Phylogeny and biogeography of Apiaceae tribe Oenantheae inferred from nuclear rDNA ITS and cpDNA psbI–5′trnK(UUU) sequences, with emphasis on the North American Endemics clade

Botany ◽  
2008 ◽  
Vol 86 (9) ◽  
pp. 1039-1064 ◽  
Author(s):  
Stephen R. Downie ◽  
Deborah S. Katz-Downie ◽  
Feng-Jie Sun ◽  
Chang-Shook Lee
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Intergenic Spacers ◽  
Rdna Its ◽  
The North

Intergeneric phylogenetic relationships within Apiaceae tribe Oenantheae were investigated using sequence data from the chloroplast DNA psbI–5′trnK(UUU) and nuclear ribosomal DNA internal transcribed spacer regions. One hundred and thirty-one accessions were examined, representing all 17 genera of the tribe and approximately one-half of its species. The cpDNA region includes four intergenic spacers and the rps16 intron and these noncoding loci were analyzed separately to assess their relative utility for resolving relationships. Separate maximum parsimony analyses of the entire psbI–5′trnK(UUU) and ITS regions, each with and without scored indels, yielded concordant trees. Phylogenies derived from maximum parsimony, Bayesian, or maximum likelihood analyses of combined chloroplast and nuclear DNA sequences for 82 accessions were highly resolved, well supported, and consistent. Among the five noncoding loci examined, the trnQ(UUG)–5′rps16 and 3′rps16–5′trnK(UUU) intergenic spacers are the most variable, with the latter contributing the greatest total number of parsimony informative characters relative to its size. The North American genera Atrema , Cynosciadium , Daucosma , Limnosciadium , Neogoezia , Oxypolis , Ptilimnium , and Trepocarpus ally with the western hemispheric and Australasian genus Lilaeopsis in a strongly supported North American Endemics clade that is a sister group to a clade composed primarily of Old World taxa ( Berula sensu lato, Cryptotaenia , Helosciadium , and Sium ). Oxypolis and Ptilimnium are not monophyletic, with the rachis-leaved members of each comprising a clade separate from their compound-leaved congeners. Dispersal-vicariance analysis suggests that the ancestors of the North American Endemics clade probably originated in Canada and the USA or in a broader ancestral area including Mexico and South America.

Phylogenetic relationships within Cicuta (Apiaceae tribe Oenantheae) inferred from nuclear rDNA ITS and cpDNA sequence data

2006 ◽  
Vol 84 (3) ◽  
pp. 453-468 ◽  
Author(s):  
Chang-Shook Lee ◽  
Stephen R. Downie
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Distinct Species ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Rdna Its ◽  
The North

The genus Cicuta (Apiaceae tribe Oenantheae Dumort.) is the most virulently poisonous group of flowering plants native to the north temperate zone. A recent treatment recognized four species ( C. bulbifera L., C. douglasii (DC.) J.M. Coult. & Rose, C. maculata L., and C. virosa L.), with C. maculata divided into four varieties. We present results of phylogenetic analyses of the nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) locus and the region bounded by the chloroplast genes psbI and trnK 5′ exon to determine taxonomic limits and relationships among these taxa, and to assess the taxonomic status of C. douglasii, a polyploid thought to be derived from C. maculata and C. virosa. Cicuta bulbifera and C. virosa are each resolved as monophyletic, the latter is a sister group to all other species. Discordance between the ITS- and plastid-derived phylogenies and lack of resolution in the ITS trees preclude unequivocal hypotheses of relationship; all trees do suggest, however, that the allotetraploid C. douglasii is polyphyletic and possibly polytopic, with all examined accessions but one nested within C. maculata. This single outstanding accession is from California and, pending further study, might warrant recognition as a distinct species. The diploid C. bulbifera may also be of hybrid origin, as revealed by significant discordance between data sets. Within C. maculata, only the western North American var. angustifolia Hook. is resolved in the ITS trees. In the cpDNA trees, C. maculata var. angustifolia comprises a strongly supported clade with C. maculata var. bolanderi (S. Watson) G.A. Mulligan and C. douglasii, both of primarily western North American distribution. The eastern North American taxa, C. maculata vars. maculata and victorinii (Fernald) B. Boivin, also comprise a clade, sister group to C. bulbifera.

