Taxonomic re-evaluation of Panicum sections Tuerckheimiana and Valida (Poaceae: Panicoideae) using morphological and molecular data (original) (raw)
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Phylogenetics of Panicoideae (Poaceae) based on chloroplast and nuclear DNA sequences
Phylogenetic relationships among major subfamilies in Poaceae and among major tribes within Panicoideae were evaluated using parsimony and Bayesian analyses of chloroplast trnL-F and atpβ-rbcL DNA sequences and a nuclear ribosomal DNA sequence, ITS1-ITS2. The Panicoideae-Aristidoideae-Chloridoideae-Micrairoideae-Arundinoideae-Danthonioideae (PACMAD) clade was well resolved. A close relationship between Aristidoideae and Chloridoideae was found. The monophyly of Micrairoideae was resolved but the relationships of three tribes (Eriachneae, Isachneae, Micraireae) within Micrairoideae were unclear, only Eriachne and Isachne were monophyletic. Panicoideae sensu stricto were supported as monophyletic and sister to a clade of Danthoniopsis and Tristachya. Within Panicoideae, only a clade of Andropogoneae + Arundinella + Garnotia was supported. None of the analyses supported the monophyletic status of Paniceae. Within Paniceae, the bristle clade (excluding Cenchrus) + Alexfloydia, and the forest shade clade sensu , were found, but their circumscription remains ambiguous. A sister relationship between the endemic and rare Australian grasses Homopholis and Walwhalleya was also resolved. Arundinelleae were found to be polyphyletic. This study supported the separation of Arundinella and Garnotia from the remaining Arundinelleae and the inclusion of both genera in their own subtribes (Arundinellinae Honda sensu stricto and Garnotiinae Pilger) within the Andropogoneae. Arundinelleae should be abandoned as a taxonomic tribe within the Centothecoid + Panicoid clade. Within Andropogoneae, five out of a total of 11 subtribes (Chionachninae, Coicinae, Dimeriinae, Germainiinae, and Tripsacinae) were monophyletic.
The use of herbarium specimens in DNA phylogenetics: Evaluation and improvement
Plant Systematics and Evolution, 1995
Abstraet: Variation in chloroplast rbcL sequences was studied in representative species of four different lineages: the tribe Rubieae (Rubiaceae), and the genera Drosera (Droseraceae), Nothofagus (Nothofagaceae) and llex (Aquifoliaceae). Each lineage has its particular non-overlapping set of rbcL polymorphic sites, indicating that common unconstrained rbcL sites are not shared. Large differences in the rate and pattern of nucleotide substitution are observed among the four lineages. The genus Ilex has the lowest rate of substitution, the lowest transition/transversion ratio, the lowest synonymous/ replacement ratio and the lowest number of substitutions at the third codon position. An apparent relationship of these measures to the age of the lineages is observed. The A + T content and codon use among the four lineages are very similar and, apparently, cannot account for the observed differences in pattems of nucleotide substitution. However, the A + T content of the two bases immediately flanking the polymorphic sites is higher in Ilex than in the other lineages. This could be correlated with the transversion/transition bias observed in Ilex. The particularly low synonymous/replacement ratio found in Ilex could also be explained by the small population sizes of species in this genus.
