378 results on '"Botany -- Identification and classification"'
Search Results
2. An evaluation of candidate plant DNA barcodes and assignment methods in diagnosing 29 species in the genus Agalinis (Robanchaceae)
- Author
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Pettengill, James B. and Neel, Maile C.
- Subjects
DNA barcoding -- Methods ,Angiosperms -- Identification and classification ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
* Premise of the study: DNA barcoding has been proposed as a useful technique within many disciplines (e.g., conservation biology and forensics) for determining the taxonomic identity of a sample based on nucleotide similarity to samples of known taxonomy. Application of DNA barcoding to plants has primarily focused on evaluating the success of candidate barcodes across a broad spectrum of evolutionary divergence. Less attention has been paid to evaluating performance when distinguishing congeners or to differential success of analytical techniques despite the fact that the practical application and utility of barcoding hinges on the ability to distinguish closely related species. * Methods: We tested the ability to distinguish among 92 samples representing 29 putative species in the genus Agalinis (Orobanchaceae) using 13 candidate barcodes and three analytical methods (i.e., threshold genetic distances, hierarchical tree-based, and diagnostic character differences). Due to questions regarding evolutionary distinctiveness of some taxa, we evaluated success under two taxonomic hypotheses. * Key results: The psbA-trnH and trnT-trnL barcodes in conjunction with the 'best close match' distance-based method best met the objectives of DNA barcoding. Success was also a function of the taxonomy used. * Conclusions: In addition to accurately identifying query sequences, our results showed that DNA barcoding is useful for detecting taxonomic uncertainty: determining whether erroneous taxonomy or incomplete lineage sorting is the cause requires additional information provided by traditional taxonomic approaches. The magnitude of differentiation within and among the Agalinis species sampled suggests that our results inform how DNA barcoding will perform among closely related species in other genera. Key words: Agalinis: conservation; DNA barcoding; monophyly; Orobanchaceae; taxonomy. doi: 10.3732/ajb.0900176
- Published
- 2010
3. A new definition and a lectotypification of the genus Cooksonia Lang 1937
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Gonez, Paul and Gerrienne, Philippe
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Plants, Fossil -- Physiological aspects ,Plants, Fossil -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature - Published
- 2010
4. Molecular taxonomy of Camellia (Theaceae) inferred from nrITS sequences
- Author
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Vijayan, Kunjupillai, Zhang, Wen-Ju, and Tsou, Chih-Hua
- Subjects
Camellia -- Natural history ,Botany -- Identification and classification ,Botany -- Analysis ,Botany -- Nomenclature ,Biological sciences - Abstract
Camellia, comprising more than 200 species, is the type genus of the family Theaceae. Currently, the interspecies relationship of the economically important genus is still a matter of great debate and controversy. In an attempt to help settle this dispute using molecular phylogeny, we analyzed ITS sequences of 112 species of Camellia. The maximum parsimony and Bayesian trees grouped these species into eight major clades and four isolates. The current study supported the monophyly of sections Thea and Furfuracea, a merged section of Theopsis and Eriandra and the formation of section Oleifera by H, -t. Chang (Flora of Reipulicae Popularis Sinicae. Tomus 49 (3), Science Press, China). The study suggested the polyphyletic nature of the sections Camellia, Paracamellia, Pseudocamellia, and Tuberculata and the paraphyletic nature of the section Chrysantha but did not support the sectional status of the three small sections, Archecamellia, Piquetia, and Sterocarpus. We also discuss the results in terms of morphology, geographic distribution and the results from an earlier molecular phylogeny analysis. Key words: Camellia; ITS; molecular phylogeny; tea; Theaceae, doi: 10.3732/ajb.0800205
- Published
- 2009
5. Profiling of phenolic compounds of somatic and reproductive tissues of Agave durangensis Gentry (Agavaceae)
- Author
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Almaraz-Abarca, Norma, Delgado-Alvarado, Eli Amanda, Hernandez-Vargas, Vicente, Ortega-Chavez, Margarita, Orea-Lara, Gildardo, de Leon, Armando Cifuentes-Diaz, Avila-Reyes, Jose Antonio, and Muniz-Martinez, Raul
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Agave -- Usage ,Agave -- Chemical properties ,Agave -- Physiological aspects ,Agave -- Research ,Bioflavonoids -- Research ,Flavones -- Research ,Flavonoids -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Science and technology - Abstract
Problem statement: In Durango, Mexico, mescal is elaborated from wild plants of Agave durangensis. This species shows a high morphological variability within and among populations, what makes its taxonomic delimitation a hard task. Approach: In this study the pollen and foliar phenolic compositions of Agave durangensis were analyzed by HPLC/DAD with the aim of determining the significance of phenol profiles to delimit this taxon. Results: The foliar phenol compositions were evaluated within and among two populations and between juvenile and adult plants. Agave asperrima Jacobi, Dasylirion sp. and juvenile samples of A. shrevei Gentry subsp. shrevei, A. shrevei Gentry subsp. matapensis Gentry and A. wocomahi Gentry, were also analyzed to stand comparisons with. The results from this study indicated that pollen and foliar tissues of Agave durangneisis were rich in kaempferol glycoside derivatives (13 and 23 different compounds can be present, respectively). Principal coordinates analysis (PCO), based on foliar profiles of adults, indicated the presence of several chemotypes within the Type locality of Agave durangensis and revealed chemical differences between the both analyzed populations. Conclusion/Recommendations: Chemical and morphological differences and biogeographical evidence suggest the recognition of two different taxonomic entities in this morphological variable group. Key words: Pollen flavonoids, foliar flavonoid profiles, Agave phenolic variability, INTRODUCTION Agave is the biggest genus of the family Agavaceae, with around 166 species, from which 125 grow in Mexico (1), (2). Relevant ethnobotanic relationships have been established between the [...]
- Published
- 2009
6. A preliminary phylogeny of the 'didymocarpoid Gesneriaceae' based on three molecular data sets: incongruence with available tribal classifications
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Moller, Michael, Pfosser, Martin, Jang, Chang-Gee, Mayer, Veronika, Clark, Alexandra, Hollingsworth, Michelle L., Barfuss, Michael H.J., Wang, Yin-Zheng, Kiehn, Michael, and Weber, Anton
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Phylogeny (Botany) -- Evaluation ,Botany -- Identification and classification ,Botany -- Evaluation ,Botany -- Nomenclature ,Biological sciences - Abstract
The 'didymocarpoid Gesneriaceae' (traditional subfam. Cyrtandroideae excluding Epithemateae) are the largest group of Old World Gesneriaceae, comprising 85 genera and 1800 species. We attempt to resolve their hitherto poorly understood generic relationships using three molecular markers on 145 species, of which 128 belong to didymocarpoid Gesneriaceae. Our analyses demonstrate that consistent topological relationships can be retrieved from data sets with missing data using subsamples and different combinations of gene sequences. We show that all available classifications in Old World Gesneriaceae are artificial and do not reflect natural relationships. At the base of the didymocarpoids are grades of clades comprising isolated genera and small groups from Asia and Europe. These are followed by a clade comprising the African and Madagascan genera. The remaining clades represent the advanced Asiatic and Malesian genera. They include a major group with mostly twisted capsules. The much larger group of remaining genera comprises exclusively genera with straight capsules and the huge genus Cyrtandra with indehiscent fruits. Several genera such as Briggsia, Henckelia, and Chirita are not monophyletic; Chirita is even distributed throughout five clades. This degree of incongruence between molecular phylogenies, traditional classifications, and generic delimitations indicates the problems with classifications based on, sometimes a single, morphological characters. Key words: atpB-rbcL spacer; Bayesian inference analysis; ITS; maximum parsimony; molecular phylogeny; Old World Gesneriaceae; taxonomy; trnL-F intron-spacer.
- Published
- 2009
7. Pentapetalum trifasciculandricus gen. et sp. nov., a thealean fossil flower from the raritan formation, New Jersey, USA (Turonian, Late Cretaceous)
- Author
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Martinez-Millan, Marcela, Crepet, William L., and Nixon, Kevin C.
