The phylogenetic position of Peucedanum sensu lato and allied genera and their placement in tribe Selineae (Apiaceae, subfamily Apioideae) (original) (raw)
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Analysis of the genus Petagnaea Caruel (Apiaceae), using new molecular and literature data
Plant Systematics and Evolution, 2009
In Southern Italy, an endemic monotypic genus belonging to family Apiaceae occurs: Petagnaea (P. gussonei), relict of Tertiary flora, belonging to subfamily Saniculoideae. At present, P. gussonei is an endangered species and is included in various lists of species deserving special protection. The genus belongs to scapose hemicryptophytes and shares a sciaphilous habitat (hygrophilous woodland). This study is aimed at doing a complete contribution about the evolutionary history of Petagnaea, using molecular markers as plastidial DNA (cpDNA), nuclear ribosomal DNA (rDNA) and data present in literature. We used nucleotide sequences from four regions of the chloroplast genome (rps16 intron, trnL (UAA) intron, atpB-rbcL intergenic spacer, and partial matK gene) to investigate possible haplotypes in Petagnaea populations.
Circumscription of Apiaceae tribe Oenantheae
South African Journal of Botany, 2004
Phylogenetic relationships within the angiosperm order Caryophyllales were investigated by comparative sequencing of two portions of the highly conserved inverted repeat (totaling some 1100 base pairs) coinciding with the region occupied by ORF2280 in Nicotiana, the largest gene in the plastid genomes of most land plants. Data were obtained for 33 species in 11 families within the order and for one species each of Plumbaginaceae, Polygonaceae, and Nepenthaceae. These data, when analyzed along with previously published ORF (open reading frame) sequences from Nicotiana, Spinacia, Epifagus, and Pelargonium using parsimony, neighbor-joining, and maximum likelihood methods, reveal that: (1) Amaranthus, Celosia, and Froelichia (all Amaranthaceae) do not comprise a monophyletic group; (2) Amaranthus may be nested within a paraphyletic Chenopodiaceae; (3) Sarcobatus (Chenopodiaceae) is allied with Nyctaginaceae ϩ Phytolaccaceae (the latter family excluding Stegnosperma but including Petiveria); and (4) Caryophyllaceae (with Corrigiola basal within the clade) are sister group to Chenopodiaceae ϩ Amaranthaceae. Basal relations within the order remain obscure. Sequence divergence values in pairwise comparisons across all Caryophyllales taxa ranged from 0.1 to 5% of nucleotides. However, despite these low values, 23 insertion and deletion events were apparent, of which five were informative phylogenetically and bolstered several of the relationships listed above. A polymerase chain reaction (PCR) survey for ORF homolog length variants in representatives from 70 additional angiosperm families revealed major deletions, of ഠ 100 to 1400 base pairs, in 19 of these families. Although the ORF is located within the mutationally retarded inverted repeat region of most angiosperm chloroplast DNAs, this gene appears particularly prone to length mutation.
Determination of phylogenetic affinity among the members of Apiaceae especially the subfamily Apioideae is much debatable. The morphological evidences on inflorescence, fruit and seed characters showed little concomitance with those derived from molecular parameters as far as groupings in clades are concerned. In the present study involving few selected Apiaceae members, a Dendrogram was computed and a putative evolutionary trend was outlined based on leaf margin insertion pattern and cotyledonary leaf features, general plant morphology as well as leaf surface micromorphology by SEM. The members of Apiaceae with broad-ovate pinnatifid to pinnatipartite leaves and ovate –lanceolate cotyledonary leaves were included in a distinct cluster but the members with pinnatisect – decompounds leaves and linear cotyledonary leaves were included in a separate cluster. Long Coriander (Eryngium foetidum) included in the subfamily Saniculoideae may represent the most primitive condition having simple entire leaf with spiny margin. The member like Long coriander might have served as progenitor stock from which Coriander, Celery, Parsley (all with ovate pinnatifid to pinnatipartite leaves) and Cumin, Fennel, Dill (all having pinnatisect to decompounds leaves with linear segments) might have originated as evidenced by gradual increase in marginal insertion. Similarly, gradual narrowing of ovate-lanceolate cotyledonary leaves might have given rise to narrow linear cotyledonary leaves. Leaf-margin insertion pattern and cotyledonary leaf features appeared to be promising in tracing phylogeny in Apiaceae especially in Apioideae. Simple entire leaf represents the primitive condition and evolution in Apiaceae supposed to have progressed towards gradual increase in marginal insertion leading to pinnately dissected, pinnatipartite and ultimately to decompound leaves with narrow linear segments. Dendrogram computed from morphological features showed concomitance with that phylogenetic trend as far as grouping and interrelationships of members are concerned. In the present study leaf margin insertion pattern and seedling morphology appeared to be instrumental in tracing the phylogeny in Apiaceae specially subfamily Apioideae while molecular systematics are not conclusive.
