Rpl16 Intron Research Articles

Chemical constituents and DNA sequence analysis of a psychotropic herbal product

In recent years, the distribution of a variety of psychotropic products, especially “spice” and “herbal blends,” which are advertised to have narcotic-like effects, has become more widespread in the Japanese illegal drug market. We recently found two synthetic annabinoids, cannabicyclohexanol and JWH-018, that serve as adulterants in herbal products purchased via the Internet. In this study, we focused on a herbal product being sold as incense, which showed unknown components by liquid chromatography-mass spectrometry (LC-MS). The product did not show any peak corresponding to the above synthetic cannabinoids, but seven other peaks were identified by high-performance liquid chromatography and LC-MS. We identified them as N-methyltyramine (1), (R)-normacromerine (2), (R)-macromerine (3), (S)-vasicine (4), mescaline (5), harmaline (6), and harmine (7) by polarimetry, LC-MS, gas chromatography-mass spectrometry, high-resolution mass spectrometry, and nuclear magnetic resonance spectroscopy. We also used DNA sequence analyses to identify the plant species of the product. As a result of the sequencing of trnL-F, internal transcribed spacer (ITS), and rpl16 intron regions, three sequences derived from Coryphantha macromeris (Cactaceae), Peganum harmala (Zygophyllaceae), and Turnera diffusa (Turneraceae) were observed. Compounds 2 and 3, both phenethylamines, were reported to cause hallucinogenic effects and are frequently found in Coryphantha genus (Cactaceae). Therefore, the plant source of these compounds was considered to be C. macromeris. Compound 5 is known to be a psychoactive phenethylamine found in peyote (Lophophora williamsii) and San Pedro cactus (Trichocereus pachanoi). The β-carboline alkaloids 6 and 7 are known to be found in the seeds of P. harmala. Therefore, there seems to be no contradiction between the chemical constituents and the plant species estimated by DNA analyses, except for compound 5. This is the first report dealing with identification of the psychoactive cactus C. macromeris and its constituent compounds in a herbal product distributed in the illegal drug market.

Phylogenetic relationships in the ‘Pinnatella’ clade of the moss family Neckeraceae (Bryophyta)

The family Neckeraceae is composed of three distinct clades, of which two, i.e. the Neckera and Thamnobryum clades, are well defined. The third clade, consisting of species belonging to Caduciella, Curvicladium, Handeliobryum, Himantocladium, Homaliodendron, Hydrocryphaea, Neckera, Neckeropsis, Pinnatella, Shevockia and Taiwanobryum, is the focus of this study. Based on sequence data from the trnS-rps4-trnT-trnL-trnF plastid cluster and the rpl16 intron as well as from nuclear ITS1&2, the phylogenetic relationships of these genera are reconstructed. The nearest relatives of this clade are resolved shedding more light on the evolution of the family. The generic composition of the clade and its individual genera are discussed; polyphyly requires redefinition of Pinnatella, Neckeropsis and Homaliodendron. The positions of Touwia and Homalia within the family are addressed in an additional analysis based on more extensive sequence data, and the corresponding new combinations are made. Several further taxonomic changes are proposed, including Circulifolium gen. nov., comprising the former Homaliodendron exiguum and H. microdendron.

Phylogeny of Camassia (Agavaceae) Inferred from Plastid rpl16 Intron and trnD–trnY–trnE–trnT Intergenic Spacer DNA Sequences: Implications for Species Delimitation

Abstract Camassia is a genus of six bulb-forming species endemic to North America that have figured prominently in the culture and sustenance of native peoples. In western North America they form a conspicuous element of wet meadows and forest openings. Species and, especially, subspecies delimitations have been problematic. Further, several hypothesized phylogenetic and biogeographic scenarios for the origin and diversification of the genus remain untested. We estimated the phylogeny of Camassia using two noncoding plastid DNA regions: rpl16 intron and trnD—trnY—trnE—trnT spacers, with the goals of evaluating 1) the delimitation of species and 2) Gould's hypotheses for the origin of species and infraspecific taxa. Maximum parsimony and Bayesian analyses provided concordant estimates of the phylogeny consistent with the monophyly of eastern American C. scilloides and western American C. howellii and C. leichtlinii. Two western American species were found to be paraphyletic—C. cusickii weakly so, but C. qu...