- Subjects
Plants, Fossil -- Identification and classification ,Plants, Fossil -- Discovery and exploration ,Dilleniidae -- Discovery and exploration ,Dilleniidae -- Identification and classification ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
The study of fossil flowers in the last 25 years has greatly increased our understanding of angiosperm diversification. Following that tradition, we here describe a new fossil taxon from the Late Cretaceous of New Jersey, Pentapetalum trifasciculandricus Martinez-Millan, Crepet et Nixon gen. et sp. nov. It includes actinomorphic pentamerous flowers with quincuncial calyx, imbricate corolla, numerous stamens of markedly different heights, and a superior tricarpellate ovary, which are morphologically consistent with the flowers of the Theaceae s.l. and of members of the order Theales sensu Cronquist. Cladistic analyses including 45 extant taxa plus the fossil, 61 morphological characters, and different combinations of the molecular markers rbcL. matK, trnL-trnF, matR, and ITS support its inclusion in the order Ericales sensu APG. Comparison with extant taxa using traditional methods of identification suggests a relation with the Theaceae s.s. (Stewartia), but the phylogenetic analyses do not support this view. Instead, the phylogenetic analysis suggests some relation to the Ternstroemiaceae/Pentaphylacaceae (Theaceae s.l.), exemplifying the importance of evaluating identifications in a phylogenetic context. The description of Pentapetalum further adds to the ample diversity of Ericales in the Late Cretaceous. Key words: Ericales; fossil flower; Late Cretaceous; Pentaphylacaceae; Raritan Formation; Theaceae; Theales; Ternstoemiaceae; Turonian.
- Published
- 2009
8. Standards for associations and alliances of the U.S. National Vegetation Classification
- Author
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Jennings, Michael D., Faber-Langendoen, Don, Loucks, Orie L., Peet, Robert K., and Roberts, David
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Botany -- Identification and classification ,Botany -- Standards ,Botany -- Nomenclature ,Biological sciences ,Environmental issues - Abstract
This article provides guidelines for the description, documentation, and review of proposals for new or revised plant associations and alliances to be recognized as units of vegetation within the U.S. National Vegetation Classification (NVC). By setting forth standards for field records, analysis, description, peer review, and archiving, the Ecological Society of America's Vegetation Classification Panel, in collaboration with the U.S. Federal Geographic Data Committee, NatureServe, and others, seeks to advance our common understanding of vegetation and improve our capability to sustain and restore natural systems. We provide definitions for the two floristic levels of the NVC hierarchy: associations and alliances. This is followed by a description of standards for field plot records and the identification and classification of vegetation types. Procedures for review and evaluation of proposed additions and revisions of types are provided, as is a structure for data archiving and dissemination. These procedures provide a dynamic and practical way to publish new or revised descriptions of vegetation types while maintaining a current, authoritative list of types for multiple users to access and apply. Key words: floristic types; national standards; plot data; U.S. National Vegetation Classification; vegetation alliance; vegetation association; vegetation classification.
- Published
- 2009
9. Assigning morphological variants of Fucus (Fucales, Phaeophyceae) in Canadian waters to recognized species using DNA barcoding
- Author
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Kucera, Hana and Saunders, Gary W.
- Subjects
Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Botany -- Morphology ,Biological sciences - Abstract
The intertidal brown algal genus Fucus (Phaeophyceae) consists of individuals with a generally dichotomously branched habit. Morphological variability within species, combined with morphological similarity between species, renders field identification difficult. In light of recent taxonomic revisions, which reduced 10 taxa traditionally recognized in Canada to four species, we tested the utility of the DNA barcode (mitochondrial cytochrome oxidase 1, 5') for assigning individuals to these species. We sequenced the DNA barcode for 125 specimens representing all morphologies recognized. We confirmed our results by sequencing the internal transcribed spacer region for 66 specimens. This is the first study to establish that the DNA barcode successfully assigns different morphologies of brown algae to known species as well as other single-gene molecular markers currently used. Furthermore, the results uncovered substantial phenotypic plasticity in Pacific Fucus distichus, from moss-like fragments embedded in estuarine mud, strap-like morphs on exposed rocky coasts, to 'spiralis'-like morphs in the upper intertidal whereas phenotypic expression for this species was more restricted in the Atlantic. Key words: Fucus, DNA barcoding, internal transcribed spacer, species identification, brown algae, cytochrome c oxidase subunit I. Les algues brunes intertidales du genre Fucus (Phaeophyceae) regroupent des individus ayant un port a ramifications dichotomiques. La variabilite morphologique intraspecifique, combinee avec une similitude entre les especes, rend l'identification au champ difficile. A la lumiere de recentes revisions taxonomiques reduisant les dix taxons generalement reconnus au Canada a quatre especes, les auteurs ont verifie l'utilite du code a barres ADN (cytochrome oxydase mitochondriale 1,5) pour attribuer les individus a ces especes. Ils ont sequence le code a barres ADN chez 125 specimens representant toutes les morphologies connues. Ils ont confirme leurs resultats en sequencant la region de l'espaceur interne transcrit chez 66 specimens. Il s'agit de la premiere etude pour etablir que le code a barres ADN attribue avec succes differentes morphologies d'algues brunes a des especes connues, en meme temps que d'autres marqueurs moleculaires a simple gene couramment utilises. De plus, les resultats demontrent une substantielle plasticite phenotypique chez le Fucus distichus du Pacifique, a partir de fragments ressemblant a une mousse enrobee dans une vase estuarienne, de formes en lacets sur des rochers cotiers, de structures spiraliformes dans la zone intertidale superieure, alors que l'expression phenotypique de cette espece est plus restreinte dans l'Atlantique. Mots-cles : Fucus, code a barres ADN, espaceur interne transcrit, identification des especes, algues brunes, sous-unite 1 de la cytochrome oxydase., Introduction The brown algal genus Fucus is a prominent component of the intertidal seaweed flora along the rocky shorelines of the cold temperate waters of the northern hemisphere. Fucus species [...]
- Published
- 2008
10. The Eocene mystery flower of McAbee, British Columbia
- Author
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Manchester, Steven R. and Pigg, Kathleen B.
- Subjects
Flowers -- Natural history ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
A distinctive, extinct type of flower and fruit is described based on coalified compression and impression fossils from the Eocene lake bed deposits of McAbee, British Columbia. Dillhoffia cachensis gen. et sp. nov. has an elongate-ellipsoidal fruit with an epigynous, completely connate funnelform calyx 1.8-2.9 cm in diameter, with an unlobed, orbicular margin. The fruit narrows apically into a single style divided into four slightly recurved stigmatic aims. Fruits are pedicellate, borne in globose heads. Stamens, pollen, and internal fruit morphology remain unknown, but the available details of gynoecial and perianth morphology present a suite of characters not encountered in any known extant genus, and the familial affinities remain uncertain. This is noteworthy, because many other elements of the same Eocene flora represent extant genera with clear familial assignments such as Cunninghamia, Ginkgo, Aesculus, Alnus, Betula, Dipteronia, Fagus, Trochodendron, and Ulmus. Key words: Eocene, paleobotany, flower, fruit, McAbee, British Columbia. Les auteurs decrivent un type de fleurs et de fruits eteints bien caracterises a partir de fossiles carbonises par impression ou compression, provenant des depots de fond du lac Eocene, a McAbee, en Colombie canadienne. Le Dillhoffia cachensis gen. et sp. nov. montre un fruit allonge ellipsoide avec un calice epigyne completement conne infundibiliforme, mesurant 1.8-2.9 cm de diametre, avec une marge orbiculaire non lobee. Les fruits s'amenuisent apicalement en simple style divise en quatre bras stigmatiques legerement recourbes. Les fruits sont portes sur des pedicelles a partir de cimes globulaires. Les etamines, le pollen, et la morphologie interne demeurent inconnus, mais les details disponibles sur la morphologie du perianthe et du gynecee presentent une suite de caracteres qu'on ne retrouve dans aucun genre existant connu, et les affinites familiales demeurent incertaines. Ceci est remarquable puisse que plusieurs autres elements de la meme flore Eocene representent des genres existant actuellement avec des attributions familiales nettes, tels que les Cunninghamia, Ginkgo, Aesculus, Alnus, Betula, Dipteronia, Fagus, Trochodendron et Ulmus. Mots-cles : Eocene, paleobotanique, fleur, fruit, McAbee, Colombie canadienne. [Traduit par la Redaction], Introduction The Eocene lake sediments of McAbee, near Cache Creek, British Columbia, yield a diverse flora including at least 14 conifers and 67 angiosperms (Dillhoff et al. 2005). Dominant dicots [...]
- Published
- 2008
11. Systematics of three North American polyploid arctic alkali grasses (Puccinellia, Poaceae): morphology, ploidy, and AFLP markers
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Consaul, Laurie L., Gillespie, Lynn J., and Waterway, Marcia J.
