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Showing papers in "Taxon in 2006"


Journal ArticleDOI
01 Aug 2006-Taxon
TL;DR: A revised classification for extant ferns is presented, with emphasis on ordinal and familial ranks, and a synopsis of included genera is provided, reflecting recently published phylogenetic hypotheses based on both morphological and molecular data.
Abstract: We present a revised classification for extant ferns, with emphasis on ordinal and familial ranks, and a synopsis of included genera. Our classification reflects recently published phylogenetic hypotheses based on both morphological and molecular data. Within our new classification, we recognize four monophyletic classes, 11 monophyletic orders, and 37 families, 32 of which are strongly supported as monophyletic. One new family, Cibotiaceae Korall, is described. The phylogenetic affinities of a few genera in the order Polypodiales are unclear and their familial placements are therefore tentative. Alphabetical lists of accepted genera (including common synonyms), families, orders, and taxa of higher rank are provided.

1,363 citations


Journal ArticleDOI
01 May 2006-Taxon
TL;DR: This work appeals for consistency, distinguishing between the terms "ploidsy / aneuploidy" referring to chromosome numbers and "DNA ploidy / DNA aneu Ploidsy" to nuclear DNA content.
Abstract: There is an ever-increasing amount of cytogenetic data in plant sciences obtained by cytometric techniques, particularly flow cytometry. However, as these methods determine nuclear DNA amount irrespective of the number of chromosomes, a discrepancy between cytometric and karyological data may occur. To avoid potential bias, we appeal for consistency, distinguishing between the terms "ploidy / aneuploidy" referring to chromosome numbers and "DNA ploidy / DNA aneuploidy" to nuclear DNA content.

178 citations


Journal ArticleDOI
01 Aug 2006-Taxon
TL;DR: Two DNA regions, the plastid trnH-psbA spacer and nuclear ribosomal ITS region, have been shown to have potential as an identification barcode for land plants, although with some significant drawbacks.
Abstract: DNA barcodes have been successfully applied to a limited number of animal groups with the application of the mitochondrial gene, cytochrome c oxidase subunit 1. Recently two DNA regions, the plastid trnH-psbA spacer and nuclear ribosomal ITS region, have been shown to have potential as an identification barcode for land plants, although with some significant drawbacks. The ideal barcode should be relatively short in length (∼700 bp), more variable between than within species, and easily amplifiable with universal primers. Building on current success, ongoing investigations are searching for the best barcode to apply to all land plants. Once established, a plant barcode may be effectively used in biodiversity inventories, conservation assessments, and applied forensic investigations. Advances in sequencing technology and the completion of the DNA barcode library have the potential to provide the public with increased access to information about the natural world.

151 citations


Journal ArticleDOI
01 May 2006-Taxon
TL;DR: The results indicate that major re-organization is necessary of the groupings within Euphorbia that have been recognised in the past, since most of them turn out to be polyphyletic.
Abstract: We use data from the internal transcribed spacer (ITS) region of the nuclear rDNA cistron and the chloroplast psbA-trnH intergenic spacer to reconstruct the phylogenetic relationships among southern African species of Euphorbia. The results indicate that major re-organization is necessary of the groupings within Euphorbia that have been recognised in the past, since most of them turn out to be polyphyletic. Furthermore, in its present circumscription, Euphorbia itself is not monophyletic, nor do the southern African species form a monophyletic group. Both datasets show that the southern African species fall into four major groups, which we recognise as subgenera: Chamaesyce Raf., Esula Pers., Euphorbia and Rhizanthium (Boiss.) Wheeler. To accommodate the southern African species, subg. Chamaesyce is divided into sect. Chamaesyce, sect. Frondosae Bruyns, sect. nov., sect. Articulofruticosae Bruyns, sect. nov. and sect. Espinosae Pax & Hoffm. Subgenus Euphorbia is divided into sect. Euphorbia, sect. Monadenium (Pax) Bruyns, sect. Goniostema H. Baill. ex Boiss. and sect. Tirucalli Boiss. To re-establish the monophyly of Euphorbia, the genera Endadenium L.C. Leach, Monadenium Pax and Synadenium Boiss. are reduced to synonymy under Euphorbia subg. Euphorbia sect. Monadenium and the species are all transferred to Euphorbia. Consequently the subtribe Euphorbiinae now consists of the single, very large, very widely distributed and very diverse genus Euphorbia. Three of the subgenera (Chamaesyce, Esula, Euphorbia) are nearly cosmopolitan, showing the great age and wide extent of the radiation that has occurred within Euphorbia. The remaining subg. Rhizanthium is mainly African.