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

Phylogeny, diversity, and species delimitation of the North American Round-Nosed Minnows (Teleostei: Dionda), as inferred from mitochondrial and nuclear DNA sequences

2012 ◽  
Vol 62 (1) ◽  
pp. 427-446 ◽  
Author(s):  
Susana Schönhuth ◽  
David M. Hillis ◽  
David A. Neely ◽  
Lourdes Lozano-Vilano ◽  
Anabel Perdices ◽  
...  
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Species Delimitation ◽  
Nuclear Dna ◽  
The North

scholarly journals Molecular systematics of western North American cyprinids (Cypriniformes: Cyprinidae)

Zootaxa ◽  
2012 ◽  
Vol 3586 (1) ◽  
pp. 281 ◽  
Author(s):  
SUSANA SCHÖNHUTH ◽  
DENNIS K. SHIOZAWA ◽  
THOMAS E. DOWLING ◽  
RICHARD L. MAYDEN
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Nuclear Dna ◽  
Modern Science ◽  
Sister Group ◽  
Molecular Data ◽  
Generic Level ◽  
Natural Classification ◽  
Extant Species ◽  
Group Relationships

The phylogenetic or evolutionary relationships of species of Cypriniformes, as well as their classification, is in a era offlux. For the first time ever, the Order, and constituent Families are being examined for relationships within aphylogenetic context. Relevant findings as to sister-group relationships are largely being inferred from analyses of bothmitochondrial and nuclear DNA sequences. Like the vast majority of Cypriniformes, due to an overall lack of anyphylogenetic investigation of these fishes since Hennig’s transformation of the discipline, changes in hypotheses ofrelationships and a natural classification of the species should not be of surprise to anyone. Basically, for most taxa noproperly supported phylogenetic hypothesis has ever been done; and this includes relationships with reasonable taxonand character sampling of even families and subfamilies. As such, like others, many western North American cyprinidgenera have had a controversial taxonomic and systematic history.Our effort to better understand the evolutionary history of this artificial geographic grouping of species (Western)surveyed taxa and characters broadly. We analyzed 127 taxa (71 species) from 36 genera, including representative taxafrom all 22 western genera hypothesized to form the Western Clade sensu Coburn and Cavender (1992). Our evaluationalso included additional sampling from a heterogeneous array of species from the western genera Algansea, Gila,Lepidomeda, Ptychocheilus and Siphateles. Resulting phylogenetic inferences, based on one mitochondrial and threenuclear genes (mtDNA: cytb; nDNA: Rag1, Rhod, S7), consistently resolved a well-supported Western Clade, but oneinclusive of Chrosomus erythrogaster. This taxon, always formed the sister group to the extant species of Gila plus 10other western genera. Our Western Clade is qualitatively different from that of prior studies and does not include thegenera Agosia, Algansea, Iotichthys, Lepidomeda, Meda, Mylocheilus, Plagopterus, Pogonichthys, Rhinichthys, Tiarogaor Yuriria. All of these taxa were, however, included in Coburn and Cavender´s (1992) Western Clade. Our broader-scalesurvey and increased character sampling were always resolved these latter taxa within one of two different major clades:the OPM Clade (sensu Mayden 1989) and the Creek Chub—Plagopterin Clade (sensu Simons et al. 2003). Ourhypothesized Western Clade places Orthodon sister to a Western Chub-Pikeminnow Clade also inclusive of Acrocheilus,Eremichthys, Gila, Hesperoleucus, Lavinia, Moapa, Mylopharodon, Ptychocheilus, Relictus and Siphateles. The lattertaxa have traditionally been recognized at the generic level, simply on the basis of their morphological distinctivenessand not on the basis of a phylogenetic evaluation of relationships. Composition of our Western Chub-Pikeminnow Cladealso reveals genetic divergences between species of some genera (Gila, Ptychocheilus, Siphateles) comparable to geneticdivergences documented between genera within the Western Clade. Relationships for these 10 genera also highlighttaxonomic inconsistencies relative to recent phylogenetic analysis and, in some cases, are in need of focused attentionusing morphology or additional molecular data to test relationships that will eventually establish a stable classification.Some of these genera are clearly unnatural relative to other genera and their classification or ranking is an obligatory change in modern science of phylogenetics.

A molecular phylogeny of the subfamily Arundinoideae (Poaceae) based on sequences of rDNA

1998 ◽  
Vol 11 (1) ◽  
pp. 41 ◽  
Author(s):  
C. Hsiao ◽  
S. W. L. Jacobs ◽  
N. P. Barker ◽  
N. J. Chatterton
Keyword(s):  
New Zealand ◽  
Molecular Phylogeny ◽  
Sequence Data ◽  
Sister Group ◽  
The Other ◽  
Its Sequence ◽  
South American ◽  
Rdna Its ◽  
The North ◽  
Poaceae Family

Phylogenetic relationships of the whole Poaceae family inferred from the sequence data of rDNA (ITS) support the hypothesis that the arundinoids are monophyletic, not polyphyletic as previously proposed. The ITS sequence phylogeny of 42 arundinoid species demonstrates an early divergence of the Aristideae and three major groupings, corresponding loosely to the tribes Aristideae, Arundineae and Danthonieae. The Arundineae are resolved into two paraphyletic clades. In one clade, Arundo, Monachather, and Dregeochloa are the sister group to Amphipogon and Diplopogon. In the other clade, Phragmites, Molinia, Gynerium, Thysanolaena, Spartochloa, and Cyperochloa are the sister group to Eriachne and Micraira. Arundo is not closely related to Phragmites. The Danthonieae clade, including taxa from Africa, Australia, New Guinea, New Zealand, the South American Cortaderia, and the North American Danthonia, appears to be monophyletic. However, the genus Merxmuellera is polyphyletic.

