ndhF Sequence Data Research Articles

Melica as an emerging model system for comparative studies in temperate Pooideae grasses.

Pooideae grasses contain some of the world's most important crop and forage species. Although much work has been conducted on understanding the genetic basis of trait diversification within a few annual Pooideae, comparative studies at the subfamily level are limited by a lack of perennial models outside 'core' Pooideae. We argue for development of the perennial non-core genus Melica as an additional model for Pooideae, and provide foundational data regarding the group's biogeography and history of character evolution. Supplementing available ITS and ndhF sequence data, we built a preliminary Bayesian-based Melica phylogeny, and used it to understand how the genus has diversified in relation to geography, climate and trait variation surveyed from various floras. We also determine biomass accumulation under controlled conditions for Melica species collected across different latitudes and compare inflorescence development across two taxa for which whole genome data are forthcoming. Our phylogenetic analyses reveal three strongly supported geographically structured Melica clades that are distinct from previously hypothesized subtribes. Despite less geographical affinity between clades, the two sister 'Ciliata' and 'Imperfecta' clades segregate from the more phylogenetically distant 'Nutans' clade in thermal climate variables and precipitation seasonality, with the 'Imperfecta' clade showing the highest levels of trait variation. Growth rates across Melica are positively correlated with latitude of origin. Variation in inflorescence morphology appears to be explained largely through differences in secondary branch distance, phyllotaxy and number of spikelets per secondary branch. The data presented here and in previous studies suggest that Melica possesses many of the necessary features to be developed as an additional model for Pooideae grasses, including a relatively fast generation time, perenniality, and interesting variation in physiology and morphology. The next step will be to generate a genome-based phylogeny and transformation tools for functional analyses.

Systematics and biogeography of Berberis s.l. inferred from nuclear ITS and chloroplast ndhF gene sequences

AbstractBerberis is the largest genus in the Berberidaceae, comprising more than 500 species. It is now recognised to include all of the compound‐leaved species formally ascribed to Mahonia, as well as simple‐leaved species comprising Berberis s.str. Berberis s.l. has a mainly Northern Hemisphere distribution, with a centre of diversity in the Sino‐Himalaya region, while Berberis s.str. extends into South America where it has a secondary centre of diversity. We analyzed nuclear ITS and chloroplast ndhF sequence data from 68 accessions of Berberis s.l. The results support the monophyly of Berberis s.l., but compound‐leaved Berberis are shown to be paraphyletic. The analysis supports Berberis higginsae, a member of North American B. sect. Horridae, as sister to all other Berberis species. Our results, interpreted in the light of fossil evidence, suggest a North American origin of Berberis s.l., but the area of origin of the simple‐leaved group remains uncertain.

Welwitschiella is a member of the African subtribe Grangeinae (Asteraceae Astereae): a new phylogenetic position based on ndhF and ITS sequence data

The African genus Welwitschiella has traditionally been placed in tribe Heliantheae. Our phylogenetic analysis of chloroplast DNA ndhF sequence data, however, reveals that it is part of tribe Astereae. In order to assess the relationships of this genus within the tribe, we produced a phylogeny based on ITS (nrDNA) sequence data of a sample including Amellus, African Conyza, Chrysocoma, Felicia spp., Mairia, Poeciliopsis, Printzia, Welwitschiella and Zyrphelis. Both parsimony and Bayesian analyses were done. The Bayesian analysis showed that African genera form a basal grade in tribe Astereae along with the Chinese Nannoglottis and South American and New Zealand genera, with Printzia being the earliest diverging member of the tribe. Mairia occupies an isolated position. Amellus, Chrysocoma, Felicia, Poecilolepis and Zyrphelis belong to subtribe Homochrominae, a South African radiation that also includes the St Helena endemics Commidendron and Melanodendron. Pteronia appears isolated, though it might be close to the Homochrominae. Welwitschiella is placed in the latest diverging African clade, subtribe Grangeinae, which also includes Grangea, Psiadia, Nidorella, and the African Conyza species except C. gouani. This subtribe is sister to the Eurasiatic subtribe Bellidinae, and together they are sister to the Astereae crown lineages of Australasia-Asia and South and North America.