137 citations


Journal ArticleDOI
01 Aug 2006-Taxon
TL;DR: A high intercontinental dispersability can be observed in Salicomioideae in particular in the Salicornia/Sarcocornia lineage with multiple colonization events in America, Australia and South Africa linked to the global aridification during the Oligocene, Late Miocene and Pliocene.
Abstract: Chenopodiaceae-Salicomioideae (14-16 gen./c. 90 spp.) are distributed worldwide in coastal and inland saline habitats. Most of them are easy to recognize by their succulent-articulated stem with strongly reduced leaves and by flowers aggregated in dense, thick spike-shaped thyrses. ITS and the atpB-rbcL spacer were sequenced for 67 species representing 14 genera of Salicomioideae and analysed with maximum parsimony and maximum likelihood, a fossil-calibrated molecular clock using the penalized likelihood method, and lineage through time plots. The evolution of stem, leaf, and flower morphology was traced using MacClade. Both molecular markers indicate that the monophyletic Salicomioideae originated in Eurasia during the Late Eocene/Early Oligocene (38.2- 28.7 Mya) and experienced a rapid radiation into its major lineages during the Early Oligocene with Allenrolfea/Heterostachys, Kalidium, Halopeplis and Halocnemum/Halostachys branching off early. Already in the Middle Miocene (19.6-14.6 Mya) all major lineages of Salicornioideae were present. These additionally include Arthrocnemum/Microcnemum, the Halosarcia lineage (which includes all Australian species except for the Australian Sarcocornia) and the Salicornia/Sarcocornia lineage. A high intercontinental dispersability can be observed in Salicomioideae in particular in the Salicornia/Sarcocornia lineage with multiple colonization events in America, Australia and South Africa linked to the global aridification during the Oligocene, Late Miocene and Pliocene. The comparatively low species number of many genera is explained by a low number of niches present in the extreme habitats of Salicomioideae, strong interspecific competition mainly by close relatives, and by Pleistocene extinctions. We detected an evolutionary trend towards increasing reduction of the leaf lamina in Salicomioideae, with an ovate or terete leaf with a decurrent base as the plesiomorphic condition. Opposite phyllotaxis has arisen at least two times in the subfamily and is strongly correlated with the pair-wise fusion of leaves (not bracts), the reduction of leaf lamina, and the articulation of stem. However, the articulated stems and reduced leaves also have evolved twice in lineages with alternate phyllotaxis, such as Allenrolfea and Kalidium caspicum. Only one shift from free to connate bracts occurred in Salicomioideae with at least one reversal within the Halosarcia lineage. The fusion of bracts is mostly accompanied by a partly or fully connation of bracts and axis resulting in club-shaped spikes in which the flowers are tightly embedded in cavities. Both molecular trees are conflicting with the traditional tribes indicating that their diagnostic characters have originated by convergent evolution. For reasons of stability and clarity we propose that only one tribe, Salicomieae, should be recognized. The traditional circumscription of most genera is supported by the molecular results except for the closely related genera of the Australian Halosarcia clade and the Sarcocornia/Salicornia complex. The monotypic Kalidiopsis clearly originated from within Kalidium, and it is therefore newly combined in Kalidium.

135 citations


Journal ArticleDOI
01 Aug 2006-Taxon
TL;DR: In their recent review, Mayr & Bock (2002) outlined comprehensively the basic conceptual differences of evolutionary (Darwinian) and cladistic (Hennigian) clas-sification.
Abstract: Taxonomy is at its crossroads in choosing criteria forclassification of taxa. The debate about recognition ofparaphyletic vs. monophyletic taxa and its nomenclatur-al consequences is continuing and is keenly disputed, ase.g., reflected by recent articles and opinion papers inTAXON (Brummitt, 2002, 2003, 2006; Nelson & al.,2003; Dias & al., 2005; Nordal & Stedje, 2005; Potter F Brummitt, 2002, 2006; Mayr & Bock,2002).In their recent review, Mayr & Bock (2002) outlinedcomprehensively the basic conceptual differences ofevolutionary (Darwinian) and cladistic (Hennigian) clas-sification. Darwinian classification requests the consid-eration of two criteria—similarity

121 citations


Journal ArticleDOI
01 Jan 2006-Taxon
TL;DR: The atpA dataset had more variable characters and resulted in a more robustly supported phylogeny than any of the other single gene datasets examined, suggesting that at pA will be exceptionally useful in more extensive studies of fern phylogeny and perhaps also in studies of other plant lineages.
Abstract: DNA sequence data and phylogenetic approaches have contributed greatly to our understanding of fern relationships. Nonetheless, the datasets analyzed to date have not been sufficient to definitively resolve all parts of the global fern phylogeny; additional data and more extensive sampling are necessary. Here, we explore the phylogenetic utility of the plastid atpA gene. Using newly designed primers, we obtained atpA sequences for 52 fern and 6 outgroup taxa, and then evaluated the capabilities of atpA relative to four other molecular markers, as well as the contributions of atpA in combined analyses. The five single-gene datasets differed markedly in the number of variable characters they possessed; and although the relationships resolved in analyses of these datasets were largely congruent, the robustness of the hypotheses varied considerably. The atpA dataset had more variable characters and resulted in a more robustly supported phylogeny than any of the other single gene datasets examined, suggesting that atpA will be exceptionally useful in more extensive studies of fern phylogeny and perhaps also in studies of other plant lineages. When the atpA data were analyzed in combination with the other four markers, an especially robust hypothesis of fern relationships emerged. With the addition of the atpA data, support increased substantially at several nodes; three nodes, which were not well-supported previously, received both good posterior probability and good bootstrap support in the combined 5-gene (> 6 kb) analyses.

