Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF

2021 ◽  
Author(s):  
Sara Fuentes-Soriano ◽  
Elizabeth A. Kellogg
Keyword(s):  
Sequence Data ◽  
Plastid Dna ◽  
Sister Relationship ◽  
Data Set ◽  
Woody Perennial ◽  
History Of ◽  
Nuclear Its ◽  
Phylogenetic Framework ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis)and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

Teuvoa, a new lichen genus inMegasporaceae(Ascomycota:Pertusariales), includingTeuvoa junipericolasp. nov.

2013 ◽  
Vol 45 (3) ◽  
pp. 347-360 ◽  
Author(s):  
Mohammad SOHRABI ◽  
Steven D. LEAVITT ◽  
Víctor J. RICO ◽  
Mehmet G. HALICI ◽  
Gajendra SHRESTHA ◽  
...  
Keyword(s):  
North America ◽  
Central Asia ◽  
New Genus ◽  
Sequence Data ◽  
Morphological Characters ◽  
Sister Relationship ◽  
New Synonyms ◽  
Nuclear Its ◽  
Relationship Of ◽  
The Relationship

AbstractThe relationship ofAspicilia uxoriswithinMegasporaceaeis assessed within a phylogenetic context. ‘Aspicilia’uxorisand other related species are recovered as sister to the genusLobothallias. str. and described here as a new genus.Teuvoa(Ascomycota,Megasporaceae) is erected based on nuclear ITS and LSU sequence data and morphological characters. In addition toTeuvoa uxoris, a second species,T. junipericola,is added to the new genus based on material collected from North America.Teuvoa junipericola, T. uxorisandT. tibeticaform a group with 8-spored asci, absence of extrolites, rather short-sized conidia and ascospores, lack of a subhypothecial algal layer, and different substratum preferences (on organic substratum) with a sister relationship to genusLobothallias. lat. (AspiciliasubgenusPachyothalliaClauzade & C. Roux). Based on spore measurements of the holotypes,Lecanora ferganensisTomin from central Asia (Kyrgyzstan, Tajikistan and Uzbekistan),Lecanora atrodiscataGintovt, from Tajikistan andLecanora takyroidesDzhur. from Turkmenistan are new synonyms toT. uxoris. A lectotype forLecanora ferganensisis designated, expanding the known distribution ofT. uxorisfrom Algeria, Morocco and Spain, into Central Asia.

Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata)

Zootaxa ◽  
2013 ◽  
Vol 3626 (1) ◽  
pp. 77-93 ◽  
Author(s):  
DAVID W. WEISROCK ◽  
J. ROBERT MACEY ◽  
MASAFUMI MATSUI ◽  
DANIEL G. MULCAHY
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Bootstrap Support ◽  
Phylogenetic Study ◽  
Taxon Sampling ◽  
12S Rrna ◽  
Sister Relationship ◽  
Data Set ◽  
History Of

The salamander family Hynobiidae contains over 50 species and has been the subject of a number of molecular phylo-genetic investigations aimed at reconstructing branches across the entire family. In general, studies using the greatest amount of sequence data have used reduced taxon sampling, while the study with the greatest taxon sampling has used a limited sequence data set. Here, we provide insights into the phylogenetic history of the Hynobiidae using both dense taxon sampling and a large mitochondrial DNA sequence data set. We report exclusive new mitochondrial DNA data of 2566 aligned bases (with 151 excluded sites, of included sites 1157 are variable with 957 parsimony informative). This is sampled from two genic regions encoding a 12S–16S region (the 3’ end of 12S rRNA, tRNAVAl, and the 5’ end of 16S rRNA), and a ND2–COI region (ND2, tRNATrp, tRNAAla, tRNAAsn, the origin for light strand replication—OL, tRNACys, tRNATyr, and the 5’ end of COI). Analyses using parsimony, Bayesian, and maximum likelihood optimality criteria produce similar phylogenetic trees, with discordant branches generally receiving low levels of branch support. Monophyly of the Hynobiidae is strongly supported across all analyses, as is the sister relationship and deep divergence between the genus Onychodactylus with all remaining hynobiids. Within this latter grouping our phylogenetic results identify six clades that are relatively divergent from one another, but for which there is minimal support for their phy-logenetic placement. This includes the genus Batrachuperus, the genus Hynobius, the genus Pachyhynobius, the genus Salamandrella, a clade containing the genera Ranodon and Paradactylodon, and a clade containing the genera Liua and Pseudohynobius. This latter clade receives low bootstrap support in the parsimony analysis, but is consistent across all three analytical methods. Our results also clarify a number of well-supported relationships within the larger Batrachu-perus and Hynobius clades. While the relationships identified in this study do much to clarify the phylogenetic history of the Hynobiidae, the poor resolution among major hynobiid clades, and the contrast of mtDNA-derived relationships with recent phylogenetic results from a small number of nuclear genes, highlights the need for continued phylogenetic study with larger numbers of nuclear loci.

scholarly journals Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽  
2019 ◽  
Vol 83 (2) ◽  
pp. 180-189 ◽  
Author(s):  
Adam W. Ferguson ◽  
Houssein R. Roble ◽  
Molly M. McDonough
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Sister Relationship ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Molecular Phylogenetic ◽  
Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