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Grasses -- Genetic aspects ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
We used flow cytometry, amplified fragment length polymorphisms (AFLP), and macromorphology from field and common garden specimens to delimit and identify parental taxa of three polyploid species of Puccinellia from the North American Arctic. Tetraploid Puccinellia bruggemannii T.J. Sorensen, hexaploid Puccinellia angustata (R. Br.) E.L. Rand & Redfield, and octoploid Puccinellia andersonii Swallen were generally separable based on ploidy and AFLP pattern, and showed allopolyploid origin. All three shared AFLP bands with at least two diploids and with Puccinellia phryganodes (Trin.) Scribn. & Merr., shown here to have both triploid and tetraploid populations in Canada. Approximately 10% of hexaploid individuals had AFLP patterns that were intermediate between P. angustata and P. bruggemannii, or P. angustata and P. andersonii, and occupied corresponding intermediate positions in morphological ordinations. Geographic distributions provide better support for introgression than for multiple polyploid events to account for these intermediate patterns. In common garden experiments, half of the characters had significantly different values between field and common garden specimens, but these plastic characters varied depending on the species pair analyzed and between experiments. Moreover, several characters were significantly different among species, but these characters were also different in each of the two experiments. Given this variation, we pooled the field and common garden data to determine important key characters by discriminant analysis of species pairs. Key words: polyploidy, Poaceae, flow cytometry, common garden experiment, amplified fragment length polymorphism. Les auteurs ont applique la cytometrie en flux, le polymorphisme de la longueur des fragments amplifies (AFLP) et la macromorphologie sur des specimens venant de la nature ou venant d'un jardin commun, afin d'identifier les taxons parentaux de trois especes polyploides de Puccinella de l'Arctique nord-americain. On peut generalement separer le P. bruggemannii, T.J. Sorensen, l'hexaploide Puccinella angustata (R. Br.) E.L. Rand & Redfield, et l'octoploide Puccinella andersonii Swallen sur la base de la ploidie et du patron AFLP, et en montrer l'origine alloploide. Ils partagent tous les trois des bandes AFLP avec au moins deux diploides et avec le Puccinella phryganodes (Trin.) Scribn. & Merr., chez lequel on demontre la presence de populations triploides et tetraploides au Canada. Environ 10 % des individus hexaploides montrent des patrons AFLP intermediaires entre le P. angustata et le P. bruggemannii, ou le P. angustata et le P. andersonii, et occupent des positions intermediaires correspondantes dans les ordinations morphologiques. Les distributions geographiques fournissent de meilleurs supports pour l'introgression que pour les evenements a polyploidie multiple pour expliquer ces patrons intermediaires. Dans les experiences en jardins communs, la moitie des caracteres montrent des valeurs significativement differentes entre les specimens venant de la nature et celles du jardin commun, mais ces caracteres plastiques varient selon la paire d'especes analysees et entre les experiences. De plus, plusieurs caracteres different significativement entre les especes, mais ces caracteres different egalement dans chacune des deux experiences. Compte tenu de cette variation, les auteurs ont regroupe les donnees de terrain avec celles des jardins communs pour determiner les caracteres cles importants, a l'aide de l'analyse discriminante des paires d'especes. Mots-cles : polyploidie, Poaceae, cytometrie en flux, experience en jardin commun, polymorphisme de la longueur des fragments amplifies. [Traduit par la Redaction], Introduction Polyploidy is a fundamental mechanism for plant speciation. Autopolyploid species, formed by the duplication of a single parental genome, can have a greater capability for genetic modification than their [...]
- Published
- 2008
12. Cytotaxonomy and cytogeography of the goldenaster genus Heterotheca (Asteraceae: Astereae)
- Author
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Semple, John C.
- Subjects
Compositae -- Genetic aspects ,Plant cytogenetics -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
Between 1948 and 2008, 668 chromosome number determinations have been reported for individuals of the goldenaster genus Heterotheca Cass. (Asteraceae: Astereae) from Canada, Mexico, and the United States, including 285 newly reported here. This common group of mostly western North American herbaceous annuals and perennials is subdivided into three sections, the most complex of which is section Phyllotheca. Differences of opinion about the taxonomy of the goldenasters, numerous synonyms, and the lack of a comprehensive treatment of the polymorphic villosa complex and other species complexes in section Phyllotheca made it difficult to organize the data into a meaningful discussion of the cytotaxonomy and cytogeography of this genus. Here I present the geographic distribution of all published counts and cytogeography maps of all species of Heterotheca, assigning taxa following recent taxonomic revisions. The sample sizes for species sampled ranged from 1 to 228 reports. All species have a base number of x = 9. Only diploids (2n = 911 or 2n = 18) were found in Heterotheca oregona (Nutt.) Shinners (the single species of sect. Ammodia) and in the three species of section Heterotheca. Both diploids and (or) tetraploids were found across 18 sampled species of section Phyllotheca, with the frequency varying among them; nine species are known only at one ploidy level (either diploid or tetraploid; three species each). Only four triploids (2n = 9111 or 2n = 27) were encountered in section Phyllotheca; two were putative interspecific hybrids. One new nomenclatural combination is proposed: Heterotheca inuloides var. leptioglossa. Key words: Heterotheca, cytogeography, cytotaxonomy, Asteraceae, Astereae, biogeography, goldenasters. Resume : Entre 1948 et 2008, on a rapporte 668 determinations de nombres de chromosomes d'individus du genre Heterotheca Cass. (Asteraceae; Asterae) du Canada, du Mexique et des Etats-Unis, incluant les 285 rapportees ici. On divise ce groupe commun d'especes annuelles et perennes, provenant surtout de l'ouest de l'Amerique du Nord, en trois sections dont la section Phyllotheca apparait la plus complexe. Il existe des differences d'opinions au sujet de la taxonomie du genre Heterotheca, de nombreux synonymes et une absence de considerations d'ensemble du complexe polymorphe villosa et autres complexes d'especes de la section Phyllotheca; ceci rend difficile l'organisation des donnees dans une discussion significative de la cytotaxonomie et la cytogeographie de ce genre. L'auteur presente la distribution geographique de tous les nombres sur des cartes cytogeographiques pour toutes les especes d'Heterotheca, attribuant les taxons selon les recentes revisions taxonomiques. Les dimensions des echantillons des especes echantillonnees vont de 1 a 228. Toutes les especes partagent le meme nombre de base, soit x = 9. On ne retrouve des diploides exclusives (2n = 911 ou 2n =18) que chez l'H. oregona (la seule espece de la sect. Ammodioa) et chez trois especes de la sect. Heterotheca. On a retrouve a la fois des diploides et des tetraploides parmi les 18 especes echantillonnees appartenant a la sect. Phyllotheca, leurs frequences variant entre elles; on connait 9 especes avec un seul degre de ploidie (diploide ou tetraploide; trois especes chacun). On n'a rencontre que quatre triploides (2n = 9111 ou 2n = 27) dans la sect. Phylloyheca; deux constituent des hybrides interspecifiques putatifs. L'auteur propose une nouvelle combinaison nomenclaturale, fHeterotheca inuloides var. leptoglossa. Mots-cles : Heterotheca, cytogeographie, cytotaxonomie, Asteraceae, Astereae, biogeographie, verge d'or. [Traduit par la Redaction], Introduction The goldenaster genus Heterotheca Cass. (Asteraceae: Astereae) includes ca. 24 species of herbaceous annuals and perennials distributed throughout much of Mexico, the United States, and the prairies and southern [...]
- Published
- 2008
13. Trans-Atlantic dispersal and large-scale lack of genetic structure in the circumpolar, arctic-alpine sedge Carex bigelowii s. l. (Cyperaceae)
- Author
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Schonswetter, Peter, Elven, Reidar, and Brochmann, Christian
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Bayesian statistical decision theory -- Evaluation ,Cyperaceae -- Identification and classification ,Cyperaceae -- Environmental aspects ,Plants -- Migration ,Plants -- Evaluation ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
Paradoxically, several of the ecologically most important plant groups in the Arctic are little understood in terms of taxonomy and biogeographic history. The circumpolar Carex bigelowii s. 1. (Cyperaceae) is abundant in the Arctic and is one of the most complicated arctic plant groups. While its ecology and population genetics have been extensively studied, its taxonomy is largely unexplored. We analyzed the large-scale geographical structuring of amplified fragment length polymorphisms (AFLPs) covering most of the distribution range. We detected high levels of genetic variation, most (66%) within populations, and a fairly weak genetic structure. Only the Central Asian populations, referred to as C. orbicularis, were strongly divergent. For the remaining populations, Bayesian clustering separated three distinct clusters (one European, one amphi-Atlantic, and one broadly amphiBeringian), probably reflecting different major glacial refugia and recent transoceanic dispersal. The isolated central European populations were most closely related to those from a larger distribution area in northern Europe. Differences in genetic diversity suggest that the Alpine and Tatra populations have experienced strong bottlenecks, whereas the Krkonose population may have been part of a continuous distribution area during the cold stages of the Pleistocene. Finally, we discuss the relevance of our results for a uniform, range-wide taxonomic concept. Key words: AFLP; arctic-alpine flora; Bayesian clustering; Carex bigelowii; Cyperaceae; plant migration; taxonomy.