An investigation was made into the relationships between six species or subspecies of the genus Hordeum that grow in the Iberian Peninsula and Balearic Islands. Plant material included samples of 19 populations of the annual species H. marinum subsp. marinum, H. marinum subsp. gussoneanum, H. murinum subsp. murinum, and H. murinum subsp. leporinum, and the perennial species H. bulbosum and H. secalinum. Relationships were analysed using PCR-based molecular markers. Thirteen sets of primers were designed and synthesized based on sequences of mapped RFLPs from genomic libraries and conserved regions of structural genes of known function in cultivated species. Primers were used to amplify genomic DNA from all populations. The number of amplified products ranged from 1 to 18 per primer and a total of 168 markers were scored. The markers revealed different degrees of relationships. Hordeum bulbosum was clearly separated from the rest. The populations of both subspecies of H. murinum were closely related. H. marinum subsp. gussoneanum appeared to be closely related to H. secalinum, yet relatively separated from its conspecific subspecies marinum. The use of a large number of DNA markers in this kind of analysis is discussed. Résumé : Une étude des relations entre six espèces ou sous-espèces du genre Hordeum qui sont présentes dans la péninsule ibérique et les îles Baléares a été réalisée. Le matériel végétal incluait des échantillons de 19 populations des espèces annuelles H. marinum subsp. marinum, H. marinum subsp. gussoneanum, H. murinum subsp. murinum et H. murinum subsp. leporinum de même que des espèce pérennes H. bulbosum et H. secalinum. Les relations ont été étudiées à l'aide de marqueurs PCR. Treize paires d'amorces ont été conçues à partir de la séquence de marqueurs RFLP dont la position était connue et qui ont été isolés d'une banque génomique de même qu'à partir de la séquence de domaines conservés chez des gènes structuraux de fonction connue chez les espèces cultivées. Les amorces ont été employées afin d'amplifier de l'ADN génomique chez toutes les populations. Le nombre de produits variait de 1 à 18 par paire d'amorces et un total de 168 marqueurs ont pu être examinés ainsi. Les marqueurs ont révélé des relations de divers ordres. Le Hordeum bulbosum était nettement séparé des autres espèces. Les populations des deux sous-espèces du H. murinum étaient très apparentées. Le H. marinum subsp. gussoneanum semblait très apparenté au H. secalinum et relativement distant du H. marinum subsp. marinum qui appartient pourtant à la même espèce. L'emploi d'un grand nombre de marqueurs moléculaires dan ce type d'analyse est discuté. Mots clés : Hordeum, orge, marqueurs moléculaires, endonucléases de restriction, variabilité, analyse de l'ADN.
DNA Extraction from Herbarium Specimens
Methods in Molecular Biology, 2013
With the expansion of molecular techniques, the historical collections have become widely used. Studying plant DNA using modern molecular techniques such as DNA sequencing plays an important role in understanding evolutionary relationships, identifi cation through DNA barcoding, conservation status, and many other aspects of plant biology. Enormous herbarium collections are an important source of material especially for specimens from areas diffi cult to access or from taxa that are now extinct. The ability to utilize these specimens greatly enhances the research. However, the process of extracting DNA from herbarium specimens is often fraught with diffi culty related to such variables as plant chemistry, drying method of the specimen, and chemical treatment of the specimen. Although many methods have been developed for extraction of DNA from herbarium specimens, the most frequently used are modifi ed CTAB and DNeasy Plant Mini Kit protocols. Nine selected protocols in this chapter have been successfully used for highquality DNA extraction from different kinds of plant herbarium tissues. These methods differ primarily with respect to their requirements for input material (from algae to vascular plants), type of the plant tissue (leaves with incrustations, sclerenchyma strands, mucilaginous tissues, needles, seeds), and further possible applications (PCR-based methods or microsatellites, AFLP).
American Journal of Botany, 2003
Panicum L. is a cosmopolitan genus with approximately 450 species. Although the genus has been considerably reduced in species number with the segregation of many taxa to independent genera in the last two centuries, Panicum remains a heterogeneous assemblage, as has been demonstrated in recent years. The genus is remarkably uniform in its floral characters but exhibits considerable variation in anatomical, physiological, and cytological features. As a result, several classifications, and criteria of what the genus should really include, have been postulated in modern literature. The purpose of this research, based on molecular data of the chloroplast ndhF gene, is to test the monophyly of Panicum, to evaluate infrageneric classifications, and to propose a robust phylogenetic hypothesis. Based on the present results, previous morphological and molecular phylogenetic studies, and inferred diagnostic morphological characters, we restrict Panicum sensu stricto (s.s.) to the former subgenus Panicum and support recognition of Dichanthelium, Phanopyrum, and Steinchisma as distinct genera. We have transfered other species of Panicum to other genera of the Paniceae. Most of the necessary combinations have been made previously, so few nomenclatural changes have been required. The remaining species of Panicum sensu lato (s.l.) are included within Panicum incertae sedis representing isolated species or species grouped within monophyletic clades. Additionally, we explore the performance of the three codon position characters in producing the supported phylogeny.
