Assessing the usefulness of histone H3, U2 snRNA and 28S rDNA in analyses of polychaete relationships

1999 ◽  
Vol 47 (5) ◽  
pp. 499 ◽  
Author(s):  
S. Brown ◽  
G. Rouse ◽  
P. Hutchings ◽  
D. Colgan
Keyword(s):  
Maximum Parsimony ◽  
Sequence Data ◽  
Histone H3 ◽  
28S Rdna ◽  
Maximum Parsimony Analysis ◽  
Data Sets ◽  
Data Set ◽  
U2 Snrna ◽  
Dna Sequence Data ◽  
Combined Data

DNA sequence data from for histone H3 (34 species), U2 snRNA (34 species) and two segments (D1 and D9–10 expansion regions) of 28S rDNA (28 and 26 species, respectively) have been collected to investigate the relationships of polychaetes. Representatives of all of the major morphologically identified clades were used, as well as members of the Sipuncula, Echiura, Turbellaria, Clitellata and Siboglinidae (formerly the phyla Pogonophora and Vestimentifera). Maximum parsimony analyses of the separate data sets gave conflicting results and none conformed closely to previous results based on morphology. Instead each data set provided corroboration of a few of the morphological groupings, usually pairing, though inconsistently, members of the same family. Higher groupings proposed on morphological grounds were rarely recovered. Maximum parsimony analysis of the combined data, excluding areas of uncertain alignment, recovered some morphological groupings such as Cirratulidae, Terebellidae, scale worms and eunicimorphs, and did not significantly contradict others. However, some expected groupings were not recovered. Surprisingly, the fanworms (Sabellidae and Serpulidae) were not shown as sister taxa, and monophyly of Phyllodocida, a morphologically well corroborated clade, required four more steps than most parsimonious trees. Aciculata was not seen in our analyses, although it was the most strongly supported large clade in Rouse and Fauchald (1997, Cladistics and polychaetes. Zoologica Scripta 26, 138–204). Trees constrained to show Aciculata as monophyletic were 18 steps longer than the most parsimonious trees. If trees are rooted on sipunculans rather than the nematode, Aciculata is nearly recovered, being rendered paraphyletic by the inclusion of the sister-pair of Oweniidae and Chaetopteridae. As suggested by some recent morphological and molecular analyses, Siboglinidae and Clitellata may well have sister groups among polychaetes. The morphologically aberrant Sternaspidae are closest to members of Terebellida in the present analyses, supporting the placement of Rouse and Fauchald. Interesting results deserving further assessment concern the placement of Chaetopteridae, Oweniidae and Sipuncula.

Phylogenetic relationships within the Terebellomorpha

2001 ◽  
Vol 81 (5) ◽  
pp. 765-773 ◽  
Author(s):  
D.J. Colgan ◽  
P.A. Hutchings ◽  
S. Brown
Keyword(s):  
Dna Sequence ◽  
Additional Data ◽  
Sequence Data ◽  
Histone H3 ◽  
28S Rdna ◽  
Maximum Parsimony Tree ◽  
U2 Snrna ◽  
Dna Sequence Data ◽  
Deep Waters ◽  
Parsimony Tree

Terebellomorpha is a clade of predominantly tube-dwelling polychaetes, some of whose species are very abundant and whose habitats range from shallow to very deep waters. The group contains five families (Terebellidae, Ampharetidae, Pectinariidae, Trichobranchidae and Alvinellidae). This study of their inter-relationships uses DNA sequence data from five gene segments. Including outgroups, sequences were available for 15 species for 15 U2 snRNA, 14 for Histone H3, 23 for the D1 expansion region of 28S rDNA, 15 for the D9-10 region of 28S rDNA and 17 for subunit I of cytochrome oxidase. Outgroups included representatives of the polychaete families Cirratulidae, Sabellidae and Siboglinidae, and the clitellate Lumbricus. These sequences include eight GenBank entries for 28S D1 and one for CO1.Generally, and in all analyses restricted to the data collected in this laboratory, but including all of these, Terebellomorpha is monophyletic. Within Terebellomorpha, the single maximum parsimony tree indicates that Alvinellidae (all data from GenBank) belongs to a clade with Terebellidae and some Trichobranchidae, contradicting morphological expectations. Terebellidae is paraphyletic with respect to Trichobranchus, this being associated with the subfamily Thelepodinae. The second trichobranchid genus Terebellides (for which only 28S D1 data is available from GenBank) is topologically very distinct to Trichobranchus. Additional data are needed to establish the family's monophyly. Also within Terebellidae, subfamily Terebellinae is paraphyletic with respect to Polycirrinae, supporting the suggestion that this subfamily's morphological simplicity is derived.