- Published
- 2008
14. Phylogenetic, morphological, and chemotaxonomic incongruence in the North American endemic genus Echinacea
- Author
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Flagel, Lex E., Rapp, Ryan A., Grover, Corrinne E., Widrlechner, Mark P., Hawkins, Jennifer, Grafenberg, Jessie L., Alvarez, Ines, Chung, Gyu Young, and Wendel, Jonathan F.
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Echinacea -- Genetic aspects ,Echinacea -- Identification and classification ,Echinacea -- Natural history ,Molecular evolution -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
The study of recently formed species is important because it can help us to better understand organismal divergence and the speciation process. However, these species often present difficult challenges in the field of molecular phylogenetics because the processes that drive molecular divergence can lag behind phenotypic divergence. In the current study we show that species of the recently diverged North American endemic genus of purple coneflower, Echinacea, have low levels of molecular divergence. Data from three nuclear loci and two plastid loci provide neither resolved topologies nor congruent hypotheses about species-level relationships. This lack of phylogenetic resolution is likely due to the combined effects of incomplete lineage sorting, hybridization, and backcrossing following secondary contact. The poor resolution provided by molecular markers contrasts previous studies that found well-resolved and taxonomically supported relationships from metabolic and morphological data. These results suggest that phenotypic canalization, resulting in identifiable morphological species, has occurred rapidly within Echinacea. Conversely, molecular signals have been distorted by gene flow and incomplete lineage soning. Here we explore the impact of natural history on the genetic organization and phylogenetic relationships of Echinacea. Key words: Asteraceae; chloroplast DNA; Echinacea; incomplete lineage sorting; phylogenetics; single-copy nuclear DNA.
- Published
- 2008
15. A review of the distribution of plasmodial and invasive tapeta in eudicots
- Author
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Furness, Carol A.
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Angiosperms -- Physiological aspects ,Dicotyledons -- Physiological aspects ,Phylogeny -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature - Published
- 2008
16. Plants and pigeonholes: classification as a practice in American ecology
- Author
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Kohler, Robert E.
- Subjects
Ecologists -- Innovations ,Classification of sciences -- Analysis ,Classification of sciences -- Methods ,Botany -- Identification and classification ,Botany -- Methods ,Botany -- Nomenclature ,Biological sciences ,Physics - Abstract
The common practice of classification that is often adopted by the ecologists in the United States to put plants and other species in different compartments on the basis of their certain characteristics is discussed. The perceptions of different categories are shown to be highly dependent on the density and geographical scope of data.
- Published
- 2008
17. Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification
- Author
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Spooner, David M., Nunez, Jorge, Trujillo, Guillermo, Herrera, Maria del Rosario, Guzman, Frank, and Ghislain, Marc
- Subjects
Genetically modified organisms -- Genetic aspects ,Genotype -- Identification and classification ,Potatoes -- Properties ,Potatoes -- Genetic aspects ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Science and technology - Abstract
Contrasting taxonomic treatments of potato landraces have continued over the last century, with the recognition of anywhere from 1 to 21 distinct Linnean species, or of Cultivar Groups within the single species Solanum tuberosum. We provide one of the largest molecular marker studies of any crop landraces to date, to include an extensive study of 742 landraces of all cultivated species (or Cultivar Groups) and 8 closely related wild species progenitors, with 50 nuclear simple sequence repeat (SSR) (also known as microsatellite) primer pairs and a plastid DNA deletion marker that distinguishes most lowland Chilean from upland Andean landraces. Neighbor-joining results highlight a tendency to separate three groups: (i) putative diploids, (ii) putative tetraploids, and (iii) the hybrid cultivated species S. ajanhuiri (diploid), S. juzepczukii (triploid), and S. curtilobum (pentaploid). However, there are many exceptions to grouping by ploidy. Strong statistical support occurs only for S. ajanhuiri, S. juzepczukii, and S. curtilobum. In combination with recent morphological analyses and an examination of the identification history of these collections, we support the reclassification of the cultivated potatoes into four species: (i) S. tuberosum, with two Cultivar Groups (Andigenum Group of upland Andean genotypes containing diploids, triploids, and tetraploids, and the Chilotanum Group of lowland tetraploid Chilean landraces); (ii) S. ajanhuiri (diploid); (iii) S. juzepczukii (triploid); and (iv) S. curtilobum (pentaploid). For other classifications, consistent and stable identifications are impossible, and their classification as species is artificial and only maintains the confusion of users of the gene banks and literature. cultivated | microsatellites | sect. Petota | Solanum tuberosum | taxonomy
- Published
- 2007
18. Random forests for classification in ecology
- Author
-
Cutler, D. Richard, Edwards, Thomas C., Jr., Beard, Karen H., Cutler, Adele, Hess, Kyle T., Gibson, Jacob, and Lawler, Joshua J.
- Subjects
Plants -- Identification and classification ,Botany -- Identification and classification ,Botany -- Methods ,Botany -- Nomenclature ,Ecological research ,Biological sciences ,Environmental issues - Abstract
Classification procedures are some of the most widely used statistical methods in ecology. Random forests (RF) is a new and powerful statistical classifier that is well established in other disciplines but is relatively unknown in ecology. Advantages of RF compared to other statistical classifiers include (1) very high classification accuracy; (2) a novel method of determining variable importance; (3) ability to model complex interactions among predictor variables; (4) flexibility to perform several types of statistical data analysis, including regression, classification, survival analysis, and unsupervised learning; and (5) an algorithm for imputing missing values. We compared the accuracies of RF and four other commonly used statistical classifiers using data on invasive plant species presence in Lava Beds National Monument, California, USA, rare lichen species presence in the Pacific Northwest, USA, and nest sites for cavity nesting birds in the Uinta Mountains, Utah, USA. We observed high classification accuracy in all applications as measured by cross-validation and, in the case of the lichen data, by independent test data, when comparing RF to other common classification methods. We also observed that the variables that RF identified as most important for classifying invasive plant species coincided with expectations based on the literature. Key words: additive logistic regression; classification trees; LDA; logistic regression; machine learning; partial dependence plots; random forests; species distribution models.
- Published
- 2007
19. A test of taxonomic predictivity: resistance to white mold in wild relatives of cultivated potato
- Author
-
Jansky, Shelley H., Simon, Reinhard, and Spooner, David M.
- Subjects
Potatoes -- Diseases ,Potatoes -- Genetic aspects ,Molds (Fungi) -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Agricultural industry ,Business - Abstract
A major justification for taxonomic research is its assumed ability to predict the presence of traits in a group for which the trait has been observed in a representative subset of the group. Taxonomy is regularly used by breeders interested in choosing potential sources of disease-resistant germplasm for cultivar improvement. We designed this study as an empirical test of prediction by associating resistance to white mold [caused by the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary] to diverse potato (Solanum spp.) taxonomies and biogeography, using 144 accessions of 34 wild relatives of potato in Solanum sections Petota and Etuberosum. Tremendous variation for resistance to white mold occurs both within and among species. No consistent association was observed between white mold resistance and taxonomic series (based on a phenetic concept), clades (based on a cladistic concept), ploidy, breeding system, geographic distance, or climate parameters. Species and individual accessions with high proportions of whitemold-resistant plants have been identified in this study, but both often exhibit extensive variation and designation of either as resistant or susceptible must take this variation into account. Therefore, taxonomic relationships and ecogeographic data cannot be reliably used to predict where additional sources of white mold resistance genes will be found.
- Published
- 2006
20. The taxonomic value of fruit wing types in the order Apiales
- Author
-
Liu, Mei "Rebecca", Plunkett, Gregory M., Lowry, Porter P., II, Van Wyk, Ben-Erik, and Tilney, Patricia M.