scholarly journals Nuclear and mitochondrial DNA sequences from two Denisovan individuals

2015 ◽  
Vol 112 (51) ◽  
pp. 15696-15700 ◽  
Author(s):  
Susanna Sawyer ◽  
Gabriel Renaud ◽  
Bence Viola ◽  
Jean-Jacques Hublin ◽  
Marie-Theres Gansauge ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Nuclear Genome ◽  
Extended Period ◽  
Sister Group ◽  
Morphological Description ◽  
Dna Sequence Data ◽  
Mtdna Sequence

Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.

Nuclear DNA Evolution and Phylogeny of the New World Nine-Primaried Oscines

The Auk ◽  
1988 ◽  
Vol 105 (3) ◽  
pp. 504-515 ◽  
Author(s):  
Anthony H. Bledsoe
Keyword(s):  
Dna Sequences ◽  
Goodness Of Fit ◽  
New World ◽  
Nuclear Dna ◽  
Thermal Dissociation ◽  
Branch Length ◽  
Sister Group ◽  
Single Copy ◽  
The North ◽  
Dissociation Curves

Abstract Estimates of phylogeny were derived from measures of dissimilarity of single-copy nuclear-DNA sequences for 13 species that represent the currently recognized major groups of New World nine-primaried oscines and an outgroup (Passer). The dissimilarity coefficients (delta mode and delta T50H) calculated from thermal dissociation curves of reassociated DNA sequences exhibited the properties of a metric. No statistically significant increase in goodness-of-fit of the raw data to a phylogeny estimated from a least-squares analysis of the 13 × 13 matrix of distances was achieved when the lengths of sister branches were allowed to vary. "Jackknife" and negative branch-length analyses identified unstable stems that resulted from non-additivity caused in part by measurement error. Such stems were collapsed to produce a more robust topology, which served as the basis for estimating the positions of taxa not included in the 13 × 13 matrix. The clade that subsumed several "typical" tanagers (e.g. Tachyphonus rufus) also included Sicalis luteola and Diuca diuca (usually allied with the North American emberizine sparrows); Cyanerpes cyaneus, two species of Diglossa, and Coereba flaveola (often split among several major groups); and Tersina viridis, Catamblyrhynchus diadema, and Nephelornis oneilli (whose affinities are often considered uncertain). This "tanager" clade and its sister group, the cardinals (represented by Cardinalis cardinalis), together formed one fork of a trichotomy. Several emberizine sparrows (e.g. Pooecetes gramineus) formed the second fork, and wood-warblers (e.g. Dendroica striata) and New World orioles (e.g. Psarocolius angustifrons) formed the third. The chaffinches (represented by Fringilla coelebs) and several cardueline finches (e.g. Carduelis pinus) together formed the sister group of the other New World nine-primaried oscines included in the study. This phylogeny implies that convergence in feeding specializations among lineages is more extensive than traditional arrangements of the assemblage would suggest.

Phylogeny of Braya and Neotorularia (Brassicaceae) based on nuclear ribosomal internal transcribed spacer and chloroplast trnL intron sequences

2004 ◽  
Vol 82 (3) ◽  
pp. 376-392 ◽  
Author(s):  
Suzanne I Warwick ◽  
Ihsan A Al-Shehbaz ◽  
Connie Sauder ◽  
James G Harris ◽  
Marcus Koch
Keyword(s):  
North American ◽  
Maximum Parsimony ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
Its Sequences ◽  
Evolutionary Relationships ◽  
Trnl Intron ◽  
The North