Combined molecular and morphological phylogeny of Ephemerellinae (Ephemerellidae: Ephemeroptera), with remarks about classification

Zootaxa ◽  
2009 ◽  
Vol 1991 (1) ◽  
pp. 28-42 ◽  
Author(s):  
T. HEATH OGDEN ◽  
JONATHAN T. OSBORNE ◽  
LUKE M. JACOBUS ◽  
MICHAEL F. WHITING
Keyword(s):  
Morphological Analysis ◽  
Sequence Data ◽  
Histone H3 ◽  
Morphological Characters ◽  
Morphological Data ◽  
Rdna Genes ◽  
Dna Sequence Data ◽  
Extant Genus ◽  
Species Groups ◽  
Combined Data

This study represents the first combined molecular and morphological analysis for the mayfly family Ephemerellidae (Ephemeroptera), with a focus on the relationships of genera and species groups of the subfamily Ephemerellinae. The phylogeny was constructed based on DNA sequence data from 3 nuclear (18S rDNA, 28S rDNA, histone H3) and 2 mitochondrial (12S rDNA, 16S rDNA) genes, and 23 morphological characters. Taxon sampling for Ephemerellidae included exemplars from all 25 extant genus groups and additional representatives from those genera with the highest diversity. Ephemerellidae appears to consist of three major clades. Ephemerella, the largest genus of Ephemerellidae, and Serratella were not supported as monophyletic, and each had representatives in two of the three major clades. However, the genera Drunella and Cincticostella were supported as monophyletic. Lineages strongly supported as monophyletic include a grouping of the Timpanoginae genera Timpanoga, Dannella, Dentatella and Eurylophella, and groupings of the Ephemerellinae genera Torleya, Hyrtanella and Crinitella and the genera Kangella, Uracanthella and Teloganopsis. The placement of the Timpanoginae genus Attenella fell within Ephemerellinae, based on molecular and combined data, but it grouped with other Timpanoginae based on morphological data alone. Further study and analysis of Ephemerellidae morphology is needed, and classification should be revised, if it is to reflect phylogenetic relationships.

scholarly journals Mitochondrial Evidence on the Phylogenetic Position of Caecilians (Amphibia: Gymnophiona)

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 765-775
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Tandem Repeats ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Maximum Parsimony Analysis ◽  
Bootstrap Support ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Data Sets ◽  
Data Set ◽  
Protein Coding

Abstract The complete nucleotide sequence (17,005 bp) of the mitochondrial genome of the caecilian Typhlonectes natans (Gymnophiona, Amphibia) was determined. This molecule is characterized by two distinctive genomic features: there are seven large 109-bp tandem repeats in the control region, and the sequence for the putative origin of replication of the L strand can potentially fold into two alternative secondary structures (one including part of the tRNACys). The new sequence data were used to assess the phylogenetic position of caecilians and to gain insights into the origin of living amphibians (frogs, salamanders, and caecilians). Phylogenetic analyses of two data sets—one combining protein-coding genes and the other combining tRNA genes—strongly supported a caecilian + frog clade and, hence, monophyly of modern amphibians. These two data sets could not further resolve relationships among the coelacanth, lungfishes, and tetrapods, but strongly supported diapsid affinities of turtles. Phylogenetic relationships among a larger set of species of frogs, salamanders, and caecilians were estimated with a mitochondrial rRNA data set. Maximum parsimony analysis of this latter data set also recovered monophyly of living amphibians and favored a frog + salamander (Batrachia) relationship. However, bootstrap support was only moderate at these nodes. This is likely due to an extensive among-site rate heterogeneity in the rRNA data set and the narrow window of time in which the three main groups of living amphibians were originated.

scholarly journals Citrus Black Rot is Caused by Phylogenetically Distinct Lineages of Alternaria alternata

2005 ◽  
Vol 95 (5) ◽  
pp. 512-518 ◽  
Author(s):  
T. L. Peever ◽  
L. Carpenter-Boggs ◽  
L. W. Timmer ◽  
L. M. Carris ◽  
A. Bhatia
Keyword(s):  
Phylogenetic Analysis ◽  
Alternaria Alternata ◽  
Sequence Data ◽  
Brown Spot ◽  
Ecological Niches ◽  
Black Rot ◽  
Data Set ◽  
Dna Sequence Data ◽  
Rough Lemon ◽  
Combined Data

