scholarly journals Figs S1-S4

2021 ◽  
Author(s):  
R. Chang
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Species Complex ◽  
Its Region ◽  
Bootstrap Support ◽  
Posterior Probabilities ◽  
Gene Sequences ◽  
Complex Sequences ◽  
Bold Type

Fig. S1. Phylogram obtained from ML analyses of the partial BT and EF gene sequences of the O. clavatum species complex. Sequences obtained in this study are printed in bold type. Maximum-likelihood bootstrap support values (1 000 replicates) above 70 % are indicated at the nodes. Bayesian inference posterior probabilities (above 0.9) are indicated by bold lines at the relevant branches. T = ex-type cultures. Fig. S2. Phylogram obtained from ML analyses of the ITS region and the partial BT gene of the O. ips species complex. Sequences obtained in this study are printed in bold type. Maximum-likelihood bootstrap support values (1 000 replicates) above 70 % are indicated at the nodes. The Bayesian inference posterior probabilities (above 0.9) are indicated by bold lines at the relevant branches. T = ex-type cultures. Fig. S3. Phylogram obtained from ML analyses of the ITS region, and the partial BT and CAL gene sequences of the Sporothrix gossypina species complex. Sequences obtained in this study are printed in bold type. Maximum-likelihood bootstrap support values (1 000 replicates) above 70 % are indicated at the nodes. Bayesian inference posterior probabilities (above 0.9) are indicated by bold lines at the relevant branches. T = ex-type cultures. Fig. S4. Phylogram obtained from ML analyses of the ITS region, and the partial BT and EF gene sequences of Endoconidiophra. Sequences obtained in this study are printed in bold type. Maximum-likelihood bootstrap support values (1 000 replicates) above 70 % are indicated at the nodes. Bayesian inference posterior probabilities (above 0.9) are indicated by bold lines at the relevant branches. T = ex-type cultures.

Towards a monophyletic classification of Lejeuneaceae III: the systematic position of Leiolejeunea

Phytotaxa ◽  
2014 ◽  
Vol 170 (3) ◽  
pp. 187 ◽  
Author(s):  
ALFONS SCHÄFER-VERWIMP ◽  
KATHRIN FELDBERG ◽  
SHANSHAN DONG ◽  
HUUB VAN MELICK ◽  
DENILSON F. PERALTA ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Its Region ◽  
Systematic Position ◽  
Leaf Cell ◽  
Oil Bodies ◽  
Sister Relationship ◽  
First Time

The derived liverwort Leiolejeunea grandiflora was recollected at the type locality in Jamaica after more than 100 years. The characteristics of its oil bodies were described for the first time based on the new collections. Each leaf cell possesses 2-4(-6) rather small, subhomogeneous to very finely segmented, subglobose to ellipsoidal, colorless oil bodies. The plants were either dioicous or autoicous. DNA sequences of two chloroplast regions (trnL-trnF, rbcL) and the nuclear ribosomal ITS region were obtained for two accessions of Leiolejeunea to enable the inference of the phylogenetic relationships of these plants. Based on Bayesian inference of phylogeny as well as maximum parsimony and maximum likelihood analyses of a dataset including 87 representatives of Lejeuneaceae, Leiolejeunea was found as the putative sister to either Echinolejeuneinae or Cheilolejeuneinae. Thus, we propose the new monogeneric subtribe Leiolejeuneinae with relationships to Cheilolejeuneinae and Echinolejeuneinae. The analyses included also one accession of the generitype of Cheilolejeunea, C. decidua [= Cheilolejeunea adnata]. This species was found in a well supported sister relationship with Cystolejeunea. To avoid nomenclatural confusion, we propose a wide genus concept for Cheilolejeunea including Aureolejeunea, Cyrtolejeunea, Cystolejeunea, Evansiolejeunea, Leucolejeunea, and Omphalanthus.

