scholarly journals A Phylogenetic Analysis of Salix (Salicaceae) Based on matK and Ribosomal DNA Sequence Data

2010 ◽  
Vol 2010 ◽  
pp. 1-12 ◽  
Author(s):  
T. M. Hardig ◽  
C. K. Anttila ◽  
S. J. Brunsfeld
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Lineage Sorting ◽  
Data Set ◽  
Infrageneric Classification ◽  
Dna Sequence Data ◽  
Phylogenetic Hypotheses ◽  
High Degree

The genus Salix has proven a fertile taxon for a host of evolutionary and ecological studies, yet much work remains in the development of a definitive phylogenetic context for those studies. We performed phylogenetic analyses, using both maximum likelihood and maximum parsimony techniques, of chloroplast-encoded matK and nuclear-encoded ribosomal DNA (rDNA) gene sequences, gathered from specimens deemed representative of the existing subgeneric classification, with the objective of identifying and elaborating the phylogenetic relationships within Salix. Comparisons between the two phylogenetic hypotheses indicate a high degree of polyphyly in the matK-based phylogeny. This we attribute to the effects of hybridization, introgression, and lineage sorting. Comparisons with previous molecule-based phylogenetic hypotheses indicate a fair degree of congruence and all are unanimous in placing Chosenia arbutifolia within the genus Salix. The phylogenetic analysis of our ITS data set has produced results that generally support the most-recent infrageneric classification.

Traditional Infrageneric Classification of Gymnopilus Is Not Supported by Ribosomal DNA Sequence Data

Mycologia ◽  
2003 ◽  
Vol 95 (6) ◽  
pp. 1204 ◽  
Author(s):  
Laura Guzman-Davalos ◽  
Gregory M. Mueller ◽  
Joaquin Cifuentes ◽  
Andrew N. Miller ◽  
Anne Santerre
Keyword(s):  
Dna Sequence ◽  
Ribosomal Dna ◽  
Sequence Data ◽  
Infrageneric Classification ◽  
Dna Sequence Data ◽  
Ribosomal Dna Sequence

Traditional infrageneric classification ofGymnopilusis not supported by ribosomal DNA sequence data

Mycologia ◽  
2003 ◽  
Vol 95 (6) ◽  
pp. 1204-1214 ◽  
Author(s):  
Laura Guzmán-Dávalos ◽  
Gregory M. Mueller ◽  
Joaquín Cifuentes ◽  
Andrew N. Miller ◽  
Anne Santerre
Keyword(s):  
Dna Sequence ◽  
Ribosomal Dna ◽  
Sequence Data ◽  
Infrageneric Classification ◽  
Dna Sequence Data ◽  
Ribosomal Dna Sequence

Rhytidhysteron mangrovei (Hysteriaceae), a new species from mangroves in Phetchaburi Province, Thailand

Phytotaxa ◽  
2019 ◽  
Vol 401 (3) ◽  
pp. 166 ◽  
Author(s):  
VINIT KUMAR ◽  
RATCHADAWAN CHEEWANGKOON ◽  
KASUN M. THAMBUGALA ◽  
GARETH E.B. JONES ◽  
RASHIKA S. BRAHMANAGE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Mangrove Forests ◽  
Morphological Comparison ◽  
Dna Sequence Data ◽  
Mangrove Tree ◽  
A New Species

During an investigation of micro-fungi inhabiting mangrove forests, a new species of Rhytidhysteron was collected and isolated from dead twigs of a mangrove tree. Rhytidhysteron mangrovei sp. nov. is introduced, described, illustrated and compared with accepted species in the genus. Morphological comparison based on the size of exciple, the appearance of ascomata and ascospore septations and size as well as the multi-gene phylogenetic analyses based on LSU, ITS and TEF DNA sequences support its establishment in Rhytidhysteron. Placement of the genus in Hysteriaceae is also well-supported. In addition, phylogenetic analysis and DNA sequence data indicate that Rhytidhysteron mangrovei is closely related to Rhytidhysteron thailandicum. However, R. mangrovei is morphologically distinct from R. thailandicum, by having a relatively smaller size of exciple and perpendicularly rough-striate ascomata.

scholarly journals Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

2019 ◽  
Author(s):  
Sigrid Liede-Schumann ◽  
Guido W. Grimm ◽  
Nicolai M. Nürk ◽  
Alastair J. Potts ◽  
Ulrich Meve ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Cape Floristic Region ◽  
Rapid Radiation ◽  
Data Set ◽  
Widespread Species ◽  
Dna Sequence Data ◽  
Phylogenetic Affinities

AbstractBackgroundDrosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum together with the highly succulent and species-rich tribe Ruschieae constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution.MethodsUsing chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species represented by multiple accessions of Drosanthemum. A well-curated, geo-referenced occurrence data set comprising the phylogenetically studied and 867 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole.ResultsPhylogenetic inference supports nine clades within Drosanthemum, seven of them group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as (pseudo-) cryptic species. In-depth analyses of sequence patterns in each gene region revealed phylogenetic affinities not obvious in the phylogenetic tree. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are molecular and morphologically diverse. In contrast, less species-rich, molecularly less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest initial rapid radiation generating the main lineages, with some clades showing subsequent diversification.