- Subjects
Rosidae -- Physiological aspects ,Rosidae -- Genetic aspects ,Phylogeny (Botany) -- Research ,Botany -- Identification and classification ,Botany -- Evaluation ,Botany -- Nomenclature ,Biological sciences - Abstract
This study shows that structural data, when carefully examined, can provide valuable characters for delimiting monophyletic groups and can complement DNA with observable features to recognize and circumscribe taxa. In the angiosperm order Apiales, traditional classification has relied heavily (often exclusively) on fruit characters. Recent molecular systematic studies, however, provided a radically different picture of relationships, calling into question the utility of fruit characters. We have studied fruit anatomy from 18 genera (Annesorhiza, Asteriscium, Astrotricha, Choritaenia, Dasispermum, Elaeoselinum, Heptaptera, Hermas, Heteromorpha, Laretia, Molopospernum, Myodocarpus, Pachypleurum, Peucedanum, Polemanniopsis, Polylophium, Rouya, and Tordylium) that represent all major taxonomic groups of Apiales characterized by winged fruits and the full range of wing types. Fruit anatomy closely corresponded with the phylogenetic position of these genera, as suggested by molecular studies. Fruit features of taxonomic importance include developmental origin of the wings, carpel shape, presence of vittae, woodiness of the endocarp, position of crystals, and type of carpophores. Despite the long history of recognizing umbellifers as a 'natural group,' few studies have been able to provide structural characters to help circumscribe the clades identified by molecular data. The interpretations presented are an important step toward erecting a stable system of classification for this difficult family. Key words: Apiaceae; Apiales; Araliaceae; classification; fruit anatomy; phylogeny; wings.
- Published
- 2006
21. Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta)
- Author
-
Robba, Lavinia, Russell, Stephen J., Barker, Gary L., and Brodie, Juliet
- Subjects
Cytochrome oxidase -- Usage ,Red algae -- Identification and classification ,Cytochrome c -- Usage ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
The red algae, a remarkably diverse group of organisms, are dill]cult to identity using morphology alone. Following the proposal to use the mitochondrial cytochrome c oxidase subunit I (cox1) for DNA barcoding animals, we assessed the use of this gene in the identification of red algae using 48 samples plus 31 sequences obtained from GenBank. The data set spanned six orders of red algae: the Bangiales, Ceramiales, Corallinales, Gigartinales, Gracilariales and Rhodymeniales. The results indicated that species could be discriminated. Intraspecific variation was between 0 and 4 bp over 539 bp analyzed except in Mastocarpus stellatus (0-14 bp) and Gracilaria gracilis (0-11 bp). Cryptic diversity was found in Bangia fuscopurpurea, Corallina officinalis, G. gracilis, M. stellatus, Porphyra leucosticta and P. umbilicalis. Interspecific variation across all taxa was between 28 and 148 bp, except for G. gracilis and M. stellatus. A comparison of cox1 with the plastid Rubisco spacer for Porphyra species revealed that it was a more sensitive marker in revealing incipient speciation and cryptic diversity. The cox1 gene has the potential to be used for DNA barcoding of red algae, although a good taxonomic foundation coupled with extensive sampling of taxa is essential for the development of an effective identification system. Key words: cytochrome c oxidase subunit I; DNA barcoding; species identification; red algae; Rubisco spacer.
- Published
- 2006
22. Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale
- Author
-
Cavender-Bares, Jeannine, Keen, Adrienne, and Miles, Brianna
- Subjects
Plant communities -- Research ,Plant communities -- Environmental aspects ,Plant conservation -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences ,Environmental issues - Abstract
Consideration of the scale at which communities are defined both taxonomically and spatially can reconcile apparently contradictory results on the extent to which plants show phylogenetic niche conservatism. In plant communities in north central Florida, we collected species abundances in 55 0.1-ha plots in several state parks. When communities were defined narrowly to include a single phylogenetic lineage, such as Quercus, Pinus, or Ilex, neighbors tended to be less related than expected (phylogenetic overdispersion)or there was no pattern. If the same communities were defined more broadly, such as when all seed plants were included, neighbors tended to be more related than expected (phylogenetic clustering). These results provide evidence that species interactions among close relatives influence community structure, but they also show that niche conservatism is increasingly evident as communities are defined to include greater phylogenetic diversity. We also found that, as the spatial scale is increased to encompass greater environmental heterogeneity, niche conservatism emerges as the dominant pattern. We then examined patterns of trait evolution in relation to trait similarity within communities for 11 functional traits for a single phylogenetic lineage (Quercus) and for all woody plants. Among the oaks, convergent evolution of traits important for environmental filtering contributes to the observed pattern of phylogenetic overdispersion. At the broader taxonomic scale, traits tend to be conserved, giving rise to phylogenetic clustering. The shift from overdispersion to clustering can be explained by the increasing conservatism of traits at broader phylogenetic scales. Key words: environmental heterogeneity; Florida; Ilex; niche conservatism; overdispersion; phylogenetic structure of communities; Pinus; Quercus; taxonomic scale; trait convergence.
- Published
- 2006
23. Molecular evidence for the systematic positions of two enigmatic mosses: Pterogonidium pulchellum (Sematophyllaceae, Musci) and Piloecium pseudorufescens (Myuriaceae, Musci)
- Author
-
Chang, Ying, Woon Khiong, Chan, Graham, Sean W., and Tan, Benito C.
- Subjects
Moss -- Identification and classification ,Moss -- Genetic aspects ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
Abstract: The systematic position of Pterogonidium pulchellum (W.J. Hooker) Muell. Hal. in the Sematophyllaceae And Piloecium pseudorufescens (Hampe) Muell. Hal. in the Myuriaceae is reexamined with new evidence derived from [...]
- Published
- 2006
24. Does plant species co-occurrence influence soil mite diversity?
- Author
-
St. John, Mark G., Wall, Diana H., and Behan-Pelletier, Valerie M.
- Subjects
Soil ecology -- Environmental aspects ,Botany -- Identification and classification ,Botany -- Environmental aspects ,Botany -- Nomenclature ,Habitat selection ,Biological sciences ,Environmental issues - Abstract
Few studies have considered whether plant taxa can be used as predictors of belowground faunal diversity in natural ecosystems. We examined soil mite (Acari) diversity beneath six grass species at the Konza Prairie Biological Station, Kansas, USA. We tested the hypotheses that soil mite species richness, abundance, and taxonomic diversity are greater (1) beneath grasses in dicultures (different species) compared to monocultures (same species), (2) beneath grasses of higher resource quality (lower C:N) compared to lower resource quality, and (3) beneath heterogeneous mixes of grasses ([C.sub.3] and [C.sub.4] grasses growing together) compared to homogeneous mixes ([C.sub.3] or [C.sub.4] grasses) using natural occurrences of plant species as treatments. This study is the first to examine the interaction between above- and belowground diversity in a natural setting with species-level resolution of a hyper-diverse taxon. Our results indicate that grasses in diculture supported a more species and phylogenetically rich soil mite fauna than was observed for monocultures and that this relationship was significant at depth but not in the upper soil horizon. We noted that mite species richness was not linearly related to grass species richness, which suggests that simple extrapolations of soil faunal diversity based on plant species inventories may underestimate the richness of associated soil mite communities. The distribution of mite size classes in dicultures was considerably different than those for monocultures. There was no difference in soil mite richness between grass combinations of differing resource quality, or resource heterogeneity. Key words: Acari; biodiversity; functional groups; microarthropods; microhabitat; mites; overyield; resource heterogeneity; resource quality; soil ecosystem; species richness.
- Published
- 2006
25. Evolutionary analysis of Pinus leiophylla: a study using an intron II sequence fragment of mitochondrial nad1
- Author
-
Mendoza, Carlos Fabian Vargas and Rodriguez-Banderas, Abril
- Subjects
Pine -- Genetic aspects ,Pine -- Research ,Pine -- Identification and classification ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
Abstract: A phylogenetic analysis was done using a mitochondrial marker to study the relationship between Pinus Leio-phylla Schiede & Deppe and Californian, Mesoamerican, European, and Asian pines. The type II [...]
- Published
- 2006
26. The anatomy of Rotoxylon dawsonii comb. Nov. (Cladoxylon dawsonii) from the upper Devonian of New York State
- Author
-
Cordi, Jennifer and Stein, William E.
- Subjects
Vascular plants -- Natural history ,Evolution -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature - Published
- 2005
27. Phylogenetic relationships in Peniocereus (Cactaceae) inferred from plastid DNA sequence data
- Author
-
Arias, Salvador, Terrazas, Teresa, Arreola-Nava, Hilda J., Vazquez-Sanchez, Monserrat, and Cameron, Kenneth M.
- Subjects
Cactus -- Identification and classification ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Science and technology - Published
- 2005
28. Male pleasure and the genders of eighteenth-century botanic exchange: A garden tour
- Author
-
Hallock, Thomas
- Subjects
Botany -- History ,United States history -- 18th century AD ,Botany -- Identification and classification ,Botany -- Analysis ,Botany -- Nomenclature ,History - Abstract
The garden tour reflected a common sentiment in which plants served as shorthand for intimate relationships that transacted across vast space and out of the remarkable epistolary network that neared two hundred correspondents. Plants served as a conduit for human affections, leading writers to affix human emotion to scientific specimens and changes in 18th century identity formation made this channeling of male pleasure through natural history almost inevitable.
