is also supported by analysis of psbA‐trnH intergenic spacer sequences. Australian alpine species are independently derived from within the two larger Australian lineages. Both major Australian lineages are present in Tasmania suggesting multiple colonisations from mainland Australia. The single lineage of New Zealand Craspedia and the low divergences between Australian and New Zealand Craspedia samples are consistent with the derivation of New Zealand Craspedia via a single dispersal event from south‐east Australia in the Late Tertiary or Quaternary. Compared with Australian Craspedia, the New Zealand species show extensive morphological divergence but little sequence divergence, suggesting a recent and rapid species radiation.
Phylogenetic relationships in the genus Crinum (Amaryllidaceae) with emphasis on tropical African species: evidence from trnL-F and nuclear ITS DNA sequence data
Authors: Kwembeya Ezekeil G. , Bjorå Charlotte S. , Stedje Brita , Nordal Inger
Published: May 2010

Fifty‐three species of Boophone Herb., Ammocharis Herb., Cybistetes Milne‐Redh. and Crinum L. were analysed cladistically using nuclear ITS and plastid trnL‐F sequences, with Amaryllis belladonna L. as an outgroup. Boophone disticha (L. f.) Herb. is sister to the subtribe Crininae (i.e., Crinum, Ammocharis, Cybistetes). Two main clades were revealed in the Crininae. The first comprises Ammocharis, Crinum baumii Harms and Cybistetes longifolia Milne‐Redh. & Schweick. Cybistetes longifolia appears in a sister relationship to Ammocharis angolensis (Baker) Milne‐Redh. & Schweick. Crinum baumii and Cybistetes longifolia are thus both referred to the genus Ammocharis under the names Ammocharis baumii (Harms) Milne‐Redh. and Ammocharis longifolia (L.) Roem. respectively. The second main clade is constituted by all other examined species of Crinum, and is split into four subclades. The first subclade includes populations of the newly discovered Zambian species, C. jasonii Bjorå & Nordal (2006), which has bell‐shaped flowers. The second subclade comprises all species with star‐shaped flowers (“Stenaster”) occurring in the southern and eastern part of Africa, Madagascar, and Australasia. The Angolan “Codonocrinum” (i.e., with bell‐shaped flowers), C. fimbriatulum Baker, is in a sister relationship to this subclade. The third subclade includes species with bell‐shaped flowers with main distribution in southern Africa, in addition to the Australian C. flaccidum Herb. The fourth subclade includes North African and tropical species with bell‐shaped flowers including Asiatic taxa. A monophyletic group with star‐shaped flowers distributed in West Africa and America is nested within this subclade. Interestingly, a narrowly endemic species, C. binghamii Nordal & Kwembeya, occurring in swamps in western Zambia is sister to this “western Stenaster” group. There is no support for the taxonomic recognition of subgeneric delimitation based on flower morphology. On the other hand, there are strong geographical and ecological trends in the phylogeny.
Towards a phylogenetic nomenclature ofTracheophyta
Authors: Cantino Philip D. , Doyle James A. , Graham Sean W. , Judd Walter S. , Olmstead Richard G. , Soltis Douglas E. , Soltis Pamela S. , Donoghue Michael J.
Published: May 2010

This is an abbreviated version of a paper that appears in full in the Electronic supplement toTaxon. Phylogenetic definitions are provided for the names of 20 clades of vascular plants (plus 33 others in the electronic supplement). Emphasis has been placed on well‐supported clades that are widely known to non‐specialists and/or have a deep origin withinTracheophytaorAngiospermae. These treatments follow the draftPhyloCodeand illustrate the application of phylogenetic nomenclature in a variety of nomenclatural and phylogenetic contexts. Phylogenetic nomenclature promotes precision in distinguishing crown, apomorphy‐based, and total clades, thereby improving communication about character evolution and divergence times. To make these distinctions more transparent without increasing the number of entirely different names that must be learned, the following naming conventions (which have been adopted in the most recent draft of thePhyloCode) are employed here: widely known names are applied to crown clades, and the corresponding total clade (i.e., crown plus stem) is named “Pan‐X”, where “X” is the name of the crown (e.g.,Pan‐Spermatophytafor the total clade of plants that share more recent ancestry with extant seed plants than with any other crown clade). If a name “X” that is based etymologically on an apomorphy is applied to the crown, the name “Apo‐X” is applied to the clade for which this trait is synapomorphic (e.g.,Apo‐Spermatophytafor the clade originating from the first plant with seeds). Crown clade names can be defined by three kinds of definitions, two of which are used here: standard node‐based and branch‐modified node‐based. The latter is particularly useful when outgroup relationships of a crown clade are better known than basal relationships within the clade. Criteria and approaches used here to choose among competing preexisting names for a clade, to select a definition type, to choose appropriate specifiers, and (in some cases) to restrict the use of a name to certain phylogenetic contexts may be widely applicable when naming other clades. The phylogenetic definitions proposed here should help focus future discussions of thePhyloCodeon real definitions rather than simplified hypothetical ones.
Experimental design in intraspecific organelle DNA sequence studies III: statistical measures of sampling success
Authors: Holt Jason A. , Stoneberg Holt Sierra D. , Bureš Petr
Published: May 2010