Troublesome tropical mints: re‐examining generic limits of Vitex and relations (Lamiaceae) in South East Asia

ABSTRACTThe relationships of Vitex and genera historically placed in Lamiaceae subfamily Viticoideae were investigated. Particular focus was given to some South East Asian genera traditionally allied to Vitex (Paravitex, Tsoongia, Viticipremna, Teijsmanniodendron) since progress with South East Asian Floras is being hampered by a lack of clarity in current generic delimitation. On the basis of maximum parsimony and Bayesian phylogenetic analyses of ITS and ndhF sequence data we provide evidence that the Viticoideae is not monophyletic, its members being spread between a number of clades which include genera currently recognised as incertae sedis (Peronema, Hymenopyramis, Petraeovitex, Tectona). The most well supported clade, the Vitex group, contains Vitex, Paravitex, Tsoongia, Viticipremna, Petitia and Teijsmanniodendron. Morphological similarities of the genera included in this group are also discussed. In light of this evidence Paravitex, Viticipremna and Tsoongia are reduced to synonymy with Vitex, the new combinations being made here. The position of Teijsmanniodendron is not resolved and its generic status is therefore upheld. Similarly, Petitia is upheld due to a lack of neotropical taxa within the sample.

First report of chromosome numbers of the Carlemanniaceae (Lamiales)

The Carlemanniaceae comprises two small genera that are restricted to East Asia: the Carlemannia and Silvianthus. These genera were previously placed in the Rubiaceae or Caprifoliaceae, but are now considered a distinct family that is probably related to the Oleaceae in the Lamiales. The family is still poorly understood with respect to its morphological characteristics. Here, we present the first report of the chromosome numbers of the family using species from both genera, i.e., Carlemannia tetragona, Silvianthus bracteatus ssp. bracteatus, and S. bracteatus ssp. clerodendroides. The species were compared with the chromosome numbers of Oleaceae and associated families using a Bayesian tree that was generated from rbcL and ndhF sequence data from Genbank. C. tetragona had 2n = 30 (x = 15), whereas the two subspecies of Silvianthus had 2n = 38 (x = 19). Comparisons of chromosome numbers support the distinctness of the Carlemanniaceae, not only from the Oleaceae (x = 11, 13, 23), but also from the Tetrachondraceae (x = 10, 11), a family that is possibly related to the Carlemanniaceae and/or Oleaceae in the Lamiales. The notable difference in chromosome number between Carlemannia and Silvianthus, as well as the differences in other characteristics (pollen, seed, and fruit morphology), suggests that the family split early in its evolution.

Phylogeny, Adaptive Radiation, and Historical Biogeography of Bromeliaceae Inferred from ndhF Sequence Data

Cladistic analysis of ndhf sequences identifies eight major clades arranged in ladderlike fashion. The traditional subfamilies Tillandsioideae and Bromelioideae are monophyletic, but Pitcairnioideae are paraphyletic, requiring the description of four new subfamilies, recircurnscription of Pitcairnioideae and Navioideae, the sinking of Ayensua, and description of the new genus Sequencia. Brocchinioideae are basalmost, followed by Lindmanioideae, both restricted to the Guayana Shield. Next is an unresolved trichotomy involving Hechtioideae from Central America, Tillandsioideae, and the remaining bromeliads in subfamilies Navioideae, Pitcairnioideae, Puyoideae, and Bromelioideae. Bromeliads arose as C 3 terrestrial plants on moist infertile sites in the Guayana Shield roughly 70 Mya, spread centripelally in the New World, and reached tropical West Africa (Pitcairnia feliciana) via long-distance dispersal about 10 Mya. Modern lineages began to diverge from each other 19 Mya and invaded drier areas in Central and South America beginning 15 Mya, coincident with a major adaptive radiation involving the repeated evolution of epiphytism, CAM photosynthesis, impounding leaves, several features of leaf/trichome anatomy, and accelerated diversification at the generic level. This bromeliad revolution occurred after the uplift of the northern Andes and shift of the Amazon to its present course. Epiphytism may have accelerated speciation by increasing ability to colonize along the length of the Andes, while favoring the occupation of a cloud-forest landscape frequently dissected by drier valleys. Avian pollination (mainly by hummingbirds) evolved at least twice ca. 13 Mya; entomophily was ancestral. Hechtia, Abromeitiella-Deuterocohnia-Dyckia-Encholirium, and Puya exhibit a remarkable pattern of concerted convergence in six anatomical and physiological leaf traits adapted to drought.