117 citations


Journal ArticleDOI
01 Feb 2006-Taxon
TL;DR: The phylogeny based on the total evidence tree including fossils supports an origin and early Tertiary diversification of Cornus in Europe and multiple trans-Atlantic migrations between Europe and North America by the early TERTiary.
Abstract: DNA sequences were generated for matK and ITS for 68 and 103 samples of Cornus to reconstruct a species level phylogeny of the genus. The results support the monophyly of most subgenera, except subg. Kraniopsis and subg. Cornus. Subgenus Kraniopsis was suggested to exclude C. peruviana from South America and subg. Afrocrania and subg. Sinocornus were nested within subg. Cornus. Four major clades corresponding to groups also recognizable by morphological differences were revealed: the big-bracted dogwoods (BB) including subg. Cynoxylon, subg. Syncarpea, and subg. Discocrania, the dwarf dogwoods (DW) including subg. Arctocrania, the cornelian cherries (CC) including subg. Cornus, subg. Sinocornus, and subg. Afrocrania, and the blue- or white-fruited dogwoods (BW) including subg. Kraniopsis, subg. Mesomora, and subg. Yinquania. This finding is consistent with previous studies with more limited sampling. The single South American species C. peruviana was found to be sister to the Asian C. oblonga of subg. Yinquania, adding a fourth intercontinental disjunction in the genus that was previously unknown. Species relationships within the subgenera were clearly resolved except for the relatively large subg. Syncarpea and subg. Kraniopsis. Phylogenetic analyses of total evidence combining morphology, matK, ITS, and previously published rbcL and 26S rDNA sequences resolved the relationships among subgenera as (BW(CC(BB,DW))). Biogeographic analyses using DIVA with or without fossils resulted in different inferences of biogeographic history of the genus, indicating the importance of fossil data in biogeographic analyses. The phylogeny based on the total evidence tree including fossils supports an origin and early Tertiary diversification of Cornus in Europe and multiple trans-Atlantic migrations between Europe and North America by the early Tertiary. It also supports that distribution of the few species in the southern hemisphere was not ancestral, but a result of migration from the north. This evidence rejects a previous hypothesis of a southern hemispheric origin of the genus.

115 citations


Journal ArticleDOI
01 Aug 2006-Taxon
TL;DR: An ongoing project to digitize information about plant specimens and make it available to botanists in the field first requires digital images and models, and then effective retrieval and mobile computing mechanisms for accessing this information.
Abstract: 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.

112 citations


Journal ArticleDOI
01 Jan 2006-Taxon
TL;DR: Comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloropleft genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.
Abstract: Three mitochondrial (atp1, matR, nad5), four chloroplast (atpB, matK, rbcL, rpoC2), and one nuclear (18S) genes from 162 seed plants, representing all major lineages of gymnosperms and angiosperms, were analyzed together in a supermatrix or in various partitions using likelihood and parsimony methods. The results show that Amborella + Nymphaeales together constitute the first diverging lineage of angiosperms, and that the topology of Amborella alone being sister to all other angiosperms likely represents a local long branch attraction artifact. The monophyly of magnoliids, as well as sister relationships between Magnoliales and Laurales, and between Canellales and Piperales, are all strongly supported. The sister relationship to eudicots of Ceratophyllum is not strongly supported by this study; instead a placement of the genus with Chloranthaceae receives moderate support in the mitochondrial gene analyses. Relationships among magnoliids, monocots, and eudicots remain unresolved. Direct comparisons of analytic results from several data partitions with or without RNA editing sites show that in multigene analyses, RNA editing has no effect on well supported relationships, but minor effect on weakly supported ones. Finally, comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloroplast genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.

110 citations


Journal ArticleDOI
01 Feb 2006-Taxon
TL;DR: A web-based program called eFloras was developed to enable access to online “electronic” floras, and through a web interface to the data, users can browse and search online floristic treatments by volume, family, and genus.
Abstract: Online floras provide research botanists with the opportunity to work on floristic treatments dynamically, and enable users to browse and search these treatments. A web-based program called eFloras (URL: http://www.efloras.org/) was developed to enable access to online “electronic” floras. Through a web interface to the data, users can browse online floristic treatments by volume, family, and genus, and can search by name, distributional data, and text. With the use of web forms, editors and authors with permissions can correct and update the data.

Journal ArticleDOI
01 Feb 2006-Taxon
TL;DR: For most insect-pollinated species, allozymes and nuclear DNA markers indicate significant genetic differentiation between populations and between geographical regions of the archipelago as discussed by the authors, which suggests a migrant pool model, where colonists are recruited from a random sample of source populations.
Abstract: Taiwan and Ryukyus constitute an archipelago lying on the western rim of the Pacific Ocean. In contrast to volcanic islands that often arise sequentially, these continental islands emerged almost simultaneously as the Luzon arc collided with the Eurasian margin some 9 million years ago (Mya). Taiwan and Ryukyus attained their modern features and their current flora and fauna from the adjacent mainland and from tropical Asia only 5-6 Mya. Quaternary glaciation led to a drop in sea level of the South China Sea and a land bridge that connected the Taiwan-Ryukyu Archipelago to the mainland, which allowed plants and animals to migrate across what was previously ocean. These islands provided refugia for northern species that migrated south during glacial periods, as indicated by unanticipated high levels of genetic diversity in island populations of plants like Cunninghamia and Pinus. For most insect-pollinated species, allozymes and nuclear DNA markers indicate significant genetic differentiation between populations and between geographical regions of the archipelago. In contrast, organelle based DNA markers suggest a migrant-pool model, where colonists are recruited from a random sample of source populations. Consistent with this model, low elevation species have high genetic heterogeneity within populations and low levels of genetic differentiation between populations. In contrast, colonization of alpine species appeared to follow a phalanx model due to the limited availability of high elevation habitats. Genetic differentiation was detected between fragmented populations of the alpine species. A scenario of stepwise colonization from the mainland to near and then distant islands remains to be tested, although several studies indicate no such pattern. These conflicting results challenge the ability to define clear conservation criteria for the rare plant species of the archipelago.