Chautemsia calcicola: A new genus and species of Gloxinieae (Gesneriaceae) from Minas Gerais, Brazil

AbstractA new species of Gesneriaceae discovered in remnants of deciduous forests on limestone outcrops in Minas Gerais, Brazil, is described and compared with morphologically related taxa. This plant presents the diagnostic features of the tribe Gloxinieae, but a unique combination of morphological traits distinguishes this taxon from previously described genera. Its phylogenetic position was inferred based on analyzing DNA sequences variation of five loci: the rpl16 intron, rps16 intron, trnL‐F intron‐spacer, a portion of the plastid‐expressed glutamine synthetase gene (ncpGS) and the ribosomal DNA internal transcribed spacer (ITS). Molecular phylogenetic analyses confirm the position of this new species in the Gloxinieae, as a sister lineage of a clade including the Brazilian genera Mandirola and Goyazia. However, tests using topological constraints do not reject the alternative relationship that places this taxon with Gloxiniopsis in a monophyletic group. To accommodate this species in the current generic circumscription of Gloxinieae, the new genus Chautemsia A.O. Araujo & V.C. Souza is created.

Phylogenetic Relationships Between and within Phacelia Sections Whitlavia and Gymnobythus (Boraginaceae)

Abstract Phylogenetic relationships between and within Phacelia sections Whitlavia and Gymnobythus are inferred based on nuclear ribosomal DNA [5.8S, and flanking internal transcribed spacers (ITS) 1 and 2] and chloroplast DNA (rpl16 intron) sequences. These two sections share morphological characters and have been thought to be closely related. The purpose of this study is to test whether each of the two sections is monophyletic as well as whether they form sister clades. Our results indicate that section Gymnobythus is monophyletic, and members of section Whitlavia form two clades that correspond to subsections previously suggested by Gillett. In the ITS dataset, the two Whitlavia groups are not sister clades, but there is little support for their placement. The rpl16 and rpl16 + ITS combined datasets provide resolution and strong support for monophyly of both sections. Both datasets indicate hybridization or a recent divergence between Phacelia parryi and Phacelia minor, as well as a close alliance bet...

The genus Bauhinia s.l. (Leguminosae): a phylogeny based on the plastid trnL–trnF region

As the largest genus in tribe Cercideae, the pantropical genus Bauhinia has been the subject of a number of regional treatments in which it has been recognized either as a single genus with several subgenera or as several distinct genera. With the aim to better understand the taxon relationships within Bauhinia and between it and related genera, we have sequenced the plastid trnL–trnF region for 85 species, which together are representative of the eight genera recognized within Bauhinia sensu lato by some workers. In addition, representative taxa were verified for the presence or absence of the plastid rpl2 intron, which previous studies indicated might be a marker for specific lineages within Bauhinia s.l. Both Bayesian and parsimony analyses indicate that Bauhinia s.l. is paraphyletic with the monospecific genus Brenierea clustered within it. This genus, usually described as sister to Bauhinia s.l., forms a clade with the genera Piliostigma and Bauhinia sensu stricto. The remaining genera ( Gigasiphon , Tylosema , Barklya , Phanera , Lasiobema , and Lysiphyllum ) form a second clade sister to the first. All of these segregate genera are monophyletic except for Phanera, which is divided into two lineages comprising the Asian Phanera species together with the genus Lasiobema , and the second comprising the American Phanera species. The relationship between the Brenierea – Bauhinia s. str. – Piliostigma clade, the Gigasiphon–Tylosema–Barklya–Phanera–Lasiobema–Lysiphyllum clade and the genus Griffonia is not well resolved, but Adenolobus is sister to this large monophyletic group and the genus Cercis is sister to all other Cercideae. Preliminary analyses of the rpl2 plastid region also support the Piliostigma – Brenierea – Bauhinia s. str. clade, suggesting a unique loss event of the intron prior to the diversification of this clade.