Pollen morphology and ultrastructure of Acalypha (Euphorbiaceae)

The pollen morphology of 73 species of Acalypha representing most of the taxonomic diversity in the genus was examined with light and scanning electron microscopy, and 14 species with transmission electron microscopy. Acalypha pollen is small (9–22 μm), subisopolar to isopolar or apolar, and oblate-spheroidal to suboblate in meridional outline. The aperture system is 2-8-colporate, with the ectocolpi short (1–5 μm) and almost equal in length to the endopore diameter. Exine ornamentation is rugulate to microrugulate or areolate with distinct scabrae localized on the margins of the muri or scattered over the pollen surface. These results show that Acalypha pollen exhibits significant variation in size, aperture number, aperture distribution and exine ornamentation, and is not homogeneous as previously reported. Two distinct types, each with two subtypes, were recognized based on tectal ornamentation. Though pollen morphology is inconsistent with a phylogeny based on ITS and ndhF sequence data, it does provide support for subgenera Linostachys and Androcephala and several small clades in the molecular phylogeny.

Phylogeny of Agavaceae Based on ndhF, rbcL, and its Sequences

Great advances have been made in our understanding of the phylogeny and classification of Agavaceae in the last 20 years. In older systems Agavaceae were paraphyletic due to overemphasis of ovary position or habit. Discovery of a unique bimodal karyotype in Agave and Yucca eventually led to a reexamination of concepts and relationships in all the lilioid monocots, which continues to the present day. Developments in cytogenetics, microscopy, phylogenetic systematics, and most recently DNA technology have led to remarkable new insights. Large-scale rbcL sequence studies placed Agavaceae with the core Asparagales and identified closely related taxa. Analysis of cpDNA restriction sites, rbcL, and ITS nrDNA sequences all supported removal of Dracaenaceae, Nolinaceae, and clarified relationships. Agavaceae s.s. presently consists of Agave, Beschorneria, Furcraea, Hesperaloe, Hesperoyucca, Manfreda, Polianthes, Prochnyanthes, and Yucca. In this paper we analyze recently obtained ndhF sequence data from Agavaceae and Asparagales and discuss the implications for classification. Parsimony analysis of ndhF data alone resolves most genera of Agavaceae and supports the inclusion of Camassia, Chlorogalum, Hesperocallis, and Hosta within Agavaceae s.l. Analysis of combined ndhF and rbcL data sets of selected Asparagales results in better resolution and stronger bootstrap support for many relationships. Combination of all available ndhF, rbcL, and ITS data in a single analysis results in the best resolution currently available for Agavaceae s.l. Implications for classification schemes past and present are discussed.

The Malagasy endemic Dendroportulaca (Portulacaceae) is referable to Deeringia (Amaranthaceae): molecular and morphological evidence

AbstractDendroportulaca mirabilis U. Eggli, a Malagasy liana described as an atypical member of Portulacaceae, was shown by ndhF sequence data to be placed within Amaranthaceae tribe Celosieae, strongly supported as sister to Deeringia polysperma. A re‐evaluation of the morphology of Dendroportulaca, including field observations, also supported its placement within Celosieae and in particular its relationship to the existing Malagasy species of Deeringia. Dendroportulaca mirabilis is herein transferred to Deeringia.

Phylogenetic relationships between Clerodendrum (Lamiaceae) and other Ajugoid genera inferred from nuclear and chloroplast DNA sequence data

Over the last two centuries the circumscription of the large, pan-tropical genus Clerodendrum (Lamiaceae) has changed frequently, as different authorities have added or removed taxa on the basis of various morphological characters. With the development of molecular methods for systematic research the process of circumscribing taxa has become increasingly analytical. When morphology signals the possibility that taxa are closely related, molecular methods can be used to test the hypothesis objectively. Aegiphila, Amasonia, Huxleya, and Kalaharia are similar morphologically to Clerodendrum. In this paper we use nuclear ribosomal ITS and chloroplast ndhF sequence data to clarify the positions of these four genera relative to Clerodendrum. We show that the Australian monotypic genus Huxleya evolved from within Clerodendrum. Accordingly, we sink Huxleya into Clerodendrum and make a new combination, Clerodendrum linifolium.