Journal ArticleDOI
01 Feb 2006-Taxon
TL;DR: It is speculated that the common distribution patterns of the cpDNA clades observed in central Honshu were formed by dynamic climatic changes and that the alpine regions of central HONShu acted as refugia for alpine plants during warm interglacial periods.
Abstract: A preliminary synthesis of the geographic distribution patterns of intraspecific cpDNA variations in Japanese alpine plants is presented by studying five species, namely, Pedicularis chamissonis, Primula cuneifolia, Loiseleuria procumbens, Cardamine nipponica, and Anemone narcissiflora. Nucleotide sequences of the noncoding regions of cpDNA recognized multiple cpDNA haplotypes in these species. Phylogenetic analyses of these haplotypes suggest two or three major cpDNA clades; each clade has a clearly disjunct distribution pattern in the northern parts of Japan, and in the central parts of Japan. The southernmost clades endemic to central Honshu in Japan were found in all the species (Central Honshu clade). We estimate that the major clades of Pedicularis chamissonis and Primula cuneifolia separated from a common ancestor before the last glacial period (>0.6 and 0.47 million years ago, respectively). We speculate that the common distribution patterns of the cpDNA clades observed in central Honshu were formed by dynamic climatic changes (e.g., glacial events in the Pleistocene) and that the alpine regions of central Honshu acted as refugia for alpine plants during warm interglacial periods.

Journal ArticleDOI
01 May 2006-Taxon

Journal ArticleDOI
01 Nov 2006-Taxon
TL;DR: The neotropical fern genus Serpocaulon (Polypodiaceae), segregated from Polypodium, is described and new combinations for the forty known species are made, and there appears to be no convenient infrageneric division of the species within SerpOCaulon.
Abstract: 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.


Journal ArticleDOI
01 Aug 2006-Taxon
TL;DR: 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 progress.
Abstract: 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.

Journal ArticleDOI
01 Feb 2006-Taxon
TL;DR: The large pantropical genus Costus is found to be polyphyletic and is divided into four genera, three of which are new and has now a more concise generic concept including morphological synapomorphies previously absent due to the polymorphic nature of the prior nonmonophyletic assemble.
Abstract: Recent cladistic analysis Of Multiple molecular data from chloroplast and nuclear genomes as well as morphological data have indicated that a reclassification of the family Costaceae is necessary in order to appropriately reflect phylogenetic relationships. The previously described genera Tapeinochilos, Monocostus, and Dimerocostus are all upheld in the new classification. Monocostus and Dimerocostus are found to be sister taxa. The large pantropical genus Costus is found to be polyphyletic and is thus divided into four genera, three of which are new (Cheilocostus, Chamaecostus, Paracostus). Costus has now a more concise generic concept including morphological synapomorphies previously absent due to the polymorphic nature of the prior nonmonophyletic assemblage. Of the three new genera, one (Parocostus) was previously recognized as a subgenus of Costus. Cheilocostus comprises several Asian taxa and is sister to Tapeinochilos, whereas Chamaecostus comprises entirely neotropical taxa and is sister to a neotropical Monocostus + Dimerocostus clade. A reevaluation of the traditional taxonomy indicates that floral characters and pollination syndromes commonly used to identify groups exhibit homoplasy when analyzed in a cladistic framework and are thus unreliable as taxonomic indicators.

Journal ArticleDOI
01 Nov 2006-Taxon

Journal ArticleDOI
01 Feb 2006-Taxon
TL;DR: A phylogenetic analysis of 39 accessions that included most species of the small austral genus Abrotanella and putative relatives including Blennosperma, Crocidium and Ischnea suggests that the BlennOSpermatinae are polyphyletic.
Abstract: Relationships of the small austral genus Abrotanella are uncertain. It was previously included in the Anthe mideae or more recently in the Senecioneae. We conducted a phylogenetic analysis of 39 accessions that included most species o? Abrotanella and putative relatives including Blennosperma, Crocidium and Ischnea. These four genera have been considered to form subtribe Blennospermatinae. Our results suggest that the Blennospermatinae are polyphyletic; Blennosperma, Crocidium and Ischnea form a well-supported clade nest ed within the Senecioneae, while Abrotanella forms another well-supported clade that is distinct from these genera and its sister is not resolved. Molecular dating o? Abrotanella suggests that the lineage initially diverged during the early Miocene. Secondary species radiations in Australasia and in southern South America that occurred 3 million years ago undoubtedly reflect long-distance dispersal, colonization and speciation. Both the ITS region and the 5' trnK/matK chloroplast DNA intron gave similar divergence estimates. The estimates were also robust to changes in the tree topology and to the different methods used to calculate divergence times.