C3 photosynthesis in Aristida longifolia: Implication for photosynthetic diversification in Aristidoideae (Poaceae)

Only a small percentage of plant species undergo C(4) photosynthesis. Despite its rarity, the C(4) pathway has evolved numerous times from C(3) ancestors, with as many as 18 independent origins in grasses alone. We report non-Kranz (C(3)) anatomy in Aristida longifolia, a species in a genus of ca. 300 species previously thought to possess only Kranz (C(4)) anatomy. Leaf blade transections of A. longifolia show widely spaced vascular bundles, nonradiate chlorenchyma, and few or no chloroplasts in cells of the sheaths surrounding the vascular bundle, all features indicative of C(3) photosynthesis. Carbon isotope ratios range from -27.68 to -29.71%, likewise indicative of C(3) photosynthesis. We also reconstruct the phylogeny of Aristidoideae, comprising Aristida, Sartidia (C(3)), and Stipagrostis (C(4)), using a sample of 11 species, including A. longifolia, and DNA sequences of the nuclear ribosomal internal transcribed spacer region and the chloroplast rpl16 intron and trnL-trnF region. Sartidia and Stipagrostis resolve as sisters, and sister to this clade is Aristida. Aristida longifolia resolves as sister to the remaining species in the genus. C(3) photosynthesis is hypothesized to be ancestral in Aristidoideae, which means the C(4) pathway evolved twice in the subfamily-in Stipagrostis and early in the diversification of the Aristida clade.

Successful DNA amplification of a more than 200‐year‐old herbarium specimen: recovering genetic material from the Linnaean era

AbstractThe limit for successful DNA extraction was tested by amplification and sequencing of an over 200‐year‐old herbarium specimen collected by Adam Afzelius, a student of Carl Linnaeus. We amplified and sequenced a 800‐bp region between 16S ribosomal DNA and the 3′ part of the trnI gene (16S‐trnI) in the chloroplast genome of Phaulopsis talbotii S. Moore (Acanthaceae). To test the replicability and to control for contamination the procedure was performed in sealed vials and with negative PCR controls. The procedure was also repeated in a separate laboratory. In addition, the chloroplast rpl16 intron was successfully amplified and sequenced and the rps16 intron amplified. Sequences of taxa closely related to Acanthaceae were found to be most similar to the produced sequences. The results suggest that molecular investigations of other 18th century botanical collections are feasible and that molecular methods could be employed for comparative studies to extant plant collections. An important application would be to identify descendants or clones of Linnaean lectotypes by comparing DNA from these with potentially remnant plants from Linnaeus' cultivations.

Phylogenetics of Dilleniaceae Using Sequence Data from Four Plastid Loci (rbcL,infA,rps4,rpl16Intron)

Dilleniaceae are an angiosperm family consisting of 10–14 genera and ∼500 described species, with a pantropical distribution extending into temperate Australia. This study addresses the infrafamilial relationships of Dilleniaceae with nucleotide sequence data from the plastid loci rbcL, infA, rps4, and the rpl16 intron. Analyses of these data using maximum parsimony and Bayesian methods resolve Tetracera, the only pantropical genus in the family, as sister to all other Dilleniaceae. Within the clade of Dilleniaceae exclusive of Tetracera, the New World endemic genera form a clade that is sister to a clade composed of the Old World endemic genera. The latter contains two major subclades: (1) a clade containing Acrotrema, Dillenia, and Schumacheria and (2) a clade containing Hibbertia and its satellite genera, Adrastaea and Pachynema, which are embedded within Hibbertia. Ancestral‐state reconstructions of six morphological characters of both biological and taxonomic significance within Dilleniaceae suggest ...