Inclusion of the Vietnamese endemic genus Grushvitzkya in Brassaiopsis (Araliaceae): evidence from nuclear ribosomal ITS and chloroplast ndhF sequences

The phylogenetic position of the recently described monotypic Vietnamese genus Grushvitzkya is evaluated using nuclear ribosomal ITS and chloroplast ndhF sequence data. Grushvitzkya stellata has often been considered as intermediate between Brassaiopsis and Trevesia, but differs in having a 5-locular ovary rather than a 2- or 6–16-locular ovary, respectively. The molecular data indicate that Grushvitzkya is deeply nested within Brassaiopsis and has a close relationship with B. phanrangensis from central and southern Indochina, and B. stellata from the regions bordering China and Vietnam. The Kimura 2-parameter distances of the ITS sequences between G. stellata and B. phanrangensis and B. stellata are 0.403 and 0.945%, respectively. Furthermore, G. stellata and B. phanrangensis have an identical ndhF sequence profile. Grushvitzkya stellata differs from B. stellata by a single nucleotide in their ndhF sequences. The available evidence is compatible with the hypothesis that Grushvitzkya diverged recently from B. phanrangensis and B. stellata. Although these three closely related species all possess stellate trichomes, G. stellata and B. phanrangensis have highly similar trichome micromorphology, with almost no difference in size, shape and branching pattern, supporting a very close relationship between the two taxa. The higher number of locules in the ovary of Grushvitzkya appears to be a secondary increase despite earlier interpretations that higher numbers are evolutionarily primitive. Grushvitzkya is herein merged with Brassaiopsis; because the combination B. stellata is occupied, a new name, Brassaiopsis grushvitzkyi, is proposed. © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003, 142, 455–463.

Family‐level relationships of Onagraceae based on chloroplast rbcL and ndhF data

Despite intensive morphological and molecular studies of Onagraceae, relationships within the family are not fully understood. One drawback of previous analyses is limited sampling within the large tribe Onagreae. In addition, the monophyly of two species-rich genera in Onagreae, Camissonia and Oenothera, has never been adequately tested. To understand relationships within Onagraceae, test the monophyly of these two genera, and ascertain the affinities of the newly discovered genus Megacorax, we conducted parsimony and maximum likelihood analyses with rbcL and ndhF sequence data for 24 taxa representing all 17 Onagraceae genera and two outgroup Lythraceae. Results strongly support a monophyletic Onagraceae, with Ludwigia as the basal lineage and a sister-taxon relationship between Megacorax and Lopezia. Gongylocarpus is supported as sister to Epilobieae plus the rest of Onagreae, although relationships within the latter clade have limited resolution. Thus, we advocate placement of Gongylocarpus in a monogeneric tribe, Gongylocarpeae. Most relationships within Onagreae are weakly resolved, suggesting a rapid diversification of this group in western North America. Neither Camissonia nor Oenothera appears to be monophyletic; however, increased taxon sampling is needed to clarify those relationships. Morphological characters generally agree with the molecular data, providing further support for relationships.

Phylogeny, concerted convergence, and phylogenetic niche conservatism in the core Liliales: insights from rbcL and ndhF sequence data.