Cladistics, 2012
Included in the PACMAD clade of the family Poaceae (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, Danthonioideae), the tribe Paniceae s.l. is one of the largest tribes of the subfamily Panicoideae, with more than 2000 species. This tribe comprises a huge morphological, cytological, and physiological diversity represented by different inflorescence types, several basic chromosome numbers, and at least four major photosynthetic pathways. The tribe Paniceae has been the subject of molecular studies that have confirmed its paraphyly: two major clades were recognized based on their basic chromosome numbers (x =9 ,x = 10). The x = 10 Paniceae clade is sister to the Andropogoneae-Arundinelleae s.s. x =1 0c l a d ea n dt h ex = 9 clade with a subsample of Paniceae genera. As a result of a recent realignment within the tribe in terms of the phylogenetic position of minor and major Paniceae genera, a reanalysis of the whole sampling is performed and new underrepresented taxa are discussed. A total of 155 genera, currently considered within subfamily Panicoideae, are represented here by almost all genera of Paniceae s.l., representatives of Andropogoneae and Arundinelleae s.s., and the endemic and small tribe Steyermarkochloeae; we also included specimens of subfamily Micrairoideae, tribes Isachneae and Eriachneae. The sampling includes as outgroups 18 genera of the PACMAD clade (excluding Panicoideae) and four genera from the BEP clade (Bambusoideae, Ehrhartoideae, Pooideae), rooting with Bromus inermis. A matrix with 265 taxa based on the combined evidence from ndhF plastid sequences (2074 bp) and 57 morphological characters was subjected to parsimony analyses. Jackknife resampling was used to calculate group support. Most clades are characterized by morphological, cytological, anatomical, and ⁄ or physiological characters. Major tribal changes are based on the basic chromosome number; the pantropical x =9 clade is here recognized as Paniceae s.s., while the American x = 10 Paniceae s.l. is restricted to the reinstated tribe Paspaleae. The optimization of the photosynthetic pathway for the Paspaleae-Andropogoneae-Arundinelleae s.s. clade, including the monotypic Reynaudia, show a plesiomorphic C 4 state while the ancestral state for Paniceae s.s. is ambiguous. If Reynaudia were not included or placed elsewhere, the ancestral photosynthetic pathway for both the Paspaleae-Andropogoneae-Arundinelleae s.s. clade and the Paniceae s.s. would be unambiguously C 3 . In order to explore character evolution further, the morphological characters were mapped onto one of the most parsimonious trees. A relationship between photosynthetic pathways and inflorescence morphology is suggested here for the first time. Based on the optimization of morphological characters and additional data, we propose names for almost all inner clades at the rank of subtribe with a few groups as incertae sedis. With this extensive sampling, we resolved the phylogenetic relationships and the assignation of synapomorphies, and improved the support in subtribe sorting; consequently a robust circumscription of the tribe Paniceae s.l. is proposed.