The demise of subfamily Hydrocotyloideae (Apiaceae) and the re-alignment of its genera across the entire order Apiales

As circumscribed by Drude, the umbellifer subfamily Hydrocotyloideae posed a major hindrance to resolving the phylogeny of order Apiales. Previous studies have suggested its polyphyly, but have not had sufficient sampling to address the issue fully. To put an end to the out-dated concept of Hydrocotyloideae, we investigated the placement of 40 of the 42 genera once placed in the subfamily, using extensive taxon sampling across the entire order. Molecular phylogenies were constructed using plastid sequences of the rpl16 intron and the trnD-trnT regions and revealed at least six hydrocotyloid lineages dispersed across both families Apiaceae and Araliaceae. The most speciose of these clades corresponds to the recently erected subfamily Azorelloideae. Another lineage includes genera grouped in Mackinlayoideae, where relationships are well resolved. Platysace appears paraphyletic with respect to Homalosciadium, and their placement is well supported as a basal lineage in Apiaceae. The type genus, Hydrocotyle, belongs to a supported clade in Araliaceae. The placements of Hermas as sister to a clade consisting of Apiaceae subfamilies Apioideae and Saniculoideae, and of Choritaenia as sister to Lichtensteinia in a clade with affinities to both Apioideae and Saniculoideae, calls into question the circumscriptions of the two subfamilies. Finally, plastid data suggest that many former hydrocotyloid genera are non-monophyletic (e.g., Azorella, Schizeilema, and Eremocharis) and are in dire need of additional phylogenetic and taxonomic studies.

Towards a more robust molecular phylogeny of Chinese Apiaceae subfamily Apioideae: Additional evidence from nrDNA ITS and cpDNA intron ( rpl16 and rps16) sequences

China contains some of the world’s greatest diversity of Apiaceae (Umbelliferae), with ten endemic genera. Our previous investigation into the phylogenetic relationships of Chinese Apiaceae subfamily Apioideae, based exclusively on nrDNA ITS sequences, revealed several major clades heretofore unrecognized in the subfamily and confirmed the phylogenetic placements of five endemic genera. To further elucidate relationships among Chinese Apioideae, ascertain the phylogenetic placements of the remaining endemic genera, and test hypotheses of relationships proposed in our earlier study, additional taxa were examined for ITS and, for smaller sets of accessions, cpDNA rpl16 and rps16 intron sequence variation. These ITS and cpDNA data matrices comprised 158 and 131 accessions, respectively, with 110 accessions included in the analysis of combined ITS and cpDNA data. Maximum parsimony and Bayesian analyses of partitioned ITS and chloroplast data sets resulted in highly consistent phylogenies, whereas analyses of combined molecular data resulted in trees of greatest resolution and overall branch support. Two major clades identified in our previous study are recognized at the tribal level: Komarovieae J. Zhou & S. R. Downie trib. nov. and Chamaesieae J. Zhou & F. D. Pu trib. nov. The monotypic tribe Chamaesieae represents one of the earliest diverging lineages of subfamily Apioideae in Asia. The Acronema and East Asia clades of previous circumscription are each expanded. Of the five Chinese endemic genera not examined previously, Chaerophyllopsis finds affinity within tribe Scandiceae subtribe Scandicinae, Chuanminshen allies with Changium and Cyclorhiza in tribe Komarovieae, Harrysmithia falls within the Acronema Clade, Melanosciadium embeds in Angelica in tribe Selineae, and Dickinsia is confirmed as a member of Apiaceae subfamily Azorelloideae. The cpDNA-based phylogenies are not sufficiently resolved in their distal portions to elucidate the tribal placement of the endemic genus Nothosmyrnium, whereas the ITS trees strongly indicate an affinity with tribe Pimpinelleae. The affinities of several Chinese endemic species are also addressed. Peucedanum delavayi, for example, is phylogenetically distant from Sinodielsia and Meeboldia, genera with which it has been allied previously, and shows close affinity to three Chinese species of Ligusticum in tribe Selineae. Aside from providing a framework for taxonomic revisions, the phylogenetic structure recovered in this study for subfamily Apioideae will lay the foundation for future investigations of evolutionary patterns of morphological characters and biogeography.