Calochortus and the family Liliaceae s.s. have often been considered each other's closest relatives, based partly on their shared possession of bulbs, visually showy flowers, winged wind-dispersed seeds, and narrow parallel-veined leaves. We present a well-supported molecular phylogeny for these groups and their close relatives in the core Liliales, based on sequence variation in the chloroplast-encoded rbcL and ndhF genes. This analysis identifies Liliaceae s.s. as monophyletic. including one clade (((Lilium, Fritillaris, Nomocharis), Cardiocrinum), Notholirion) that appears to have diversified in the Himalayas roughly 12 million years ago and another ((Erythronium, Tulipa), (Gagea, Lloydia)) that arose in East Asia at about the same time. Medeola and Clintonia are sister to Liliaceae s.s. and bear rhizomes, inconspicuous flowers, fleshy animal-dispersed fruits, and broad reticulate-veined leaves. Calochortus is sister to Tricyrtis; both Tricyrtis and the neighboring clade of Prosartes-Streptopus-Scoliopus share several of the traits seen in Medeola-Clintonia. The core Liliales thus provide compelling examples of both concerted convergence and phylogenetic niche conservatism. Invasion of open, seasonal habitats was accompanied by the independent evolution of bulbs, showy flowers, wind-dispersed seeds, and narrow parallel-veined leaves in Calochortus and Liliaceae s.s. Conversely, persistence in shady habitats was accompanied by the retention of rhizomes, inconspicuous flowers, animal-dispersed seeds, and broad reticulate-veined leaves in their sister groups. We advance arguments for the context-specific adaptive value of each of these traits, as well as evidence of parallel trends in other groups. Concerted convergence--convergence in several different traits, favored by the same shared set of ecological conditions, in two or more lineages--is an important evolutionary process that can mislead evolutionary analyses based solely on phenotypic variation.

Phylogeny of the Portulacaceous Cohort Based on ndhF Sequence Data

Abstract The Portulacaceae, Basellaceae, Cactaceae, and Didiereaceae form a monophyletic group within the Caryophyllales, and evidence exists that the first may be paraphyletic if the latter three are recognized at the familial level. Several taxonomic treatments of the Portulacaceae based on morphological features have failed to produce consensus regarding infrafamilial relationships. The present paper employs sequences of the chloroplast gene ndhF to produce a molecular phylogeny of the portulacaceous cohort, focusing on the relationship among major lineages of the Portulacaceae and the three families potentially derived from within them. Results of this analysis supported two major clades within the monophyletic cohort. The first included Portulaca, Anacampseros and its relatives, much of Talinum, Talinella, and Cactaceae; the second, weakly supported, included the remaining genera of Portulacaceae, Basellaceae, and Didiereaceae. This phylogeny also showed that several generic circumscriptions remain i...

Polyphyly of the Genus Dentaria (Brassicaceae): Evidence from trnL Intron and ndhF Sequence Data

Abstract Members of the traditional genus Dentaria (Brassicaceae) comprise about twenty species disjunctly distributed in three biogeographical areas: eastern North America, western North America, and Eurasia. The group has variously been treated as a distinct genus, as a subgenus of Cardamine, or as several sections within Cardamine. Using chloroplast DNA sequence data from the trnL intron and ndhF gene we examine the evolutionary relationships of traditional Dentaria species to Cardamine sensu stricto and the validity of Schulz's sectional treatment of Cardamine (including Dentaria). Sequence data were obtained from nine Dentaria species, representing all three disjunct biogeographical groups and two of Schulz's sections, and six other Cardamine species representing a range of morphological variation within the genus and three of Schulz's sections. Results from maximum parsimony analysis show multiple origins for Dentaria within Cardamine and do not correspond well to Schulz's sectional classification. ...

On the circumscription of the Blennospermatinae (Asteraceae, Senecioneae) based on ndhF sequence data

SummarySwenson, U. & Bremer, K.: On the circumscription of the Blennospermatinae (Asteraceae, Senecioneae) based on ndhF sequence data. – Taxon 48: 7‐14. 1999. – ISSN 0040‐0262.The subtribe Blennospermatinae is usually defined to comprise four genera (Abrotanella, Blennosperma, Crocidium, and Ischnea). The placement of Abrotanella in the Blennospermatinae has been disputed, and the monogeneric subtribe Abrotanellinae was recently erected. A cladistic analysis of ndhF sequence data provides strong support for grouping Blennosperma with the Senecioneae, while Abrotanella is only weakly associated with the Senecioneae and does not form a monophyletic group with Blennosperma. Crocidium and Ischnea (not sequenced) are morphologically close to Blennosperma. Hence, the Blennospermatinae are best circumscribed to include only Blennosperma, Crocidium, and Ischnea, but not Abrotanella. The tribal position of Abrotanella remains uncertain.