Phylogeny of Apiaceae subtribe Daucinae and the taxonomic delineation of its genera
Scandiceae subtribe Daucinae encompasses umbellifers that have fruits with prominent secondary ridges projecting into wings (former tribe Laserpitieae) or spines (former tribe Caucalideae pro parte). It comprises several economically or medicinally important genera including Cuminum, Daucus, Laser, Laserpitium and Thapsia among others. Recent molecular studies, based mostly on nrDNA ITS sequences, revealed that neither Daucus nor Laserpitium are monophyletic. To address issues of relationships and apply respective nomenclatural changes, we obtained additional ITS sequences as well as inde- pendent data from three plastid markers—rps16 intron, rpoC1 intron and rpoB-trnC intergenic spacer—for a comprehensive sample of the subtribe. We examined data for 260 accessions representing all genera of Daucinae and 81 of its ca. 93 species. Phylogenetic trees were estimated using maximum likelihood and Bayesian inference methods. The results indicate that former Laserpitieae constitute a paraphyletic grade at the base of the spiny-fruited members of Daucinae while traditionally delimited Daucus and Laserpitium are polyphyletic. To maintain a monophyletic Daucus, we suggest including the following genera and species into its synonymy: Agrocharis, Melanoselinum, Monizia, Pachyctenium, Pseudorlaya, Rouya, Tornabenea, Athamanta dellacellae and Cryptotaenia elegans. The species of Laserpitium occur in seven clades and only six species of the Laserpitium s.str. clade retain the generic name. Several species are transferred to Ekimia, Laser and Thapsia; additionally, a monospecific genus Siler is restored and a new genus, Silphiodaucus, is established. The inclusion of Ammodaucus into Thapsia suggested in an earlier study is not supported. The position of Laserpitium pseudomeum requires further study.
Tribes and Clades Within Apiaceae Subfamily Apioideae: The Contribution of Molecular Data
Edinburgh Journal of Botany, 2001
Phylogenetic analyses of chloroplast gene (rbcL, matK ), intron (rpl16, rps16, rpoC1) and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences and chloroplast DNA restriction sites, with supplementary data from variation in size of the chloroplast genome inverted repeat, have been used to elucidate major clades within Apiaceae (Umbelliferae) subfamily Apioideae Drude. This paper summarizes the results of previously published molecular cladistic analyses and presents a provisional classification of the subfamily based on taxonomic congruence among the data sets.