- Published
- 2005
29. Molecular phylogenetics of subtribe Aeridinae (Orchidaceae): insights from plastid matK and nuclear ribosomal ITS sequences
- Author
-
Hidayat, Topik, Yukawa, Tomohisa, and Ito, Motomi
- Subjects
Orchids -- Identification and classification ,Orchids -- Genetic aspects ,Orchids -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Science and technology - Published
- 2005
30. A Middle English rosemary treatise in verse and prose
- Author
-
Keiser, George R.
- Subjects
Rosemary -- History ,Botany -- Identification and classification ,Botany -- History ,Botany -- Nomenclature ,Anthropology/archeology/folklore ,History ,Literature/writing - Abstract
In England of the fourteenth, fifteenth, and sixteenth centuries the increasing accessibility of books among the professional and middle classes led to a great and persistent demand for vernacular herbals [...]
- Published
- 2005
31. Karyomorphology of Maianthemum sensu lato (Polygonatae, Ruscaceae)
- Author
-
Meng, Ying, Nie, Ze-Long, Yang, Yong-Ping, and Gu, Zhi-Jian
- Subjects
Botany -- Identification and classification ,Botany -- Research ,Botany -- Genetic aspects ,Botany -- Nomenclature ,Science and technology - Published
- 2005
32. Paraphyly of Cyrtomium (Dryopteridaceae): evidence from rbcL and trnL-F sequence data
- Author
-
Lu, Jin-Mei, Li, De-Zhu, Gao, Lian-Ming, Cheng, Xiao, and Wu, Ding
- Subjects
Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Science and technology - Published
- 2005
33. Viburnum phylogeny based on combined molecular data: implications for taxonomy and biogeography
- Author
-
Winkworth, Richard C. and Donoghue, Michael J.
- Subjects
Phylogeny (Botany) -- Research ,Botany -- Identification and classification ,Botany -- Analysis ,Botany -- Nomenclature ,Biological sciences - Abstract
We investigated Viburnum phylogeny using separate and combined analyses of DNA sequence data from two chloroplast and three nuclear loci. Separate analyses of nuclear and chloroplast data sets resulted in gene trees that were generally congruent with one another and with trees from two previous analyses. Our gene trees do differ in the position of section Pseudotinus, as well as in species relationships within sections Pseudotinus and Lentago. However, tests for incongruence indicate that differences between the nuclear and chloroplast data are not significant. Furthermore, gene trees from combined analyses were highly similar to those found in separate analyses, suggesting that these localized differences do not affect other parts of the tree. Our analyses provide convincing support for numerous relationships, although there is still uncertainty at the base of the tree. To facilitate future study, we propose informal names for 12 well-supported species groups, as well as for several higher-level clades. We also discuss the biogeographic implications of our phylogeny, focusing on repeated, although apparently temporally incongruent, patterns of disjunction between the Old and New Worlds. Key words: biogeography; data combination; phylogeny; taxonomy; Viburnum.
- Published
- 2005
34. Molecular phylogeny of Incarvillea (Bignoniaceae) based on ITS and trnL-F sequences
- Author
-
Chen, Shaotian, Guan, Kaiyun, Zhou, Zhekun, Olmstead, Richard, and Cronk, Quentin
- Subjects
Phylogeny (Botany) -- Research ,Botany -- Identification and classification ,Botany -- Analysis ,Botany -- Nomenclature ,Biological sciences - Abstract
Incarvillea is a herbaceous and temperate member of Bignoniaceae, previously divided into four subgenera, Niedzwedzkia, Amphicome, Incarvillea, and Pteroscleris. Niedzwedzkia and Amphicome have in the past been treated as independent genera. Different relationships have been proposed for the four subgenera. Here, maximum parsimony analysis using ITS and trnL-F sequences resulted in similar trees and showed that the genus is monophyletic. Analysis of the combined data resulted in a single tree with five major clades highly supported and well resolved. The relationships of the five major clades are (subgenus Niedzwedzkia (Incarvillea olgae (subgenus Amphicome (subgenus Incarvillea, subgenus Pteroscleris)))). All four subgenera are well supported for monophyly, with the exception of subgenus Incarvillea, represented here by I. sinensis and L olgae. Incarvillea olgae is not closely related to I. sinensis, a conclusion supported by morphology. The two basal monotypic suhgenera are found in Central Asia. The most species-rich subgenus, Pteroscleris, has 10 species in the Himalaya-Hengduan Mountains and may have dispersed early from central Asia to eastern Asia. Short branch lengths on the molecular trees within Pteroscleris suggest a recent and rapid radiation of this rosette-forming subgenus, perhaps connected with the uplift of the Himalaya-Hengduan massif. Key words: Bignoniaceae; classification; Himalaya-Hengduan Mountains; Incarvillea; ITS; phylogenetics; radiation; trnL-F.
- Published
- 2005
35. Why are plant names changing so much?
- Author
-
Weakley, Alan S.
- Subjects
Botany -- Identification and classification ,Botany -- Forecasts and trends ,Botany -- Nomenclature ,Market trend/market analysis ,Biological sciences - Published
- 2005
36. An analysis of flavonoid compounds in leaves of Japonolirion (Petrosaviaceae)
- Author
-
Iwashina, Tsukasa, Kitajima, Junichi, Kato, Takako, and Tobe, Hiroshi
- Subjects
Bioflavonoids -- Physiological aspects ,Flavones -- Physiological aspects ,Flavonoids -- Physiological aspects ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Science and technology - Published
- 2005
37. Molecular variation of Spiranthes sinensis (Orchidaceae) in Japan, with special reference to systematic treatment of seasonally differentiated groups and a dwarf form, f. gracilis, from Yakushima Island
- Author
-
Tsukaya, Hirokazu
- Subjects
Orchids -- Identification and classification ,Orchids -- Genetic aspects ,Orchids -- Research ,Plant populations -- Identification and classification ,Plant populations -- Genetic aspects ,Plant populations -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Science and technology - Published
- 2005
38. The evolution of plant development
- Author
-
Friedman, William E., Moore, Richard C., and Purugganan, Michael D.
- Subjects
Botany -- Identification and classification ,Botany -- Nomenclature ,Botany -- Anatomy ,Roots (Botany) ,Meristem ,Flowers ,Evolution ,Biological sciences - Abstract
The last decade has witnessed a resurgence in the study of the evolution of plant development, combining investigations in systematics, developmental morphology, molecular developmental genetics, and molecular evolution. The integration of phylogenetic studies, structural analyses of fossil and extant taxa, and molecular developmental genetic information allows the formulation of explicit and testable hypotheses for the evolution of morphological characters. These comprehensive approaches provide opportunities to dissect the evolution of major developmental transitions among land plants, including those associated with apical meristems, the origins of the root/shoot dichotomy, diversification of leaves, and origin and subsequent modification of flower structure. The evolution of these major developmental innovations is discussed within both phylogenetic and molecular genetic contexts. We conclude that it is the combination of these approaches that will lead to the greatest understanding of the evolution of plant development. Key words: apical meristem; flower; leaf: origin; plant systematics; root: shoot.
- Published
- 2004
39. Assessing red algal supraordinal diversity and taxonomy in the context of contemporary systematic data
- Author
-
Saunders, Gary W. and Hommersand, Max H.
- Subjects
Botany -- Identification and classification ,Botany -- Nomenclature ,Red algae ,Biological diversity ,Biological sciences - Abstract
The wondrously diverse eukaryotes that constitute the red algae have been the focus of numerous recent molecular surveys and remain a rich source of undescribed and little known species for the traditional taxonomist. Molecular studies place the red algae in the kingdom Plantae; however, supraordinal classification has been largely confined to debate on subclass vs. class level status for the two recognized subgroups, one of which is widely acknowledged as paraphyletic. This narrow focus has generally masked the extent to which red algal classification needs modification. We provide a comprehensive review of the literature pertaining to the antiquity, diversity, and systematics of the red algae and propose a contemporary classification based on recent and traditional evidence. Key words: Bangiophyceae; Compsopogonophyceae; Cyanidiophyta; Eurhodophytina; Florideophyceae; Metarhodophytina; Rhodophyta; Rhodoplantae.