Journal ArticleDOI
01 Feb 2006-Taxon
TL;DR: Investigation of higher level relationships within the Syzygium group, using parsimony and Bayesian analyses of cpDNA sequences from the matK and ndhF genes and the rpl 16 intron, generated for a total of 87 species from the SyZombie group and eight outgroup taxa finds four major well supported clades.
Abstract: With as many as 1000 included species, Syzygium s.l. (including Syzygium and segregate genera such as Acmena, Acmenosperma, Cleistocalyx, Piliocalyx, and Waterhousea) comprises one of the major lineages within Myrtaceae, and is an important component of the Old-World tropical rainforest flora. As with other large genera, high species richness, an extensive distribution and relative homogeneity in morphology have hindered attempts to divide Syzygium s.l. Here, we investigate higher level relationships within the group, using parsimony and Bayesian analyses of cpDNA sequences from the matK and ndhF genes and the rpl 16 intron, generated for a total of 87 species from the Syzygium group and eight outgroup taxa. Within the ingroup, four major well supported clades are found, which form a basal polytomy along with S. wesa and monotypic Anetholea. Generally, the molecular data provide little support for traditional divisions of Syzygium s.l., and the recognition of segregate groups such as Acmena, Acmenosperma, Cleistocalyx, Piliocalyx and Waterhousea. While homoplasy amongst morphological characters has misled attempts to divide the group, detailed and critical assessments of placental, ovular and seed morphology may provide novel insights into evolutionary relationships, and are an important future step in the development of a sound higher level taxonomy for Syzygium s.l.

Journal ArticleDOI
01 Aug 2006-Taxon
TL;DR: A molecular-based phylogeny of Canarian Descurainia was constructed using DNA sequences from nuclear ribosomal internal transcribed spacer (ITS) and seven non-coding chloroplast regions and chloroplast data suggest that both intra-island adaptive radiation and inter-islands colonization have played a prominent role in the evolution of DesCurainia in the Canary Islands.
Abstract: Descurainia Webb & Berthel. (Brassicaceae) comprises approximately 45 species distributed throughout temperate areas of the world. In contrast to the small-flowered herbaceous taxa which constitute the majority of the genus, the seven species endemic to the Canary Islands are relatively large-flowered woody perennials. A molecular-based phylogeny of Canarian Descurainia was constructed using DNA sequences from nuclear ribosomal internal transcribed spacer (ITS) and seven non-coding chloroplast regions. The results of parsimony and Bayesian analyses suggest that species of Descurainia in the Canary Islands are recently derived via a single colonization event. The closest continental relative is D. tanacetifolia, a perennial herb from the mountains of southwestern Europe. Chloroplast data suggest that both intra-island adaptive radiation and inter-island colonization have played a prominent role in the evolution of Descurainia in the Canary Islands. The most likely ancestral location of the island progenitor was the lowland scrub zone on Tenerife.

Journal ArticleDOI
01 Feb 2006-Taxon
TL;DR: The western Eurasian-western North American disjunction of Oreobliton/Aphanisma is more likely to have resulted from the fragmentation of a Beringian than a North Atlantic ancestral range, and it is postulate that the evolution into dry habitats of OreOBliton and Aphanisma took place in parallel in western Eurasia and western North America.
Abstract: Chenopodiaceae subfam. Betoideae is distributed in both western Eurasia (four genera) and western North America (one genus). To understand the origin of this disjunction, the phylogeny of the subfamily was reconstructed and dated using ndhF, matK/trnK, tmL-trnF spacer, and ITS sequence variation, penalized likelihood and Langley-Fitch, and calibration with three different fossils. Maximum Parsimony and Maximum Likelihood analyses of the molecular data show that Betoideae are monophyletic, but that relationships of the Himalayan Acroglochin, traditionally included in Betoideae because of the shared possession of a circumscissile capsule, are uncertain. Among the betoidean genera, Beta (excl. sect. Procumbentes) is sister to a clade of Hablitzia, Patellifolia (= Beta sect. Procumbentes), Oreobliton, and Aphanisma. Apart from the strongly supported sister group relationship between the North African Oreobliton and the Califomian Aphanisma interrelationships among these four genera are not unambiguously resolved. The crown group age of Betoideae was estimated to 38.4-27.5 my using different DNA sequences, and the age of the Oreobliton/Aphanisma split to 15.4-8.1 my. Considering all evidence available, we conclude that the western Eurasian-western North American disjunction of Oreoblitom/Aphanisma is more likely to have resulted from the fragmentation of a Beringian than a North Atlantic ancestral range. Irrespective of the geographical location of this ancestral range we postulate that the evolution into dry habitats of Oreobliton and Aphanisma took place in parallel in western Eurasia and western North America. Evidence for this may be the very different life form and habitat of the two genera, of which Oreobliton is a subshrub of rocky ground at montane altitude, and Aphanisma an annual from coastal habitats. Hablitzia, a perennial vine of deciduous forests in the Caucasus area, is sister to Patellifolia/ Oreobliton/Aphanisma in the ndhF and ITS data sets. The habitat requirements of Hablitzia may be similar to those of the ancestor of the subfamily. Comparing the age of the Oreobliton/Aphanisma disjunction with ages estimated for East Asian-eastern North American disjunctions, we conclude that in many cases these two types of disjunction represent different ecological trajectories of essentially the same historical phenomenon.