Statistical methods are proposed for analyzing the experimental design, preliminary results, and final results of phylogenetic studies of organelle DNA sequence at low taxonomic levels. Such studies require sampling numerous individuals, many of which share identical haplotypes. The proportions of the haplotypes sampled can help answer the following questions: (1) Is one haplotype so dominant that the particular DNA region is without meaningful variation within the scope of the study? (2) Were all prevalent haplotypes found? (3) What are the proportions of each haplotype within the studied group? (4) What percentage of the studied group can be confidently asserted to belong to the haplotypes that were found? Examples are given in which the statistics techniques are applied to data drawn from the botanical literature. Tables are included as a quick reference for the researcher who wishes to circumvent calculation. A Microsoft® Excel 2000 spreadsheet (titled “HaploPro. xls”) for performing some of the more complicated calculations is offered online. Finally, the limitations of these methods and their applicability to nuclear DNA and other characters studies are discussed.
Gentianella stiriaca, a case of reticulate evolution in the northeastern and eastern Central Alps
Authors: Greimler Josef , Jang Chang-Gee
Published: May 2010

We gathered morphological and genetic evidence for introgressive patterns inGentianella stiriaca, a taxon thought to have resulted from reticulate relationships between two or three species (G. aspera, G. austriaca, G. rhaetica). Multivariate analyses including morphometric and classical differential characters were poorly resolving and showed thatG. stiriacawas mostly distributed withinG. rhaeticaandG. aspera. Using only the categorical classical differential characters, three well‐separated morphological groups (G. aspera, G. austriaca, G. rhaetica) were identified, however, with half of theG. stiriacasamples close toG. rhaetica. In contrast, AFLP data revealed several groups that were not concordant with morphological groups. Neighbour Joining, PCoA and Bayesian admixture analysis (BAPS) each identified a northeastern gene pool ofG. asperaincluding northern samples ofG. stiriaca, and a southeastern gene pool ofG. rhaeticaincluding southeasternG. stiriaca. Both gene pools show some admixture fromG. austriaca. The genetic data support an old hypothesis of multiple hybrid origin and introgressive processes in the evolution ofG. stiriaca. We discuss the effect of Pleistocene climate changes on the patterns of variation and introgression inGentianella. We consider “G. stiriaca” a polytopic variant that does not deserve specific rank. Following the morphological species concept we propose including it inG. rhaeticato which it is most similar.
Ombronesus stuvensis, a new genus and species of the Ptychomniaceae (Bryophyta) from south west Chile
Authors: Bell Neil E. , Pedersen Niklas , Newton Angela E.
Published: May 2010

A new genus of the Ptychomniaceae (Ptychomniales) is described from Juan Stuven Island, south west Chile. Molecular phylogenetic analyses and morphology independently confirm the position of the taxon in the family, but features of the sporophyte (in particular a highly reduced endostome), a unique combination of gametophytic characters and a significant number of molecular autapomorphies indicate that the plant is clearly distinct from previously described genera. Molecular data demonstrate that the new genus is one of the earlier diverging lineages within the order, part of a basal grade that includes Hampeella, Ptychomniella, Tetraphidopsis, and Cladomniopsis, although its precise position remains ambiguous. The Ptychomniales occupy a key phylogenetic position as one of the earliest diverging pleurocarpous lineages with features that are intermediate between the most basal, predominantly orthotropic pleurocarps and the more derived plagiotropic taxa. The new taxon is thus of considerable phylogenetic significance and contributes to the nature conservation value of the locality.
The taxonomic utility of staminal features in Vaccinieae (Ericaceae)
Authors: Vander Kloet Sam P. , Avery Trevor S.
Published: May 2010