Molecular systematics of Gagea and Lloydia (Liliaceae; Liliales): implications of analyses of nuclear ribosomal and plastid DNA sequences for infrageneric classification

Gagea is a Eurasian genus of petaloid monocots, with a few species in North Africa, comprising between 70 and approximately 275 species depending on the author. Lloydia (thought to be the closest relative of Gagea) consists of 12-20 species that have a mostly eastern Asian distribution. Delimitation of these genera and their subdivisions are unresolved questions in Liliaceae taxonomy. The objective of this study is to evaluate generic and infrageneric circumscription of Gagea and Lloydia using DNA sequence data. A phylogenetic study of Gagea and Lloydia (Liliaceae) was conducted using sequences of nuclear ribosomal internal transcribed spacer (ITS) and plastid (rpl16 intron, trnL intron, trnL-F spacer, matK and the psbA-trnH spacer) DNA regions. This included 149 accessions (seven as outgroups), with multiple accessions of some taxa; 552 sequences were included, of which 393 were generated as part of this research. A close relationship of Gagea and Lloydia was confirmed in analyses using different datasets, but neither Gagea nor Lloydia forms a monophyletic group as currently circumscribed; however, the ITS and plastid analyses did not produce congruent results for the placement of Lloydia relative to the major groups within Gagea. Gagea accessions formed five moderately to strongly supported clades in all trees, with most Lloydia taxa positioned at the basal nodes; in the strict consensus trees from the combined data a basal polytomy occurs. There is limited congruence between the classical, morphology-derived infrageneric taxonomy in Gagea (including Lloydia) and clades in the present phylogenetic analyses. The analyses support monophyly of Gagea/Lloydia collectively, and they clearly comprise a single lineage, as some previous authors have hypothesized. The results provide the basis for a new classification of Gagea that has support from some morphological features. Incongruence between plastid and nuclear ITS results is interpreted as potentially due to ancient hybridization and/or paralogy of ITS rDNA.

Phylogeny of the Australian Camphorosmeae (Chenopodiaceae) and the Taxonomic Significance of the Fruiting Perianth

Molecular and morphological data were used to reconstruct the phylogeny of Camphorosmeae (Chenopodiaceae) in Australia, a tribe adapted to and widespread in the temperate arid and semiarid areas of the continent. A total of 71 species, representing nearly half of the species and all 14 currently recognized endemic genera, were sampled. Of seven molecular markers tested (ETS, ITS, the trnL‐trnF spacer, the trnP‐psaJ spacer, the rpS16 intron, the rpL16 intron, and the trnS‐trnG spacer), only the nuclear ETS and ITS provided enough variation for phylogenetic studies in the group. Phylogenetic hypotheses inferred from molecular data do not support the current taxonomy of Camphorosmeae in Australia. Neobassia, Threlkeldia, Osteocarpum, and Enchylaena should be subsumed into the species‐rich genera Sclerolaena and Maireana. Of 15 morphological characters, only the fruiting perianth provided some support for the taxonomic implications of the DNA‐based phylogeny. Indumentum characters, which were reported to be of taxonomic significance in several groups in Chenopodiaceae, did not provide support for the molecular phylogeny of Camphorosmeae in Australia.

Phylogeny of Tricalysia (Rubiaceae) and its Relationships with Allied Genera Based on Plastid DNA Data: Resurrection of the Genus Empogona1

Abstract Recent studies on the circumscription of the tribe Coffeeae (Rubiaceae) revealed a weakly supported clade containing Tricalysia A. Rich. and the allied genera Argocoffeopsis Lebrun, Calycosiphonia Pierre ex Robbr., Belonophora Hook. f., Diplospora DC., Discospermum Dalzell, Nostolachma T. Durand, and Xantonnea Pierre ex Pit. The phylogenetic relationships of Tricalysia and these allied taxa are investigated further using sequence data from four plastid regions (trnL-F intron and intergenic spacer, rpL16 intron, accD-psa1 intergenic spacer, and PetD). Our results demonstrate that Tricalysia sensu Robbrecht is not monophyletic. The genus name Tricalysia should be restricted to taxa from subgenus Tricalysia; subgenus Empogona (Hook. f.) Robbr. is sister to the genus Diplospora and is recognized at the generic level. The 34 necessary new combinations for Empogona Hook. f. are provided: E. acidophylla (Robbr.) J. Tosh & Robbr., E. aequatoria (Robbr.) J. Tosh & Robbr., E. africana (Sim) J. Tosh & Robbr...