Journal ArticleDOI
01 May 2006-Taxon
TL;DR: The results support the monophyly of the South American species with the southern O. obtusangulus as sister to the rest, and the transformed branch lengths of the ITS tree indicate a recent (5.5–6 mya) origin of theSouth American clade, followed by a northward migration and diversification of species along the Andes.
Abstract: Nuclear ribosomal DNA Internal Transcribed Spacer (ITS) and plastid trnL intron and trnL-F intergenic spacer regions were sequenced for 14 species of Oreobolus (Cyperaceae) from throughout most of its distribution range (South America, Australasia, and Hawai’i), with the exception of the Malesian species; Costularia laxa was used as outgroup. Phylogenetic trees were produced for ITS and trnL-F datasets using maximum parsimony and maximum likelihood. We estimated species divergence times by enforcing a molecular clock on the Maximum Likelihood ITS tree, using the appearance of O. furcatus in Hawai’i, no earlier than 5.1 mya, as a calibration point. Our results support the monophyly of the South American species with the southern O. obtusangulus as sister to the rest. This South American clade is sister to the Australian O. pumilio, and the Australasian and Hawaiian species sampled form a basal grade. Oreobolus oligocephalus is embedded within Oreobolus, rejecting its separation in the monotypic genus Schoenoides. The transformed branch lengths of the ITS tree indicate a recent (5.5–6 mya) origin of the South American clade, followed by a northward migration and diversification of species along the Andes.

Journal ArticleDOI
01 Aug 2006-Taxon
TL;DR: The phylogeny of Corymbia and related eucalypt groups was investigated using nuclear ETS sequences, and combined ETS and ITS sequences, finding patterns of relationship and distribution are consistent with differentiation of major lineages of CoryMBia prior to the isolation of taxa in eastern and south-western Australia.
Abstract: The generic classification of the eucalypts, especially recognition of the genus Corymbia, has been controversial. The phylogeny of Corymbia and related eucalypt groups was investigated using nuclear ETS sequences, and combined ETS and ITS sequences. Both the ETS and combined datasets support the monophyly of Corymbia. Three major eucalypt clades are confirmed: Corymbia + Angophora; Eucalyptus s.s.; and the Eucalyptopsis group. Within Corymbia, relationships are broadly consistent with phylogenies based on morphological and anatomical characters; sections Ochraria, Blakearia, and Politaria are all supported as monophyletic; sect. Rufaria is monophyletic with the inclusion of the monotypic sect. Apteria. Within Eucalyptus s.s., relationships are generally consistent with those shown by previous molecular studies. Within the Eucalyptopsis group, Allosyncarpia is sister to the clade Stockwellia + Eucalyptopsis. Relationships between the major eucalypt clades are equivocal, but combined analysis of ETS and ITS data shows Corymbia + Angophora as sister to Eucalyptus-the rainforest taxa of the Eucalyptopsis group being outside this clade. Patterns of relationship and distribution are consistent with differentiation of major lineages of Corymbia prior to the isolation of taxa (now relictual) in eastern and south-western Australia, arguably before the midMiocene.

Journal ArticleDOI
01 Jan 2006-Taxon
TL;DR: P phylogenetic analyses utilizing two molecular and morphological datasets and one morphological dataset combined in a total evidence analysis show Drymonia is weakly supported and is shown here to be morphologically diverse and in need of further evaluation.
Abstract: Episcieae is the most diverse tribe of Gesneriaceae, with 22 genera and over 700 species, or roughly 21% of all Gesneriaceae. The tribe is restricted to the Neotropics and is characterized by axillary flowers derived from a pair-flowered cyme inflorescence by reduction, a three-trace trilacunar node with split lateral bundles, superior ovaries, and with most members having a haploid chromosome number of n = 9 [n = 8 in Codonanthe and Nematanthus]. Most traditionally recognized genera in Episcieae are either known to be non-monophyletic or have not been represented adequately in phylogenetic analyses to test their monophyly. This paper presents phylogenetic analyses utilizing two molecular [the internal transcribed spacer region of 18S-26S nuclear ribosomal DNA (ITS) and the trnH-psbA intergenic spacer for 155 species] and one morphological (99 characters for 120 species) datasets, combined in a total evidence analysis. All traditionally recognized genera of Episcieae except for the monotypic genus Lampadaria are represented. Of the 21 sampled genera in Episcieae, 16 are represented by the generic type species. The genera Glossoloma and Crantzia are segregated from the genus Alloplectus as traditionally recognized. Other genera that are strongly supported as monophyletic include Alsobia, Columnea (with the inclusion of C. dielsii), Corytoplectus, and Episcia. Drymonia is weakly supported and is shown here to be morphologically diverse and in need of further evaluation. Evolution of fruit structure is examined in the context of the phylogenetic results presented here with two previously unreported features that are here referred to as capsules with tardily dehiscent and non-dehiscent endocarps. Three independent origins of resupinate flowers are inferred for Glossoloma, Nematanthus, and Crantzia. Strongly supported clades have centers of diversity in southeastern Brazil (Nematanthus, Codonanthe, Codonanthopsis, and Paradrymonia anisophylla), northern South America (Alloplectus, Drymonia, Columnea, Neomortonia), Central America (Alsobia, Oerstedina, Rufodorsia, Cobananthus), and two clades with diversity in the Guiana Shield [(Paradrymonia, Nautilocalyx, Chrysothemis) and (Lembocarpus, Cremersia, Rhoogeton)]. Neomortonia, a genus of three species, is poorly supported due to conflict among datasets.