Phylogenetic analysis revealed that isolates of Alternaria alternata causing black rot of citrus were associated with six well-supported evolutionary lineages. Isolates recovered from brown spot lesions on Minneola tangelo, leaf spot lesions on rough lemon, and healthy citrus tissue and noncitrus hosts were related closely to isolates from black-rotted fruit. Phylogenies estimated independently from DNA sequence data from an endopolygalacturonase gene (endoPG) and two anonymous regions of the genome (OPA1-3 and OPA2-1) had similar topologies, and phylogenetic analysis was performed on the combined data set. In the combined phylogeny, isolates from diverse ecological niches on citrus and noncitrus hosts were distributed in eight clades. Isolates from all lineages, regardless of ecological or host association, caused black rot in fruit inoculation assays, demonstrating that small-spored Alternaria isolates associated with different ecological niches on citrus and other plant hosts are potential black rot pathogens. These data also indicated that the fungi associated with black-rotted fruit do not form a natural evolutionary group distinct from other Alternaria pathogens and saprophytes associated with citrus. The use of the name A. citri to describe fungi associated with citrus black rot is not justified and it is proposed that citrus black rot fungi be referred to as A. alternata.

scholarly journals Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1817-1833 ◽  
Author(s):  
Michel C Milinkovitch ◽  
Richard G LeDuc ◽  
Jun Adachi ◽  
Frederic Farnir ◽  
Michel Georges ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Data Sets ◽  
Sperm Whales ◽  
Sister Relationship ◽  
Data Set ◽  
Baleen Whales ◽  
Dna Sequence Data ◽  
Character Weighting

Different phylogenetic analyses of the same genetic data set can yield conflicting results, depending on the choice of parameter settings and included taxa. This is particularly true in studies involving data sets where levels of homoplasy are high and likely to obscure the phylogenetic signal. Filtering of this phylogenetic noise can be attempted, with varying degrees of success, by using different weighting schemes and ingroup/outgroup choices, but it can be difficult to decide objectively which approach is best. Using a cytochrome b data set from cetaceans and artiodactyls, we examined the effects of a suite of parameter settings on the outcome of phylogenetic analyses. We tested 2968 combinations among the seven parameters that most often vary among phylogenetic studies. It is our contention that this sensitivity analysis identifies portions of the multidimensional parameter space where phylogenetic signal is most reliably recovered, and simple rules are given to guide the choice of settings. Portions of this data set have been used in previous studies with conflicting results, namely the monophyly vs. paraphyly of one of the two major recognized cetacean suborders, the toothed whales. This analysis strongly supports the sister relationship between sperm whales and baleen whales.

Generic Delimitations and Relationships of the Cape Genera Capnophyllum, Dasispermum, and Sonderina, the North African Genera Krubera and Stoibrax, and a New Monotypic Genus of the Subfamily Apioideae (Apiaceae)

2009 ◽  
Vol 34 (3) ◽  
pp. 580-594 ◽  
Author(s):  
Anthony R. Magee ◽  
Ben-Erik van Wyk ◽  
Patricia M. Tilney ◽  
Stephen R. Downie
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Monotypic Genus ◽  
North African ◽  
African Species ◽  
Dna Sequence Data ◽  
The North ◽  
Relationship Of

Generic circumscriptions and phylogenetic relationships of the Cape genera Capnophyllum, Dasispermum, and Sonderina are explored through parsimony and Bayesian inference analyses of nrDNA ITS and cpDNA rps16 intron sequences, morphology, and combined molecular and morphological data. The relationship of these genera with the North African genera Krubera and Stoibrax is also assessed. Analyses of both molecular data sets place Capnophyllum, Dasispermum, Sonderina, and the only southern African species of Stoibrax (S. capense) within the newly recognized Lefebvrea clade of tribe Tordylieae. Capnophyllum is strongly supported as monophyletic and is distantly related to Krubera. The monotypic genus Dasispermum and Stoibrax capense are embedded within a paraphyletic Sonderina. This complex is distantly related to the North African species of Stoibrax in tribe Apieae, in which the type species, Stoibrax dichotomum, occurs. Consequently, Dasispermum is expanded to include both Sonderina and Stoibrax capense. New combinations are formalized for Dasispermum capense, D. hispidum, D. humile, and D. tenue. An undescribed species from the Tanqua Karoo in South Africa is also closely related to Capnophyllum and the Dasispermum–Sonderina complex. The genus Scaraboides is described herein to accommodate the new species, S. manningii. This monotypic genus shares the dorsally compressed fruit and involute marginal wings with Capnophyllum, but is easily distinguished by its erect branching habit, green leaves, scabrous umbels, and fruit with indistinct median and lateral ribs, additional solitary vittae in each marginal wing, and parallel, closely spaced commissural vittae. Despite the marked fruit similarities with Capnophyllum, analyses of DNA sequence data place Scaraboides closer to the Dasispermum–Sonderina complex, with which it shares the erect habit, green (nonglaucous) leaves, and scabrous umbels.