Molecular phylogenetics of the Onobrychis genus (Fabaceae: Papilionoideae) using ITS and trnL–trnF DNA sequence data

2014 ◽  
Vol 62 (3) ◽  
pp. 235 ◽  
Author(s):  
S. Safaei Chaei Kar ◽  
F. Ghanavati ◽  
M. R. Naghavi ◽  
H. Amirabadi-zade ◽  
R. Rabiee
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Sequence Data ◽  
Group I ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Cultivated Species ◽  
Relationship Of

Onobrychis, comprising more than 130 species, is a genus of the family Fabaceae. At this time, the interspecies relationship of this biologically important genus is still a subject of great discussion and debate. To help resolve this disagreement, we used molecular phylogeny to analyse internal transcribed spacer (ITS) and trnL–trnF sequences of 76 species of Onobrychis. Bayesian interference, maximum parsimony and maximum likelihood analyses of nuclear ITS and plastid trnL–trnF DNA sequence data generated trees with strong posterior probability for two groups: Onobrychis subgen. Sisyrosema (including: Heliobrychis, Hymenobrychis, Afghanicae and Anthyllium sections) along with Laxiflorae section in Group I and Onobrychis subgen. Onobrychis (except Laxiflorae section) in the other (Group II). The Laxiflorae section roots back to the ancestral node for Sisyrosema subgen. O. viciifolia (cultivated species), which is closely associated with O. cyri var. cyri, suggesting that the latter may be a wild progenitor of O. viciifolia. The present study supported the paraphyly of subgenera Onobrychis and Sisyrosema. The study proposed the paraphyletic nature of the sections Onobrychis, Dendrobrychis, Heliobrychis and Hymenobrychis. Together with our molecular phylogenetic analyses we present a review of Onobrychis morphology and discuss and compare our results with those of earlier morphological and molecular phylogenetic analyses.

The invasive coconut mite Aceria guerreronis (Acari: Eriophyidae): origin and invasion sources inferred from mitochondrial (16S) and nuclear (ITS) sequences

2005 ◽  
Vol 95 (6) ◽  
pp. 505-516 ◽  
Author(s):  
D. Navia ◽  
G.J. de Moraes ◽  
G. Roderick ◽  
M. Navajas
Keyword(s):  
Sequence Data ◽  
Common Source ◽  
Aceria Guerreronis ◽  
Dna Sequence Data ◽  
Coconut Mite ◽  
Ocean Region ◽  
Invasion Routes ◽  
History Of ◽  
Nuclear Its ◽  
Production Areas

AbstractOver the past 30 years the coconut mite Aceria guerreronis Keifer has emerged as one of the most important pests of coconut and has recently spread to most coconut production areas worldwide. The mite has not been recorded in the Indo-Pacific region, the area of origin of coconut, suggesting that it has infested coconut only recently. To investigate the geographical origin, ancestral host associations, and colonization history of the mite, DNA sequence data from two mitochondrial and one nuclear region were obtained from samples of 29 populations from the Americas, Africa and the Indo-ocean region. Mitochondrial DNA 16S ribosomal sequences were most diverse in Brazil, which contained six of a total of seven haplotypes. A single haplotype was shared by non-American mites. Patterns of nuclear ribosomal internal transcribed spacer (ITS) variation were similar, again with the highest nucleotide diversity found in Brazil. These results suggest an American origin of the mite and lend evidence to a previous hypothesis that the original host of the mite is a non-coconut palm. In contrast to the diversity in the Americas, all samples from Africa and Asia were identical or very similar, consistent with the hypothesis that the mite invaded these regions recently from a common source. Although the invasion routes of this mite are still only partially reconstructed, the study rules out coconut as the ancestral host of A. guerreronis, thus prompting a reassessment of efforts using quarantine and biological control to check the spread of the pest.

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.

Eritreo-Arabian Affinities of the Socotran Flora as Revealed from the Molecular Phylogeny of Aerva (Amaranthaceae)

2006 ◽  
Vol 31 (3) ◽  
pp. 560-570 ◽  
Author(s):  
Mike Thiv ◽  
Mats Thulin ◽  
Norbert Kilian ◽  
H. Peter Linder
Keyword(s):  
Indian Ocean ◽  
Sequence Data ◽  
Plastid Dna ◽  
Molecular Dating ◽  
Tropical Asia ◽  
Biogeographic Patterns ◽  
Dna Sequence Data ◽  
Biogeographic History ◽  
History Of ◽  
Taxonomic Groups

We investigated the colonization of the Indian Ocean archipelago of Socotra through phylogenetic analysis of Aerva (Amaranthaceae) based on nuclear and plastid DNA sequence data. The biogeographic history of the genus was tracked using ancestral area reconstructions and molecular dating. Three independent colonization lineages from the Eritreo-Arabian subregion of the Sudano-Zambesian Region were revealed: one endemic clade comprising Aerva revoluta / A. microphylla and once within A. lanata and A. javanica. Our results provide further support for the dominance of Eritreo-Arabian affinities in the flora of Socotra, in contrast to more rare affinities to Madagascar, the Mascarenes, southern Africa, and tropical Asia. Our data point towards colonization via dispersal, rather than a vicariance origin of the island elements. The overall biogeographic patterns of Aerva show only limited concordance with other taxonomic groups distributed on Indian Ocean islands.