- Published
- 2004
40. Analysis of fern spore banks from the soil of three vegetation types in the central region of Mexico
- Author
-
Ramirez-Trejo, Maria Del Rosario, Perez-Garcia, Blanca, and Orozco-Segovia, Alma
- Subjects
Mexico -- Environmental aspects ,Spores (Botany) -- Distribution ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Soils -- Sampling ,Soils -- Research ,Company distribution practices ,Biological sciences - Abstract
The vertical structure of fern spore banks was studied in a xerophilous shrubland, montane rain forest, and pine-oak forest in Hidalgo, Mexico, using the emergence method. Soil samples were collected in April 1999 at depths of 0-10, 10-20, and 20-30 cm. Viable spores decreased significantly with depth in all vegetation types, and the highest number of prothallia and sporophytes was found in the uppermost layer. The montane rain forest and the xerophilous shrubland had the largest and the richest banks, respectively. Twenty-three fern taxa were registered in the aboveground vegetation, 12 in the soil banks, and 43.5% were in both. Aboveground and in the soil bank, the xerophilous shrubland, the montane rain forest, and the pine-oak forest had, 17 and 7, 1 and 6, and 7 and 3 taxa, respectively. These were distributed differentially in relation to depth. The Sorensen index indicated a similarity of 61.5% between the xerophilous shrubland and the montane rain forest, and the Czeckanovsky index indicated 19.75%. The presence of viable spores in the soil of all vegetation types confirmed the existence of natural spore banks. Long-distance dispersal was an important factor determining the specific composition of the xerophilous shrubland and the pine-oak forest. Key words: ferns; Mexico; soil propagule banks; spores; vegetation types.
- Published
- 2004
41. Intergeneric and infrafamilial phylogeny of subfamily Monsteroideae (Araceae) revealed by chloroplast trnL-F Sequences
- Author
-
Tam, Sheh-May, Boyce, Peter C., Upson, Tim M., Barabe, Denis, Bruneau, Anne, Forest, Felix, and Parker, John S.
- Subjects
Phylogeny (Botany) -- Research ,Araceae -- Genetic aspects ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
The chloroplast trnL-F region was used as an independent data set for phylogenetic analysis of 118 aroid taxa. We investigated the intergeneric relationships of subfamily Monsteroideae (Araceae) and used this as a basis for an interspecific phylogenetic study of Rhaphidophora Hassk., the largest genus of the Monsteroideae. Results of the molecular tree were useful for inferring subfamilial and tribal circumscription and evolution in Araceae. Our results show that family Araceae consists of five clades that correspond to the subfamilies traditionally recognized. Starting from the most basal clade, these correspond to subfamilies Gymnostachydoideae and Orontioideae (proto aroids), with Lemna sp. (Lemnaceae) embedded in the Araceae and sister to the true aroids consisting of Pothoideae sister to Monsteroideae, immediately sister to Lasioideae and Aroideae. There is less agreement with existing tribal classifications. Complex relationships exist between members of the Monsteroideae. Our results show that Rhaphidophora and Epipremnum are paraphyletic with species of Rhaphidophora sampled, forming three informal groups with other genera of the Monstereae. Phylogenetic results may be used to suggest taxonomic changes to the current systematics of the monsteroids. Key words: Araceae; classification; intergeneric; Monstereae; Monsteroideae; phylogeny; trnL-F region.
- Published
- 2004
42. Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits
- Author
-
Miadlikowska, Jolanta and Lutzoni, Francois
- Subjects
Phylogeny (Botany) -- Research ,Fungi -- Genetic aspects ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
To provide a comprehensive molecular phylogeny for peltigeralean fungi and to establish a classification based on monophyly, phylogenetic analyses were carried out on sequences from the nuclear ribosomal large (LSU) and small (SSU) subunits obtained from 113 individuals that represent virtually all main lineages of ascomycetes. Analyses were also conducted on a subset of 77 individuals in which the ingroup consisted of 59 individuals representing six families, 12 genera, and 54 species potentially part of the Peltigerineae/ Peltigerales. Our study revealed that all six families together formed a strongly supported monophyletic group within the Lecanoromycetidae. We propose here a new classification for these lichens consisting of the order Peltigerales and two suborders--Collematineae subordo nov. (Collemataceae, Placynthiaceae, and Pannariaceae) and Peltigerineae (Lobariaceae, Nephromataceae, and Peltigeraceae). To accommodate these new monophyletic groups, we redefined the Lecanorineae, Pertusariales, and Lecanorales sensu Eriksson et al. (Outline of Ascomycota--2003, Myconet 9: 1-103, 2003). Our study confirms the monophyly of the Collemataceae, Lobariaceae, Nephromataceae, and Peltigeraceae, and the genera Nephroma, Sticta, and Peltigera. However, Leptogium, Lobaria, Pseudocyphellaria, and Solorina were found to be nonmonophyletic genera. Reconstruction of ancestral symbiotic states within the Peltigerales, using maximum likelihood (ML) and a Bayesian approach to account for phylogenetic uncertainty, revealed an evolutionary scenario in which bimembered associations with cyanobacteria were ancestral, followed by multiple independent acquisitions of green algae to form tripartite symbioses and rare subsequent losses of the cyanobiont to form bimembered symbioses with green algae. Key words: ancestral state reconstruction; Collematineae; Lecanoromycetidae; lichen symbiosis; molecular phylogenetic classification of ascomycetes; nuclear ribosomal large (LSU nrDNA) and small (SSU nrDNA) subunits; Peltigerales; Peltigerineae.
- Published
- 2004
43. Patterns of evolution in western North American Mimulus (Phrymaceae)
- Author
-
Beardsley, Paul M., Schoenig, Steve E., Whittall, Justen B., and Olmstead, Richard G.
- Subjects
North America -- Environmental aspects ,Plant chromosomes -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
A well-supported phylogeny is presented from both chloroplast DNA (the trnL/F region) and two regions of nuclear rDNA (ITS [internal transcribed spacer] and ETS [external transcribed spacer]) with nearly complete sampling for Mimulus (Phrymaceae) in western North America. Three separate genera are derived from within the clade that contains all the Mimulus species in western North America. The taxonomic status of the proposed sections of Mimulus and the relationships of many taxonomically difficult species are considered with observations on morphological evolution. Discordance between data sources provides support for the hypothesis that M. evanescens is a hybrid between M. latidens and M. breviflorus. In two major clades (Eunanus and Diplacus), patterns of genetic variation do not match the current taxonomy. The clustering of taxa in Eunanus is strongly associated with geographic distributions. Mimulus aurantiacus sensu Thompson, M. nanus, and M. floribundus are found to be progenitor species to other species that appear to be derived from within them. Polyploidy and aneuploidy events are clustered near the tips of the phylogeny. Thus, these two mechanisms are concluded to have played a relatively small role in the evolution of persistent lineages in Mimulus. The phylogenetic distribution of rare taxa is also examined. Key words: chromosome evolution; cryptic diversity; ETS; ITS; Mimulus; Phrymaceae; polyploidy; trnL/F.
- Published
- 2004
44. Floral development and molecular phylogeny support the generic status of Tasmannia (Winteraceae)
- Author
-
Doust, Andrew N. and Drinnan, Andrew N.
- Subjects
Phylogeny (Botany) -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
The taxonomic status of and evolutionary relationship between Tasmannia and Drimys (Winteraceae) have been subjects of controversy for many years. In this paper, a molecular phylogenetic analysis of the family with sequences of previously unpublished Tasmannia and Drimys species confirms earlier conclusions that Tasmannia and Drimys do not form a monophyletic group, despite the fact that they appear to share distinctive inflorescence and floral orphological attributes. Examination of alternative hypotheses of relationships with likelihood-ratio tests and parametric bootstrapping supports the separation of Tasmannia and Drimys. A detailed analysis of floral development in Tasmannia lanceolata and T. xerophila indicates that timing and position of sepal initiation differs between them, but that the position of subsequent organ initiation predictably follows from sepal position. This is in contrast to Drimys winteri, where a prolonged delay between sepal and petal initiation leads to the production of many phyllotactic patterns. The prolonged period of calyx tube growth leading to the formation of a calyptra in Tasmannia and Drimys probably evolved in parallel in the two lineages. Key words: Drimys; floral development; molecular phylogeny; parametric bootstrapping; SH test; Tasmannia; Winteraceae.