Journal ArticleDOI
01 May 2006-Taxon
TL;DR: The phylogeny of usneoid lichens with black pigmentation in the cortex was reconstructed using Bayesian and maximum parsimony analyses of nuclear ITS rDNA sequences and indicates that Neuropogon is polyphyletic with a core group nested within Usnea subgen.
Abstract: The phylogeny of usneoid lichens with black pigmentation in the cortex was reconstructed using Bayesian and maximum parsimony analyses of nuclear ITS rDNA sequences. Fifty new partial sequences of 14 taxa were generated and assembled with 74 sequences from GenBank. Our results indicate that Neuropogon is polyphyletic with a core group nested within Usnea subgen. Usnea as sister-group to section Usnea. In addition an undescribed species is basal to the section Usnea clade and the Neuropogon species U. acanthella and U. durietzii have unresolved relationships in the Usnea subgen. Usnea clade. Monophyly of Neuropogon not nested within Usnea subgen. Usnea is rejected using three independent tests. Consequently, it is proposed to synonymise Neuropogon with Usnea. We recommend a conservative approach regarding nomenclatural changes from phylogenetic studies especially at the generic level when few taxa are studied.

Journal ArticleDOI
01 Feb 2006-Taxon
TL;DR: Acevedo-Rodríguez, Pedro and Mark T. Strong as discussed by the authors presented an updated revision for the monocotyledon and gymnosperm flora (excluding Orchidaceae and Poaceae) for the biogeographical region of Puerto Rico (including all islets and islands) and the Virgin Islands.
Abstract: Acevedo-Rodríguez, Pedro and Mark T. Strong. Monocots and Gymnosperms of Puerto Rico and the Virgin Islands. Contributions from the United States National Herbarium, volume 52: 415 pages (including 65 figures). The present treatment constitutes an updated revision for the monocotyledon and gymnosperm flora (excluding Orchidaceae and Poaceae) for the biogeographical region of Puerto Rico (including all islets and islands) and the Virgin Islands. With this contribution, we fill the last major gap in the flora of this region, since the dicotyledons have been previously revised. This volume recognizes 33 families, 118 genera, and 349 species of Monocots (excluding the Orchidaceae and Poaceae) and three families, three genera, and six species of gymnosperms. The Poaceae with an estimated 89 genera and 265 species, will be published in a separate volume at a later date. When Ackerman’s (1995) treatment of orchids (65 genera and 145 species) and the Poaceae are added to our account of monocots, the new total rises to 35 families, 272 genera and 759 species. The differences in number from Britton’s and Wilson’s (1926) treatment is attributed to changes in families, generic and species concepts, recent introductions, naturalization of introduced species and cultivars, exclusion of cultivated plants, misdeterminations, and discoveries of new taxa or new distributional records during the last seven decades. Seven new taxa are described: Agave minor Proctor, Bulbostylis capillaris subsp. insulana M.T. Strong, Cyperus pulguerensis M.T. Strong, Guzmania lingulata var. concolor Proctor & Cedeño-Mald., Pitcairnia angustifolia var. simplicior Proctor & Cedeño-Mald., Pitcairnia jareckii Proctor & Cedeño-Mald., and Zephyranthes proctorii Acev.-Rodr. & M.T. Strong; and two new combinations are made: Cyperus subtenuis (Kük.) M.T. Strong and Rhynchospora divaricata (Ham.) M.T. Strong. Twenty one of the accepted names (or their basionyms) in this work are lectotypified: Aechmea lingulata (L.) Baker, Aechmea nudicaulis (L.) Griseb., Alocasia plumbea Van Houtte, Crocosmia × crocosmiiflora (Lemoine ex Morren) N.E. Brown, Cyperus confertus Sw., Cyperus subtenuis (Kük.) M.T. Strong, Cyperus urbanii Boeck., Eleocharis rostellata (Torr.) Torr., Guzmania monostachia (L.) Mez, Heteranthera limosa (Sw.) Willd., Heteranthera reniformis Ruiz & Pav., Hohenbergia antillana Mez., Neomarica northiana (Schneev.) Sprague, Rajania cordata L., Rhynchospora ciliata (G. Mey.) Kük., Rhynchospora odorata C. Wright ex Griseb., Spathiphyllum wallisii Regel, Tillandsia fasciculata Sw., Tillandsia polystachya (L.)L., and Xanthosoma helleborifolium (Jacq.) Schott. Four names are neotypified: Caladium bicolor (Aiton) Vent., Eleutherine bulbosa (Mill.) Urb., Smilax coriacea Spreng., and Spirodela polyrhiza (L.) Schleid. One name is epitypified: Anthurium scandens (Aubl.) Engl. Fifteen synonyms of accepted taxa are lectotypified: Amaryllis equestris Aiton, Bulbostylis curassavica var. pallescens Kük. & Ekman ex Urb., Bulbostylis ekmanii Kük., Bulbostylis papillosa Kük., Crinum amabile Donn ex Ker-Gawl, Cyperus ehrenbergii Kunth, Cyperus filiformis var. densiceps Kük., Eleocharis sintenisii Boeck., Pistia occidentalis Blume, Pitcairnia ramosa J. Jacq., Psilocarya rufa Nees, Rhynchospora longispicata Boeck., Scleria microcarpa var. subeciliata C.B.Clarke, Scleria grisebachii C.B. Clarke, and Xanthosoma atrovirens K. Koch & Bouché. Thirty-two of the taxa treated are newly reported for the flora area: Aechmea fasciata (Lindl.) Baker, Agave vivipara L., Bulbostylis stenocarpa Kük., Calathea crotalifera S. Watson, Carex longii Mack., Commelina rufipes var. glabrata (D.R. Hunt) Faden & D.R. Hunt, Costus malortieanus H. Wendl., Costus scaber Ruiz & Pav., Cyperus floridanus Britton ex Small, Cyperus papyrus L., Cyperus squarrosus L., Cyperus tenuis Sw., Cyperus unifolius Boeck., Eleocharis debilis Kunth, Eleocharis minutiflora Boeck., Eleocharis oligantha C.B. Clarke, Fuirena robusta Kunth, Furcraea stratiotes J. B. Petersen, Halophila engelmannii Asch., Heliconia rostrata Ruiz & Pav., Hydrocleys nymphoides (Willd.) Buchenau, Kyllinga nemoralis (J.R. & G. Forst.) Dandy ex Hutchinson & Dalz., Maranta gibba Sm., Rhynchospora domingensis Urb., Rhynchospora fascicularis subsp. fascicularis var. distans (Michx.) Chapm., Rhynchospora radicans subsp. microcephala (Bertero ex Spreng.) W.W. Thomas, Ruppia didyma Sw., Scleria brittonii Core, Scleria havanensis Britton, Scleria verticillata Muhl. ex Willd., Spathiphyllum wallisii Regel., and Xyris curtissii Malme.