scholarly journals Molecular phylogeny uncovers an overlooked species in the macrolichen family Parmeliaceae (Ascomycota) from India

2018 ◽  
Author(s):  
Pradeep K. Divakar ◽  
Ana Crespo
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Fungal Species ◽  
Species Boundaries ◽  
Data Set ◽  
Dna Sequence Data ◽  
Distinct Lineage ◽  
Phylogenetic Framework ◽  
Phenotypic Features ◽  
A New Species

Several obligately sexualy reproducing lichen-forming fungal species are disjunctly distributed in pantropical regions. Here, we aim to re-examine species boundaries within the sexually reproducing, disjunctly distributed species, Hypotrachyna intercalanda. We gathered a three-locus DNA sequence data set of Hypotrachyna subgen. Parmelinopsis, especially including the samples from India, and these data were analysed in a phylogenetic framework. Our results show that specimens of H. intercalanda, as currently circumscribed, do not form a monophyletic group but fall into two well-supported independent clades. Morphological and chemical features were re-evaluated. Corroborating with the phenotypic features, the sample recovered in clade 2 occurring in southern India are described as a new species, viz. Hypotrachyna upretii Divakar and A. Crespo sp. nov. Our study adds a further example of a previously overlooked, geographically distinct, lineage that was uncovered using molecular data. Additionally, our study underlines the need of critical reexamination of phenotypic features of samples falling into different clades.

scholarly journals A genome-skimmed phylogeny of a widespread bryozoan family, Adeonidae

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Russell J. S. Orr ◽  
Marianne N. Haugen ◽  
Björn Berning ◽  
Philip Bock ◽  
Robyn L. Cumming ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Mitochondrial Genomes ◽  
Sequence Information ◽  
A Genome ◽  
Ribosomal Operon ◽  
History Of ◽  
Genome Skimming ◽  
Phylogenetic Hypotheses ◽  
Cheilostome Bryozoans

Abstract Background Understanding the phylogenetic relationships among species is one of the main goals of systematic biology. Simultaneously, credible phylogenetic hypotheses are often the first requirement for unveiling the evolutionary history of traits and for modelling macroevolutionary processes. However, many non-model taxa have not yet been sequenced to an extent such that statistically well-supported molecular phylogenies can be constructed for these purposes. Here, we use a genome-skimming approach to extract sequence information for 15 mitochondrial and 2 ribosomal operon genes from the cheilostome bryozoan family, Adeonidae, Busk, 1884, whose current systematics is based purely on morphological traits. The members of the Adeonidae are, like all cheilostome bryozoans, benthic, colonial, marine organisms. Adeonids are also geographically widely-distributed, often locally common, and are sometimes important habitat-builders. Results We successfully genome-skimmed 35 adeonid colonies representing 6 genera (Adeona, Adeonellopsis, Bracebridgia, Adeonella, Laminopora and Cucullipora). We also contributed 16 new, circularised mitochondrial genomes to the eight previously published for cheilostome bryozoans. Using the aforementioned mitochondrial and ribosomal genes, we inferred the relationships among these 35 samples. Contrary to some previous suggestions, the Adeonidae is a robustly supported monophyletic clade. However, the genera Adeonella and Laminopora are in need of revision: Adeonella is polyphyletic and Laminopora paraphyletically forms a clade with some Adeonella species. Additionally, we assign a sequence clustering identity using cox1 barcoding region of 99% at the species and 83% at the genus level. Conclusions We provide sequence data, obtained via genome-skimming, that greatly increases the resolution of the phylogenetic relationships within the adeonids. We present a highly-supported topology based on 17 genes and substantially increase availability of circularised cheilostome mitochondrial genomes, and highlight how we can extend our pipeline to other bryozoans.

scholarly journals X-Ray Observations Of Stellar Flares

1983 ◽  
Vol 71 ◽  
pp. 255-272 ◽  
Author(s):  
Bernhard M. Haisch
Keyword(s):  
Optical Emission ◽  
Light Curves ◽  
Data Set ◽  
Time Resolved ◽  
X Ray ◽  
Uv Emission ◽  
Stellar Flares ◽  
History Of ◽  
Relationship Of ◽  
Lower Limits

ABSTRACTThe history of stellar X-ray flare observations prior to EINSTEIN is reviewed. X-ray light curves as measured by the IPC are then presented for all time resolved flare events discovered as of July 1982 in the EINSTEIN data set. These light curves are analyzed in terms of solar-like loop models to derive densities, temperatures, loop lengths, magnetic field strength lower limits, etc. The failure of the model to adequately represent the observations in the case of the YZ CMi flares is discussed. The relationship of X-ray to optical emission and X-ray to UV emission is considered from both an observational and a theoretical viewpoint. It is concluded that the characterization of a flare by a single, time averaged ratio, Lx /Lopt , is not physically significant.

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