- Published
- 2004
45. Implications of ITS sequences and RAPD markers for the taxonomy and biogeography of the Oxytropis campestris and O. arctica (Fabaceae) complexes in Alaska
- Author
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Jorgensen, Janet L., Stehlik, Ivana, Brochmann, Christian, and Conti, Elena
- Subjects
Plant populations -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
Taxonomic consensus is lacking on the Oxytropis arctica and O. campestris species complexes, two polyploid complexes found in the interior and arctic areas of Alaska. One classification has emphasized flower size, whereas flower color is considered a key diagnostic character in another classification. Our analyses of internal transcribed spacer (ITS) sequences and random amplified polymorphic DNA (RAPD) markers provided no support for either classification system. The trees generated from ITS sequences and the phenogram derived from RAPD markers suggest that most recognized taxa in the two complexes are probably polyphyletic, including O. arctica van barnebyana, which is listed as threatened in Alaska. The only consistent pattern detected by both types of molecular markers was a geographic split dividing the northeastern arctic populations from most other populations (48.60 55.03% in AMOVA analyses). This genetic subdivision probably reflects a Pleistocene barrier formed by the northern coastal ice shield. Our molecular data, in conjunction with the previously reported variation of ploidy levels in these groups, suggest a scenario of recent and multiple origins of polyploidy. It is possible that most Alaskan populations of these two complexes are best referred to as a single taxonomic species despite morphological differentiation within the complexes. Key words: Alaska, USA; arctic plant species complex; Fabaceae; ITS; morphological characters; Oxytropis; Pleistocene glaciations; RAPDs.
- Published
- 2003
46. Patterns of prey capture and prey availability among populations of the carnivorous plant Pinguicula moranensis (Lentibulariaceae) along an environmental gradient
- Author
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Alcala, Raul E. and Dominguez, Cesar A.
- Subjects
Plant biomass -- Research ,Carnivorous plants -- Genetic aspects ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
In this study we explored the effect of the physical environment and the availability of prey (biomass and taxonomic composition) on the patterns of prey capture and reproduction on five populations of Pinguicula moranensis (Lentibulariaceae) in areas ranging from pine-oak forests to desert scrublands. Environmental variation was summarized using principal factor analysis. Prey availability and prey capture increased toward the shadiest, most humid, and fertile population. The probability of reproduction and average bud production per population did not follow the same tendency because both fitness components peaked at the middle of the environmental gradient. These results suggest that the benefits derived from carnivory are maximized at sites fulfilling a trade-off between light, moisture, and prey availability. We also found that the taxonomic composition of both the available prey and that of the prey captured by plants varied among populations. The results also indicated that the prey captured by plants are not a random sample of prey available within populations. Overall, the results from this study revealed a marked amount of heterogeneity in the physical and biotic environment among the populations of P. moranensis, which has the potential to affect the outcome of the interaction between this carnivorous species and its prey. Key words: carnivorous habit; environmental heterogeneity; insectivorous plants; Lentibulariaceae; Pinguicula.
- Published
- 2003
47. Incongruence between cladistic and taxonomic systems
- Author
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Grant, Verne
- Subjects
Plant genetics -- Research ,Numerical taxonomy -- Research ,Cladistic analysis -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
Cladistic and taxonomic treatments of the same plant group usually exhibit a mixture of congruences and incongruences. The question arises in the case of the incongruences as to which version is right and which is wrong. Many cladists believe that cladistics is a superior approach and gives the best results. There are several conceptual and methodological differences between cladistics and taxonomy that cause incongruence. One important conceptual difference is the use of different criteria for grouping: order of branching vs. similarity and difference (clades vs. taxa). Another is the policy regarding paraphyletic groups: to ban them in cladistics but ignore the ban in taxonomy. These two differences automatically lead to some incongruences. One approach is not right and the other wrong; each is operating by its own standards. However, when cladists apply the paraphyly rule to a taxonomic system and conclude that it needs revision to eliminate paraphyly, as cladists often do, they are judging the taxonomic system by a wrong standard. Several differences between the two schools in the use and handling of characters can also cause incongruence. First consider phenetic characters. Taxonomy uses a very wide range of these, whereas phenetic cladistics sets restrictions on the selection of characters, which deprive it of potentially useful evidence. Taxonomic systems generally rest on a broader empirical foundation than phenetic cladistic systems. Next, consider molecular cladistics, which is the leader in the use of DNA evidence. Two sources of incongruence between molecular cladistics and taxonomic systems can come into play here. First, the molecular evidence used in cladistics comes mainly from cytoplasmic organelles, whereas taxonomic systems are based on characters that are determined mainly by the chromosomal genome. More generally, the database in a molecular cladogram is, in itself, too narrow to serve as a foundation for an organismic classification. In cases of incongruence, the molecular evidence can be a reliable indicator of taxonomic relationships sometimes, misleading other times, and may afford no clear basis for a systematic decision. In this situation, it is helpful, indeed necessary, to integrate the molecular evidence with the phenetic evidence and bring more characters to bear on the question. Key words: cladistics; molecular systematics; paraphyly; phylogenetics; systematics; taxonomy.
- Published
- 2003
48. Phylogenetic study of Fulgensia and allied Caloplaca and Xanthoria species (Teloschistaceae, lichen-forming ascomycota)
- Author
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Gaya, Ester, Lutzoni, Francois, Zoller, Stefan, and Navarro-Rosines, Pere
- Subjects
Phylogeny (Botany) -- Research ,Lichens -- Genetic aspects ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
Fulgensia Massal. & De Not. is a widespread genus with considerable morphological and ecological heterogeneity across species. For this reason, the taxonomic delimitation of this genus has been controversial. Relationships among species of Fulgensia, Caloplaca Th. Fr., and Xanthoria (Fr.) Th. Ft. (Lecanorales) were investigated based on a comprehensive phylogenetic analysis of 62 DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) region using maximum parsimony (MP) and likelihood (ML). Ambiguously aligned (INAASE coded characters) and unambiguous regions were analyzed separately and combined when using MP as the optimization criterion. All our analyses confirm the polyphyly of this genus as three distinct lineages: Fulgensia sensu stricto, F. australis, and F. schistidii. We report here that Caloplaca, Fulgensia, and Xanthoria together form two main sister lineages. One lineage includes Fulgensia schistidii (part of the C saxicola group), Xanthoria, and most of the lobed Caloplaca species belonging to the Gasparrinia group. A second main lineage comprises the remaining Caloplaca species, Fulgensia sensu stricto, and F. australis. Therefore, the traditional generic level classification schemcs for the family Teloschistaceae appear to be highly artificial. All three genera were found to be nonmonophyletic. We demonstrate here that the ITS is appropriate to resolve relationships across the Teloschistaceae. However, a combination of an MP analysis, in which ambiguously aligned regions are accommodated using INAASE, with an ML analysis, in which phylogenetic confidence is estimated using a Bayesian approach, is needed. Key words: ambiguous alignments; Caloplaca; Fulgensia; internal transcribed spacer; lichen-forming fungi; Markov chain Monte Carlo Bayesian inference; molecular phylogenetics; Teloschistaceae; Xanthoria.
- Published
- 2003
49. Development of ovule, embryo sac, and endosperm in Triteleia (Themidaceae) relative to taxonomy
- Author
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Berg, Rolf Y.
- Subjects
Plant embryology -- Research ,Botany -- Identification and classification ,Botany -- Research ,Botany -- Nomenclature ,Biological sciences - Abstract
Six of 14 species of Triteleia were studied. All possess septal nectaries, raphides in the ovary wall, an anatropous and crassinucellatc ovule with a micropyle formed by the inner integument only, and parietal cells. A short and thick nucellus, which is not penetrated by the embryo sac, has a one-layered apical epidermis and thickens from its subepidermal layer. The permanently two-layered inner integument is made up of normal, i.e., not greatly enlarged, cells. The embryo sac is of the Polygonum type, and the endosperm is of the helobial type. Embryo development is of the Asterad type in Triteleia laxa and 72 ixioides. From an embryological point of view, Triteleia is closely related to Muilla maritima because the two taxa are alike in all characteristics, except for the number of layers in the apical nucellar epidermis. Triteleia is only distantly related to Dipterostemon, Dichelostemma, and Brodiaea, judging from the numerous differences in embryology. Both Triteleia and Muilla maritima are embryologically more primitive than the Dipterostemon-Dichelostemma-Brodiaea group. Embryologically, the Themidaceae are more similar to the Hyacinthaceae than to Allium. However, all embryological similarities with Hyacinthaccae are in plesiomorphic characters. Key words: Allium; embryo sac; embryology; endosperm; seed development; taxonomy; Themidaceae; Triteleia.
- Published
- 2003
50. Inside-out flowers characteristic of Lacandonia schismatica evolved at least before its divergence from a closely related taxon, Triuris brevistylis. (Development)
- Author
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Vergara-Silva, Francisco, Espinosa-Matias, Silvia, Ambrose, Barbara A., Vazquez-Santana, Sonia, Martinez-Mena, Alejandro, Marquez-Guzman, Judith, Martinez, Esteban, Meyerowitz, Elliot M., and Alvarez-Buylla, Elena R.
- Subjects
Angiosperms -- Genetic aspects ,Plant genetics -- Research ,Botany -- Identification and classification - Published
- 2003
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