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.

Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data

Phytotaxa ◽  
2018 ◽  
Vol 376 (6) ◽  
pp. 254 ◽  
Author(s):  
RATIDZAYI TAKAWIRA-NYENYA ◽  
LADISLAV MUCINA ◽  
WARREN M. CARDINAL-MCTEAGUE ◽  
KEVIN R. THIELE
Keyword(s):  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Plastid Dna ◽  
Trnl Intron ◽  
Dna Sequence Data ◽  
Molecular Phylogenetic ◽  
Phylogenetic Hypotheses ◽  
Generic Description

The evolutionary history of the dracaenoid genera Dracaena and Sansevieria (Asparagaceae, Nolinoideae) remains poorly resolved, despite long-recognised issues with their generic boundaries and increased attention paid by both horticulturalists and taxonomists. In this study we aim to: (1) elucidate evolutionary relationships within and between Dracaena and Sansevieria using molecular phylogenetic inference of both nuclear (nDNA) and plastid (cpDNA) markers, (2) examine the infrageneric classifications of each genus, and (3) revise the circumscription of the dracaenoids in light of morphological and phylogenetic evidence. In total, we sampled 21 accessions of Dracaena (ca. 19 species), 27 accessions of Sansevieria (ca. 26 species), and six outgroup taxa. Phylogenetic analyses were based on nucleotide sequences of two non-coding plastid DNA regions, the trnL-F region (trnL intron and trnL-trnF intergenic spacer) and rps16 intron, and the low-copy nuclear region At103. Phylogenetic hypotheses were constructed using maximum parsimony, maximum likelihood, and Bayesian inference. Individual datasets were analysed separately and, after testing for congruence, as combined datasets. We recovered instances of soft incongruence between nDNA and cpDNA datasets in Sansevieria, but general trends in the dracaenoids were congruent, although often poorly supported or resolved. The dracaenoids constitute a strongly supported monophyletic group. Dracaena was resolved as a paraphyletic grade embedded with two clades of Sansevieria, a primary clade comprising most species, and a secondary clade including S. sambiranensis, a distinctive species from Madagascar. The backbone of our phylogeny was only resolved in nDNA analyses, but combined analyses recovered strongly supported species groups. None of the previous infrageneric classifications were supported by our phylogeny, and biogeographic groupings were frequently more significant than morphology. More work is needed to resolve internal relationships in the dracaenoids, but we support a recent proposal to recognise a broadened circumscription of Dracaena that includes Sansevieria. We provide a generic description for the recircumscribed Dracaena and new combinations for several species of Sansevieria in Dracaena.

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.

The phylogenetic and taxonomic position of Lilaeopsis (Apiaceae), with notes on the applicability of ITS sequence data for phylogenetic reconstruction

2002 ◽  
Vol 15 (2) ◽  
pp. 181 ◽  
Author(s):  
Gitte Petersen ◽  
Ole Seberg ◽  
Sidsel Larsen
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Its Sequences ◽  
Its Sequence ◽  
Dna Sequence Data ◽  
Coding Regions ◽  
Phylogenetic Hypotheses

The relationships of the genusLilaeopsis Greene have been difficult to determine primarily due to its simple morphology with entire, linear to spathulate leaves, simple umbels and lack of carpophore. Consequently, the genus has been referred to both Hydrocotyloideae and Apioideae. DNA sequence data from different genes (rbcL and matK) and non-coding regions (rpoC1 intron and ITS) were explored in order to determine the phylogenetic relationships of Lilaeopsis. Separate and combined analyses of rpoC1 intron, rbcL and matK data give almost congruent results with respect to a clade including Lilaeopsis. The three species of Lilaeopsis included in the analyses form a monophyletic group within the Oenanthe clade and hence belong to the Apioideae. Presently, the Mexican genus Neogoezia Hemsl. is considered its most likely sister group. Optimisation alignment of the ITS sequence data results in widely different phylogenetic hypotheses, but on the basis of congruence tests, two very similar trees can be selected. These trees are, however, incongruent with the trees obtained from analyses of the chloroplast sequences. As alignment of the ITS sequences is problematic even within the Oenanthe clade, the reliability of phylogenies on the basis of ITS data of higher taxonomic levels in the Apiaceae is questioned. However, for phylogenetic analysis within Lilaeopsis ITS sequences may prove useful and unproblematic.

scholarly journals Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

2021 ◽  
Vol 9 (3) ◽  
pp. 666
Author(s):  
Niccolò Forin ◽  
Alfredo Vizzini ◽  
Federico Fainelli ◽  
Enrico Ercole ◽  
Barbara Baldan
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Illumina Miseq ◽  
Botanical Garden ◽  
Molecular Study ◽  
Its2 Sequence ◽  
Type Specimens ◽  
Its1 Sequence ◽  
Dna Sequence Data ◽  
Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

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