Phylogenetic Analysis and Relationships in Hydrophyllaceae Based on ndhF Sequence Data

An analysis of evolutionary relationships within the angiosperm family Hydrophyllaceae was completed. A parsimony search using DNA sequence data from the chloroplast gene ndhF from 65 accessions yielded 3,227 most parsimonious trees distributed over six tree islands. Hydrophyllaceae, excluding Hydrolea and Codon, are nested within a paraphyletic Boraginaceae sensu lato. These core Hydrophyllaceae are restricted to the New World and have the derived feature of capsular fruits with parietal placentation and many small seeds. Two large clades can be recognized-a clade of annual and perennial herbs including Phacelia, tribe Hydrophylleae, and related genera, and a clade containing Nama and the woody, shrubby gen- era Eriodictyon, Turricula, and Wigandia. The second clade corresponds to the tribe Nameae sensu Gray, but the first has not been formally recognized. Evolutionary relationships based on ndhF are compared to current clas- sification systems and inferences about evolution based on published morphological and anatomical studies.

Phylogenetic Relationships of Clerodendrum s.l. (Lamiaceae) Inferred from Chloroplast DNA

Seventy-nine accessions representing forty-seven taxa of Clerodendrumn s.l. (Lamiaceae) and seven putative outgroup genera are included in an analysis of chloroplast DNA restriction sites for ten enzymes. Parsimony analysis of 456 potentially informative characters identifies four large discrete clades (Clades I-IV) within Clerodenidruim s.l. and shows that Clerodendruim s.l. is polyphyletic. Clades I and II comprise Asian and African taxa respectively. Clade III comprises coastal species from Africa, Asia and central America and presents an hypothesis of relationship within Clerodendrutm that has not previously been explicit in classifications of the genus. Clade IV, comprising subg. Cyclonema and sect. Konocalyx (subg. Clerodendrrnm pro parte) emerges as a lineage distinct from the rest of Clerodendrtni. Traditional sections Squamnata, Odontocalyx (subg. Clerodendrutm), Cyclonenia and Stacheocymosa (subg. Cycloinema) are well-supported mono- phyletic groups. Subgenus Clerodenidrutm and sections Clerodendrutm and Axilliflora (subg. Clerodendrnm pro parte) are shown to be polyphyletic. The polyphyly of Clerodendruni s.l. is also supported by a separate analysis of chloroplast ndhF sequences, in which a smaller sampling of Clerodendruman is included in a broader sample of labiate genera. The ndhF sequence data suggest that Tetraclea belongs in Clade I of Clerodendruni and support the monophyly of the recently circumscribed subfamily Teucriodeae.

Familial placement of Cyrtandromoea, Titanotrichum and Sanango, three problematic genera of the Lamiales

SummarySmith, J. F., Brown, K. D., Carroll, C. L. & Denton, D. S.: Familial placement of Cyrtandromoea, Titanotrichum and Sanango, three problematic genera of the Lamiales. – Taxon 46: 65‐74. 1997. – ISSN 0040‐0262.Cladistic relationships among Gesneriaceae and related families are investigated using ndhF sequence data, to establish the affinity of three genera whose familial placement was uncertain on the basis of morphological evidence alone. A first analysis, including 18 outgroup species from the Buddlejaceae, Scrophulariaceae, Bignoniaceae, and Acanthaceae resulted in eleven most‐parsimonious trees of 5740 steps each. Recent classifications had placed Cyrtandromoea in Scrophulariaceae or Gesneriaceae, Titanotrichum as a monogeneric tribe in Gesneriaceae, and Sanango in either Scrophulariaceae, Gesneriaceae, Loganiaceae, or Buddlejaceae, Sequence data from the chloroplast ndhF gene indicate that they are Gesneriaceae: Cyrtandromoea belongs to the Klugieae, the monogeneric Titanotricheae are perhaps sister to the remainder of the Cyrtandroideae, and Sanango is placed in the Gesnerieae as was predicted by recent morphological and chemical analyses.