The use of staminal features as generic characters in Vaccinieae are reviewed and assessed using 108 OTUs belonging to 97 taxa, scored for 17 characters and then subjected to a variety of phenetic analyses. Our results suggest that such staminal features quo genetic characters are highly overrated and that any generic revision contemplated for Vaccinieae ought to encompass a much wider selection of characters.
Gymnosperms and cladistic biogeography of the Mexican Transition Zone
Authors: Contreras-Medina Raúl , Vega Isolda Luna , Morrone Juan J.
Published: May 2010

Distributional patterns of 81 species of three genera of Mexican gymnosperms (Ceratozamia, Dioon, Pinus) were analyzed to evaluate their contribution to the cladistic biogeography of the Mexican Transition Zone, applying Brooks Parsimony Analysis (BPA) and parsimony analysis of paralogy‐free subtrees (PAPS). BPA showed three main groups of areas: clade A is comprised of the Baja California, Great Basin, and Mojavean provinces; clade B includes the Valle de Tehuacán‐Cuicatlán, Balsas Basin, Planicie Costera del Noreste, Planicie Costera del Noroeste, Costa del Golfo de México, and Costa Pacífica provinces, located along the coasts and in the central lowlands of Mexico; and clade C includes the Appalachian, Atlantic and Gulf Coastal, Yucatán Peninsula, Caribbean, Californian, Vancouverian, Eastern Central America, Soconusco, Serranías Transístmicas, Serranías Meridionales, Sierra Madre Occidental, Altiplano, and Sierra Madre Oriental provinces, corresponding to the montane areas of the Mexican Transition Zone, Central America and some areas of the U.S.A. PAPS showed three groups of areas: clade D includes the Vancouverian, Appalachian, and Atlantic and Gulf Coastal provinces; clade E the Balsas Basin, Planicie Costera del Noreste, and Planicie Costera del Noroeste provinces; and clade F the Serranías Transístmicas, Soconusco, Serranías Meridionales, Sierra Madre Occidental, Altiplano, Sierra Madre Oriental, Baja California, Californian, Great Basin and Mojavean provinces. Comparing both analyses, three common area relationships emerge: (1) Appalachian and Atlantic and Gulf Coastal provinces, (2) Great Basin, Mojavean and Baja California provinces, and (3) Altiplano, Sierra Madre Oriental and Sierra Madre Occidental provinces. Differences between the general area cladograms can be accounted for by dispersal having a stronger influence in BPA, and the PAPS general area cladogram showing a clearer vicariant signal. The general area cladograms obtained support some area relationships not explained in previous studies, and may complement the historical distributional patterns of the biota of the Mexican Transition Zone.
The nomenclature of Sorghum bicolor (L.) Moench (Gramineae)
Authors: Wiersema John H. , Dahlberg Jeff
Published: May 2010

The currently used subspecific names for the annual wild and weedy relatives of domesticated sorghum either lack valid publication or have not had their priority established over competing names of equivalent priority. These problems are resolved with valid publication of the new combination Sorghum bicolor subsp. verticilliflorum and establishment of its priority and that of S. bicolor subsp. drummondii over competing synonyms.
Typification of Euphorbia pilosa L. (Euphorbiaceae)
Authors: Geltman Dmitry V.
Published: May 2010

The illustration from J.G. Gmelin’s Flora Sibirica (1749) is designated as the lectotype of Euphorbia pilosa L.
Typification of the names of some infraspecific taxa in the Tortula subulata complex (Pottiaceae, Bryophyta) and their taxonomic disposition
Authors: Cano María J.
Published: May 2010