Journal ArticleDOI
01 Feb 2006-Taxon
TL;DR: Together analysis of the plastid regions, Blepharodon lineare and Funastrum clausum are confirmed as sister group to the rest of Metastelmatinae and Oxypetalinae, respectively, and indicates that Ditassa is polyphyletic.
Abstract: According to analyses of plastid DNA, New World Asclepiadoideae (Apocynaceae) fall into four clades; most species, however, are included in just one clade endemic to the New World that comprises Metastelmatinae, Oxypetalinae and Gonolobinae (the MOG clade). Looking for better support and resolution inside the MOG core group, we sequenced the nuclear ribosomal DNA region ITS and increased the number of plastid regions (trnS-G and matK) sequenced. Because of high levels of intra-individual polymorphisms and complex alignment among subtribes, ITS could not be used at the subtribal level. According to combined analysis of the plastid regions, Blepharodon lineare and Funastrum clausum are confirmed as sister group to the rest of Metastelmatinae and Oxypetalinae, respectively. The analysis indicates that Ditassa is polyphyletic. A highly supported clade composed of shrubby species with minute leaves that were traditionally classified in Ditassa comes out as sister to the rest of the subtribe apart from B. lineare. These data clearly support the recognition of a new genus in Metastelmatinae.

Journal ArticleDOI
01 May 2006-Taxon
TL;DR: The evolutionary distinctiveness and phylogeneticposition of Marantaceae within Zingiberales is strongly supported by morphological and molecular data analyses and is likely due to secondary intercontinentaldispersal events.
Abstract: The evolutionary distinctiveness and phylogeneticposition of Marantaceae within Zingiberales is stronglysupported by morphological and molecular data analyses(Kress, 1990, 1995; Kress & al., 2001). Cannaceae, amonogeneric family with about 10 species (Kubitzki,1998; but see Tanaka, 2001), are the closest relative ofMarantaceae. These two families are sister to the familypair Zingiberaceae and Costaceae. Marantaceae includes31 genera and ~535 species distributed throughout warmtemperate and tropical parts of the world (Andersson,1998) with 14 genera in the New World, 11 genera inAfrica (including Madagascar), and eight genera in Asia.Only the genera Thalia and Halopegia occur on morethan one continent. The current geographic distributionof the family is likely due to secondary intercontinentaldispersal events (Kress & Specht, in press; Prince K Watt, 1892; van denBerg, 1984; W. J. Kress, pers. obs.).Andersson (1998) described Marantaceae as prima-rily “jungle weeds”, taking advantage of light gaps tocomplete their life cycle. He noted two genera, Thaliaand Halopegia , that are “confined to open marshes”although the latter often occurs in shady habitats as wellin tropical Asia. The growth habits of some African andAsian Marantaceae are somewhat different from thosefound in the Americas. “Marantaceae forests”, which arelarge expanses of herbaceous vegetation dominated by