Phylogenetic Relationships in the Genus Paspalum (Poaceae: Panicoideae: Paniceae): An Assessment of the Quadrifaria and Virgata Informal Groups

Paspalum, an American genus of the x = 10 Paniceae clade, includes about 330 species, four subgenera, and 27 informal groups. Within the genus, the Quadrifaria and Virgata groups are well-represented in South and Central America. Interspecific variability make the delimitation of these groups difficult; hence several species have been included or excluded from Quadrifaria or Virgata depending on the taxonomic treatment. In previous analyses, the Quadrifaria and Virgata groups of Paspalum were polyphyletic. Here we present a new appraisal of the classification of both groups based on the phylogenetic analyses of DNA data from the chloroplast: the rpl16 intron, and the region comprising the trnL and trnF genes. A monophyletic Virgata clade is recovered, consisting of nearly all the species listed in an unpublished manuscript. The Quadrifaria group is restricted to P. quadrifarium and P. quarinii. Other clades grouped species traditionally treated within Virgata or Quadrifaria, although their phylogenetic placement needs to be reevaluated. Within most of the clades, diploid and polyploid species seemingly derive from a common ancestor denoting an autopolyploid origin. Alloploidy is also possible although reticulate evolution needs to be explored. The wide distribution of the I genome suggests that this is a plesiomorphic state in Paspalum.

Phylogeny and Character Evolution in Nierembergia (Solanaceae): Molecular, Morphological, and Cytogenetic Evidence

Nierembergia (Solanaceae) contains 21 species found primarily in South America, with one species occurring disjunctly in Mexico. Among other features, a pollination system not found elsewhere in the Solanaceae typifies this genus. In most species, nectaries are absent, but oil-producing elaiophores are present on the corolla limb and these attract oil-collecting bees. Molecular phylogenetic hypotheses based on nuclear ITS and chloroplast rpl16 intron data support the monophyly of Nierembergia, which is sister to a clade composed of Bouchetia plus Hunzikeria. The data reconstruct two clades within the genus: one composed primarily of herbaceous species with broad stigmas and the second containing woody species with crescent-shaped stigmas. Morphological homoplasy is frequent among the species of the herbaceous clade, while the woody clade is morphologically cohesive. Chromosome counts are confirmed and karyotype features are given for 13 Nierembergia species (including six varieties) and for Bouchetia anomala, Leptoglossis linifolia, and Petunia axillaris. The two clades are also supported by karyotypic features: one has asymmetrical karyotypes, small chromosomes, and two chromosome pairs with nucleolar organizing regions (NOR) and the other has symmetrical karyotypes, large chromosomes, and only one NOR.

Phylogenetic Analysis of Pachycereus (Cactaceae, Pachycereeae) based on Chloroplast and Nuclear DNA Sequences

The phylogenetic relationships of Pachycereus (Cactaceae) species and relatives from subtribe Pachycereinae were studied using DNA sequence data. The plastid rpl16 intron, trnL intron, trnL-F intergenic spacer, and nuclear rDNA internal transcribed spacer region (ITS) were sequenced for 30 species, representing the four genera of subtribe Pachycereinae (Carnegiea, Cephalocereus, Neobuxbaumia ,a ndPachycereus) as well as three additional outgroup genera from subtribe Steno- cereinae. Phylogenetic analyses support neither the monophyly of Pachycereus as currently circumscribed nor Pachycereinae unless Stenocereus aragonii and S. eichlamii are included within it. However, these results suggest that the subtribe can be divided into three major clades. The first includes Pachycereus hollianus and P. lepidanthus, which is sister to a large clade combining species from the Pachycereus and Cephalocereus groups. Within this large clade Cephalocereus and Neobuxbaumia together with Pachycereus fulviceps are sister to the remaining species of Pachycereus as well as Stenocereus aragonii, S. eichlamii, and Carnegiea gigantea. Our results suggest that Pachycereus is paraphyletic and that several other genera (Backebergia, Lemai- reocereus, Lophocereus ,a ndPseudomitrocereus) may be resurrected to accommodate these new phylogenetic insights. A number of morphological and anatomical characters support these relationships, indicating that future analyses combining both molecular and morphological characters will be particularly useful in resolving relationships within this group of columnar cacti.