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast trnL intron were used to examine the evolutionary relationships and generic delimitations of Braya, Neotorularia, Dichasianthus, and Sisymbriopsis. Several species, especially the North American - Asian Braya (= Neotorularia) humilis (C.A. Mey.) B.L. Rob., were previously assigned to more than one genus. Sequence data were obtained from all Braya species, except Braya pilosa Hook., seven species of Neotorularia, one of Dichasianthus, and two of Sisymbriopsis. Maximum parsimony analyses showed a poly phyletic origin for Neotorularia, with the genus split into three or four major clades. For both the ITS and trnL sequence data, three species (Neotorularia brachycarpa (Vassilcz.) Hedge & J. Léonard, Neotorularia gamosepala (Hedge) O'Kane & Al-Shehbaz, and Neotorularia humilis (C.A. Mey.) Hedge & J. Léonard) fell within the Braya clade; Neotorularia korolkowii (Regel & Schmalh.) Hedge & J. Léonard formed a separate clade with Dichasianthus subtilissimus (Popov) Ovcz. & Yunussov, while Neotorularia torulosa (Desf.) Hedge & J. Léonard, Neotorularia contor tuplicata (Stephan ex Willd.) Hedge & J. Léonard, Neotorularia dentata (Freyn & Sint.) Hedge & J. Léonard, and Neotorularia tetracmoides (Boiss. & Hausskn.) Hedge & J. Léonard formed either one clade (trnL data) or two clades (ITS data). Sisymbriopsis was not monophyletic, although ITS and trnL data showed a weakly supported relationship between Sisymbriopsis mollipila (Maxim.) Botsch. and one of the Neotorularia clades. Except for Braya forrestii W.W. Sm., which is well supported as sister to the remainder of the Braya clade (ITS data), ITS and trnL sequences showed poor resolution within Braya. Additive ITS sequences indicated allopolyploid origins for Braya fernaldii Abbe, Braya longii Fernald, and three accessions of Braya glabella Richardson (all species with 2n = 56). Morphology and molecular data strongly suggest expanding Braya to include N. humilis, N. brachycarpa, and N. gamosepala; delimiting Neotorularia to include N. torulosa, N. contortuplicata, N. dentata, N. korolkowii, N. tetracmoides, D. subtilissimus, and S. mollipila; and revising Sisymbriopsis.Key words: Braya, Neotorularia, Dichasianthus, Sisymbriopsis, ITS, trnL, Brassicaceae.

Relationships of North American members of Rhodiola (Crassulaceae)

Botany ◽  
2014 ◽  
Vol 92 (12) ◽  
pp. 901-910 ◽  
Author(s):  
Joel P. Olfelt ◽  
William A. Freyman
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Phylogenetic Analyses ◽  
Black Hills ◽  
Trnl Intron ◽  
The North ◽  
Alpine Habitats ◽  
Rare And Endangered ◽  
Chloroplast Dna Sequences ◽  
Rhodiola Integrifolia

Taxa of Rhodiola L. (Crassulaceae) generally grow in arctic or alpine habitats. Some Rhodiola species are used medicinally, one taxon, Rhodiola integrifolia Raf. subsp. leedyi (Rosend. & J.W.Moore) Moran, (Leedy’s roseroot), is rare and endangered, and the group’s biogeography in North America is intriguing because of distributional disjunctions and the possibility that Rhodiola rhodantha (A.Gray) H.Jacobsen (2n = 7II) and Rhodiola rosea L. (2n = 11II) hybridized to form Rhodiola integrifolia Raf. (2n = 18II). Recent studies of the North American Rhodiola suggest that the group’s current taxonomy is misleading. We analyzed nuclear and chloroplast DNA sequences (internal transcribed spacer (ITS), trnL intron, trnL–trnF spacer, trnS–trnG spacer) from the North American Rhodiola taxa. We combined our data with GenBank sequences from Asian Rhodiola species, performed parsimony, maximum likelihood (ML), and Bayesian phylogenetic analyses, and applied a Bayesian clock model to the ITS data. Our analyses reveal two major Rhodiola clades, suggest that hybridization between R. rhodantha and R. rosea lineages was possible, show two distinct clades within R. integrifolia, and demonstrate that a Black Hills, South Dakota, Rhodiola population should be reclassified as Leedy’s roseroot. We recommend that R. integrifolia be revised, and that the Black Hills Leedy’s roseroot population be managed as part of that rare and endangered taxon.

A SYSTEMATIC REVIEW OF THE NORTH AMERICAN SPECIES OF THE OREODYTES ALASKANUS CLADE (COLEOPTERA: DYTISCIDAE: HYDROPORINAE)

1993 ◽  
Vol 125 (5) ◽  
pp. 847-867 ◽  
Author(s):  
Yves Alarie
Keyword(s):  
Systematic Review ◽  
North American ◽  
Sister Group ◽  
North American Species ◽  
Abdominal Sternite ◽  
The North ◽  
Subjective Synonym

AbstractNorth American members of the Oreodyies alaskanus clade are revised. The species O. productotruncatus (Hatch) and O. recticollis (Fall) are recognized as valid and those names are removed from junior synonymy with O. alaskanus (Fall.). Oreodytes leechi Zimmerman is considered a new junior subjective synonym of O. recticollis. Lectotype designations are provided for O. alaskanus and O. recticollis. Palaearctic O. dauricus (Motschulsky) is included within the O. alaskanus clade whose members are characterized by the protibia having the inner margin sinuate and strongly narrowed proximally, Oreodytes kanoi Kamiya, from Japan, is suggested as the sister-group of members of the O. alaskanus clade based on the shared presence in the female of a last abdominal sternite with an emargination at the apex.

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