DNA technology and studies in phylogenetic relationships of tropical plant: Prospect in Indonesia***
Phylogenetic is one of the most preferable methods in systematic to reconstruct evolutionary relationships of groups of biological organisms in order to understand the biodiversity. Until recently, morphological characters have long been preserved in most phylogenetic studies. With the recent advance of molecular techniques such as polymerase chain reaction (PCR) and DNA sequencing, the use of DNA sequences in phylogenetic studies has rapidly increased and been performed at all taxonomic levels. DNA sequences have drawn attention to many researchers due to in facts that, i.e.,: (1) they offer an increased precision by permitting better homology assessment of characters; (2) they have the large differences in substitution rates in different loci, providing the large number of characters; and (3) They provide an independent source with which to test hypotheses on the evolution of form, leading to a new and better supported-work of phylogeny of plant. In respect with many genes are recently available for such studies, the investigator is faced with a question which gene or genome must be selected; this should fit with phylogenetic problem of materials under study. Common choices in plants include the chloroplast genome (cpDNA) or components of the chloroplast genome, the nuclear ribosomal DNA genes (nrDNA), or nuclear-encoded, single-copy genes. Indonesia as a tropical country is inhabited by the large number and great diversity of plant. Many large and important tropical Indonesian plant group present challenges to systematists interested in understanding the evolution, and they, therefore, await exploration. However, phylogenetic studies dealing with these plant groups using molecular data are few. These include ongoing work by Adi Pancoro and Topik Hidayat and their colleagues at Institute Technology of Bandung (ITB), Indonesia University of Education (UPI), and Herbarium Bogoriense on various groups of angiospermae. Several molecular phylogenetic studies that have been done by the Pancoro group's research will be presented.
2007
Phylogenetic relationships among 85 species representing 35 genera in the grass tribe Andropogoneae were estimated from maximum parsimony and Bayesian analyses of nuclear ITS and chloroplast trnL-F DNA sequences. Ten of the 11 subtribes recognized by Clayton and Renvoize (1986) were sampled. Independent analyses of ITS and trnL-F yielded mostly congruent, though not well resolved, topologies. Arundinella is sister to Andropogoneae in the trnL-F phylogeny and is nested within the tribe in the ITS and combined data trees. Tristachya is sister to Andropogoneae ϩ Arundinella in the ITS phylogeny. Four clades are common to the ITS and trnL-F phylogenies and the trees from the combined data set. Clade A consists of Andropogon, Diectomis, Hyparrhenia, Hyperthelia, and Schizachyrium. Within this clade, Andropogon distachyos, Hyparrhenia, and Hyperthelia form clade C. Clade B consists of Bothriochloa, Capillipedium, and Dichanthium, and clade D includes Chrysopogon and Vetiveria. Analysis of the combined data resulted in an unsupported larger clade comprising clades A and B plus Cymbopogon, and a sister clade of Heteropogon, Iseilema, and Themeda. This larger clade is similar to the core Andropogoneae clade previously reported (Spangler et al. 1999; Mathews et al. 2002). Based on our sample, which represents 41% of the tribe's genera, most of Clayton and Renvoize's (1986) subtribes are not monophyletic.
Plant taxonomy and systematics, particularly classification is essentially based on the morphological criteria of plants. Criteria derived from other plant features such as anatomy, chromosomes and the characteristics of pollens, embryos and seeds have provided important information for the taxonomic delimitation of many plant groups. However, the use of these criteria as sources of taxonomic information, have been gradually overtaken by the modern use of molecular data derived from the DNA and proteins. These data because of the sequential transfer of genetic code from DNA to proteins provide the means for elucidating the genetic basis for all biological diversity and a universal standard for comparing all forms of life. Characters derived from proteins have been obtained by four approaches i.e. serological comparisons, native or denatured protein electrophoresis, allozymes and isozymes polymorphism, also revealed by electrophoresis and amino acid sequencing. However, characters derived from proteins are gradually replaced by the more powerful and more informative DNA data. Systematic information from DNA have been obtained by a number of approaches; the most common are the restriction fragment analysis, restriction fragment length polymorphism (RFLP), nucleotide sequencing of chloroplast and nuclear genes and the analysis of DNA amplification products produced by using polymerase chain reaction (PCR) by the random amplification of polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and amplified fragment length polymorphism (AFLP). In this article, I comment on the contribution of the different types of taxonomic information and describe the sources of molecular data particularly the methods used to obtain evidence from the DNA properties. The implications of the DNA based information on the systematics of selected groups of plants are also briefly described. The article also includes recommendations for the application of DNA data in systematic studies.