Molecular phylogenetics of tribe Epidendreae with emphasis on subtribe Laeliinae (Orchidaceae)
2000
In this project, the phylogenetic relationships of tribe Epidendreae, especially subtribe Laeliinae were assessed by using DNA sequence data. At the tribal level, I used data from three DNA regions, namely internal transcribed spacers of nuclear ribosomal DNA (ITS), and plastid matK (gene and spacers) and trnL-F (intron, exon and spacer). After individual and combined phylogenetic analysis using parsimony, it was possible to delimit Epidendreae as an exclusively Neotropical tribe (composed of subtribes Laeliinae, Pleurothallidinae, Ponerinae, Bletiinae and Chysinae). It is still unclear whether Coeliinae and Calypsoeae should be also included in Epidendreae. All Old World subtribes placed in Epidendreae in Dressler's (1993) system belong to different tribes of subfamily Epidendroideae. The revised subtribe Bletiinae is composed only of Bletia, Hexalectris and Basiphyllaea. All Old World genera previously placed in Bletiinae belong also to Old World groups. Arpophyllum (previously Arpophyllinae) and Meiracyllium (previously Meiracyllinae) should be included in Laeliinae. Neocogniauxia and Dilomilis belong to a clade sister to Pleurothallidinae. Ponera, Isochilus and Helleriella (previously in the Scaphyglottis alliance within Laeliinae) belong to a recircumscribed version of Ponerinae, which is sister to Bletiinae. Two other datasets were collected to investigate in more detail phylogenetic relationships within Laeliinae. The first dataset used 295 ITS sequences to assess generic delimitation and species phylogenies. Because the levels of variation were low, there was little resolution along the spine of the tree, and few generic groups achieved strong internal support. However, most species groups obtained were coincident with previous taxonomic groups at the infrageneric level, but several genera were found to be polyphyletic, including Cattleya, Laelia, Encyclia, and Schomburgkia. A second analysis of Laeliinae used the same three gene regions as in the Epidendreae study. This analysis found increased support for generic groups, confirmed polyphyly of several genera, and clarified unusual relationships in the ITS study. It also confirmed the suspicion that some ITS sequences were paralogous copies, although the underlying cause of the paralogy remains uncertain. Comparison of the three studies emphasise the importance of both taxon and character sampling in phylogenetic reconstruction. Firstly, I would like to thank God for all. I would like to thank my supervisor at Kew, Prof. Mark W. Chase, for receiving me in his lab, and especially for his support and advice. Mark always followed closely the development of every part of this project and was available every time he was needed. I would also like to thank my supervisor at Reading, Dr. Alastair Culham, for constructive criticism and for reading the drafts of my thesis in difficult circumstances.
Systematic Botany, 2004
Phylogenetic analyses of 159 DNA sequences from the nuclear rDNA internal transcribed spacer region were conducted to evaluate the monophyly of the herbaceous, perennial genera of Apiaceae subfamily Apioideae endemic to North America (north of Mexico) and to determine the relationships of those elements that currently comprise Cymopterus within the group. The results of a previous phylogenetic study were equivocal in suggesting monophyly for these perennial, endemic taxa and revealed Cymopterus to be polyphyletic, with its species closely linked with those of Aletes, Lomatium, Musineon, Oreoxis, Orogenia, Podistera, Pseudocymopterus, Pteryxia, and Tauschia. Herein, we expand sampling to include comprehensive representation of Aletes, Cymopterus, Musineon, Oreoxis, Orogenia, Podistera, Pseudocymopterus, and Pteryxia, and greater representation of Lomatium and Tauschia. We also include all members of two genera not examined previously, Glehnia and Oreonana, as well as additional outgroup genera from the Angelica clade of the apioid superclade. Our results indicate that the perennial, endemic apioid umbellifers of North America constitute a (weakly supported) monophyletic group, with Angelica and the meso-American Arracacia clade comprising two of several possible sister groups. The two subspecies of Glehnia littoralis ally with Angelica and Peucedanum japonicum; Oreonana shows af nity with several species of Cymopterus and Lomatium. The lack of resolution in the ITS trees precludes unambiguous hypotheses of relationship among these perennial, endemic umbellifers but does show that many of these genera, where resolved, are not monophyletic. Indeed, Cymopterus and Lomatium are highly polyphyletic and permeate all major clades resolved in the molecule-derived trees. Evidence from branch lengths and low sequence divergence suggests that this group of North American umbellifers underwent rapid radiation, likely during the geoclimatic events of the Late Tertiary and Quaternary.
Plant Systematics and Evolution, 1999
Evolutionary relationships among 116 representatives (80 genera) ofApiaceae (Umbelliferae) subfam.Apioideae were investigated by comparative sequencing of the two internal transcribed spacers of the 18S–26S nuclear ribosomal DNA repeat. The resultant phylogenies, inferred using maximum parsimony and neighbor-joining methods, clarified the relationships of several genera whose phylogenetic placements have heretofore been problematic. Comparisons between the phylogenies inferred and the distribution of