Phylogenetics of <I>Otatea</I> Inferred from Morphology and Chloroplast DNA Sequence Data, and Recircumscription of Guaduinae (Poaceae: Bambusoideae)

Abstract Representative taxa of the five genera of Guaduinae, a subtribe of Neotropical woody bamboos, were sampled to investigate the phylogenetic relationships of the species of the genus Otatea using morphological and molecular (cpDNA intergenic spacer trnH-psbA and the rpl16 intron) evidence. Phylogenetic analysis of a combined data set retrieved 53 most parsimonious trees in which subtribe Guaduinae is monophyletic if two species of Anlonemia (A. clarkiae and A. fulgor) are included. They were previously classified within subtribe Arthrostylidiinae. Guaduinae is supported by the lack of papillae from the abaxial surface, by an almost solid style, a short rachis extension, and oral setae present in culm and foliage leaves. Monophyly of the genera in Guaduinae (Eremocanlon, Guadna, Apoclada, Otatea, and Olmeca) was corroborated. Otatea species formed a monophyletic clade, supported by culms with three subequal ascending branches and pubescent lemmas. Eight species in Guaduinae (the four species in Otat...

A Molecular Phylogenetic Study of Arnica (Asteraceae): Low Chloroplast DNA Variation and Problematic Subgeneric Classification

DNA sequences from five chloroplast DNA regions (the rpl16 and rps16 introns and the psbA-trnH, ycf4-cemA, and trnT-L spacers), and the nuclear ribosomal internal and external transcribed spacer (ITS and ETS) regions, were analyzed using maximum parsimony and Bayesian methods to explore the putatively complicated history of the mainly North American genus Arnica. The chloroplast regions were found to contain minimal variation in Arnica. Of 3710 nucleotides, only 119 were variable and 45 informative. However, combined with the ribosomal DNA data, the analysis yielded a number of well-supported clades. Strong support for the monophyly of Arnica was found in both the separate and combined analyses but none of the five currently recognized subgenera was resolved as monophyletic in any of the analyses. Arnica (Whitneya) dealbata and A. mallotopus (Mallotopus japonicus), two species that were previously placed outside Arnica, were confidently confirmed as members of the genus. The analyses revealed that A. nevadensis (subg. Austromontana) is most closely related to A. dealbata and that A. mallotopus forms a strongly supported clade with A. unalaschcensis (subg. Andropurpurea). Earlier biogeographical hypotheses that suggested an arctic origin and southward spread of the genus are not supported by our analyses. Hybridization, homoplasy, and rapid evolution are possible explanations for conflicts between the chloroplast and nuclear ribosomal data sets and for low support of the deeper nodes.

A localized loss of the chloroplast rpl16 intron in Mammillaria series Stylothelae (Cactaceae) delineates members of the M. crinita group

Within the cactus genus Mammillaria, the circumscription of series Stylothelae has been controversial. This has resulted in circumscriptions that group species into a single series with various species groups (M. crinita Group, M. bombycina Group, M. glassii Group, and M. mercadensis Group) and circumscriptions that split the series into a number of subsequent series. Utilizing PCR sequencing methods, the authors investigated phylogenetic relationships in the Stylothelae and discovered the deletion of the entire rpl16 intron of the chloroplast in a number of members of the series. To date, this deletion has not been documented elsewhere in the Cactaceae. Specifically, the deletion of the rpl16 intron in the Stylothelae is restricted to those species that have either been treated as a distinct species group (M. crinita Group) within the series, or as a unique series in their own right (series Stylothelae sensu stricto).