Types for the names Barbula saxicola Lamy, Barbula subulata var. longifolia Kindb., Syntrichia alpina Brid., Tortula inermis var. submarginata Schiffn., and Tortula subulata var. compacta Schiffn., are designated here. Syntrichia alpina is considered conspecific with T. subulata Hedw., with which Tortula inermis var. submarginata and T. subulata var. compacta are also synonymized, as is Barbula subulata var. longifolia with T. schimperi M.J. Cano & al. Barbula saxicola is here considered to apply to the species currently known as Dialytrichia fragilifolia (Bizot & Cl. Roux) F. Lara; as B. saxicola has priority, this necessitates the new combination D. saxicola (Lamy) M.J. Cano.
Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes
Authors: Schuettpelz Eric , Pryer Kathleen M.
Published: May 2010

In an effort to obtain a solid and balanced approximation of global fern phylogeny to serve as a tool for addressing large‐scale evolutionary questions, we assembled and analyzed the most inclusive molecular dataset for leptosporangiate ferns to date. Three plastid genes (rbcL, atpB, atpA), totaling more than 4,000 bp, were sequenced for each of 400 leptosporangiate fern species (selected using a proportional sampling approach) and five outgroups. Maximum likelihood analysis of these data yielded an especially robust phylogeny: 80% of the nodes were supported by a maximum likelihood bootstrap percentage ≥ 70. The scope of our analysis provides unprecedented insight into overall fern relationships, not only delivering additional support for the deepest leptosporangiate divergences, but also uncovering the composition of more recently emerging clades and their relationships to one another.
The systematics of Knoxieae (Rubiaceae)—molecular data and their taxonomic consequences
Authors: Kårehed Jesper , Bremer Birgitta
Published: May 2010

The tribe Knoxieae consists of genera formerly included in (at least) four tribes of the Rubiaceae (the coffee family). Apart fromKnoxiaitself, which is mainly Indomalesian, the group is from Africa and Madagascar. Most genera are herbaceous or shrubby, but small trees are also present. They generally have fimbriate, colleter‐tipped stipules and five‐merous flowers with unequal calyx lobes. We present a molecular phylogeny of the group (based on two chloroplast markers,rps16andtrnT‐F, and the nuclear ITS) and discuss the morphological support for the resulting groups and the taxonomic consequences of the phylogeny. Two hundred and sixty‐one new sequences from 90 species have been obtained. Of the 19 genera of the Knoxieae, all but three (two monotypic and one with two species) are represented. The generaCalanda, Chlorochorion, Neopentanisia, andParaknoxiaare merged withPentanisia. Pentasis shown to be not monophyletic and is split into the new generaPhyllopentas, Dolichopentas, andRhodopentas. We also suggest thePentassubgeneraMegapentasandChamaepentadoidesbe included inChamaepentas. The genusCarphaleais also shown to be not monophyletic and for the African members of the genus (sectionDirichletia) the nameDirichletiashould be used.Placopodais suggested to be merged withDirichletia. Triainolepisis enlarged to includeParatriainaandThyridocalyx. The tribal position ofLathraeocarpais discussed. Twenty‐nine new combinations for species and seven for infraspecific taxa are made. A key to the genera of Knoxieae is provided.
An ITS phylogeny of tribe Senecioneae (Asteraceae) and a new delimitation of Senecio L.
Authors: Pelser Pieter B. , Nordenstam Bertil , Kadereit Joachim W. , Watson Linda E.
Published: May 2010

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.
Cytinaceae are sister to Muntingiaceae (Malvales)
Authors: Nickrent Daniel L.
Published: May 2010

The holoparasitic family Cytinaceae (Cytinus and Bdallophyton) was previously shown to be allied with Malvales, however its closest photosynthetic ancestor was not determined. A molecular phylogenetic study was conducted using nuclear small‐subunit rDNA and three chloroplast genes (the latter missing from the holoparasites but included to stabilize the overall tree topology) using Cytinaceae and exemplars from all recognized families from an expanded Malvales. Using maximum parsimony and maximum likelihood methods, Cytinaceae were resolved with strong support as sister to the newly described Muntingiaceae. Potential morphological synapomorphies include trichome types, mature pollen released as tetrads, inferior ovaries, intrusive parietal placentation with many ovules, and fruit type. Given that all Muntingiaceae are neotropical, it is likely that the ancestor of Cytinaceae arose in the New World and migrated to continental Africa prior to the separation of Africa from South America.