A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny 

Phytotaxa ◽  
2014 ◽  
Vol 174 (4) ◽  
pp. 187 ◽  
Author(s):  
Lakshmi Attigala ◽  
Jimmy K. Triplett ◽  
Hashendra-Suvini Kathriarachchi ◽  
Lynn G Clark
Keyword(s):  
Sri Lanka ◽  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Sri Lankan ◽  
Data Set ◽  
Woody Bamboos ◽  
Cpdna Markers ◽  
Combined Data

Kuruna, a new temperate woody bamboo (Poaceae, Bambusoideae, Arundinarieae) genus from Sri Lanka, is recognized based on chloroplast sequence data from five markers (coding: ndhF 3’ end; non-coding: rps16-trnQ, trnC-rpoB, trnD-trnT, trnT-trnL). This genus represents the twelfth major lineage of temperate woody bamboos and is characterized by pachymorph culm bases with short necks, unicaespitose clumps, culm leaf girdles ca. 1 mm wide, usually abaxially hispid culm leaves with non-irritating hairs, persistent foliage leaf sheaths, complete branch sheathing and acute to biapiculate palea apices. Maximum Parsimony, Bayesian Inference and Maximum Likelihood analyses of a combined data set consistently strongly supported the monophyly of this Sri Lankan temperate woody bamboo clade. Although the Kishino-Hasegawa test is unable to reject the alternative hypothesis of monophyly of the Sri Lankan clade plus Bergbambos tessellata from South Africa, Kuruna and Bergbambos are distinguishable by a combination of morphological characters. A few additional cpDNA markers not previously used in phylogenetic analyses of Arundinarieae were tested to evaluate their utility in this taxonomically difficult tribe.

From 18S ribosomal sequence data to evolution of morphology among the fungi

1995 ◽  
Vol 73 (S1) ◽  
pp. 677-683 ◽  
Author(s):  
Mary L. Berbee ◽  
John W. Taylor
Keyword(s):  
Sequence Data ◽  
Morphological Evolution ◽  
Strong Support ◽  
Morphological Characters ◽  
Geological Time ◽  
Data Set ◽  
Dna Sequence Data ◽  
Sequence Of Events ◽  
History Of ◽  
Time Of Divergence

From ribosomal DNA sequence data we can estimate ascomycete relationships, the time of divergence of major ascomycete lineages, and the history of morphological evolutionary change. Groups long accepted by mycologists such as the filamentous ascomycetes with fruiting bodies, (the plectomycetes and pyrenomycetes) are supported by 18S rDNA sequence data. After generating a phylogenetic tree showing relationships, the geological time of divergence of major fungal lineages may be estimated, inferring elapsed time using the calibrated percent substitutions between sequences. Determining the pathway of evolution of morphological characters is more difficult than inferring the relationships among these taxa. To establish the history of morphological evolution, we need accurate trees receiving strong support from our data set. We also need taxa with the intermediate characters to reveal the sequence of events in morphological evolution. Soon, however, we may be able to take a more direct approach to evolution of morphological characters, sequencing the genes that code for the character. Key words: fungus evolution, ascomycete phylogeny.

Combining cross-crystal averaging and MRSAD to phase a 4354-amino-acid structure

2016 ◽  
Vol 72 (2) ◽  
pp. 182-191
Author(s):  
Jason Nicholas Busby ◽  
J. Shaun Lott ◽  
Santosh Panjikar
Keyword(s):  
Radiation Damage ◽  
Model Building ◽  
Data Sets ◽  
Low Resolution ◽  
Data Set ◽  
C Protein ◽  
Large Size ◽  
Anomalous Signal ◽  
Difference Fourier ◽  
Combined Data

The B and C proteins from the ABC toxin complex ofYersinia entomophagaform a large heterodimer that cleaves and encapsulates the C-terminal toxin domain of the C protein. Determining the structure of the complex formed by B and the N-terminal region of C was challenging owing to its large size, the non-isomorphism of different crystals and their sensitivity to radiation damage. A native data set was collected to 2.5 Å resolution and a non-isomorphous Ta6Br12-derivative data set was collected that showed strong anomalous signal at low resolution. The tantalum-cluster sites could be found, but the anomalous signal did not extend to a high enough resolution to allow model building. Selenomethionine (SeMet)-derivatized protein crystals were produced, but the high number (60) of SeMet sites and the sensitivity of the crystals to radiation damage made phasing using the SAD or MAD methods difficult. Multiple SeMet data sets were combined to provide 30-fold multiplicity, and the low-resolution phase information from the Ta6Br12data set was transferred to this combined data set by cross-crystal averaging. This allowed the Se atoms to be located in an anomalous difference Fourier map; they were then used inAuto-Rickshawfor multiple rounds of autobuilding and MRSAD.

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