Revisiting the phylogeny and taxonomy of Osmanthus (Oleaceae) including description of the new genus Chengiodendron

Phytotaxa ◽  
2020 ◽  
Vol 436 (3) ◽  
pp. 283-292 ◽  
Author(s):  
YONG-FU LI ◽  
MIN ZHANG ◽  
XIAN-RONG WANG ◽  
STEVEN PAUL SYLVESTER ◽  
QI-BAI XIANG ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
New Genus ◽  
Morphological Character ◽  
Strong Support ◽  
Its Region ◽  
Phylogenetic Placement ◽  
Morphological Patterns

Osmanthus (Oleaceae) is considered one of the most confusing genera with regards to circumscription and phylogenetic placement of taxa within the subtribe Oleinae of Oleaceae, with controversies mainly focused on the attribution of section Leiolea. In the present study, we analyzed 71 samples that represent the broad taxonomic, biogeographic, and morphological patterns in the subtribe Oleinae. Based on concatenation of four plastid genes (trnL-F, trnT-L, trnS-G, and matK) and comparison with the ITS region, Bayesian Inference, Maximum Likelihood and Maximum Parsimony phylogenies were inferred. Morphological character traits and geographical distributions of taxa were also studied. These results provide strong support for the segregation of the Leiolea clade (Osmanthus marginatus, O. matsumuranus and O. minor) of sect. Leiolea from Osmanthus. Therefore, the Leiolea clade is instated as the new genus Chengiodendron, with a taxonomic treatment provided. This study provides a clearer understanding of the phylogenetic relationships of genera in the subtribe Oleinae.

Sanghuangporus vitexicola sp. nov. (Hymenochaetales, Basidiomycota) from tropical Taiwan

Phytotaxa ◽  
2020 ◽  
Vol 475 (1) ◽  
pp. 43-51
Author(s):  
SHENG-HUA WU ◽  
CHIA-LING WEI ◽  
CHIUNG-CHIH CHANG
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Identification Key ◽  
Monophyletic Group ◽  
Pore Surface ◽  
Vitex Negundo ◽  
A New Species

Sanghuangporus vitexicola (Hymenochaetales) is described as a new species based on collections made from Pingtung County, tropical South Taiwan. All studied basidiocarps grew on living trunks of Vitex negundo. This new species is characterized by having perennial, pileate basidiocarps; pore surface yellowish brown, pores 6–8 per mm; context 0.7–1.5 cm thick; setae ventricose to subulate, dark brown, 17–30 × 5–8 μm; basidiospores broadly ellipsoid, brownish, smooth, 4.2–4.8 × 3.2–3.7 μm, with 0.2–0.5 μm thick walls. Maximum likelihood and Bayesian inference phylogenies inferred from the internal transcribed spacer (ITS) region of rDNA indicated that six strains of Sanghuangporus viexicola formed a monophyletic group which is sister to S. zonatus. An identification key to known species of Sanghuangporus is provided.

Towards a monophyletic classification of Lejeuneaceae I: subtribe Leptolejeuneinae subtr. nov.

Phytotaxa ◽  
2014 ◽  
Vol 156 (3) ◽  
pp. 165 ◽  
Author(s):  
JOCHEN HEINRICHS ◽  
ALFONS SCHÄFER-VERWIMP ◽  
ALEKSANDRA CZUMAY ◽  
SHANSHAN DONG ◽  
ARMIN SCHEBEN ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Maximum Parsimony ◽  
Its Region ◽  
Bootstrap Support ◽  
Phylogenetic Position ◽  
Likelihood Methods ◽  
Monophyletic Lineage ◽  
Current Classification ◽  
Maximum Likelihood Methods

We employed sequences of two chloroplast regions (trnL-trnF, rbcL) and the nuclear ribosomal ITS region of seven accessions of Leptolejeunea to explore its phylogenetic position. Maximum parsimony and maximum likelihood analyses led to similar topologies but deeper nodes received good bootstrap support only with maximum likelihood methods. Leptolejeunea formed an early diverging, robust monophyletic lineage within Lejeuneaceae tribe Lejeuneeae. Contrary to earlier belief, it is not closely related to Drepanolejeunea. To amend the current classification of Lejeuneeae into subtribes, we propose Leptolejeuneinae, subtr. nov.

Schoenus (Cyperaceae) is not monophyletic based on ITS nrDNA sequence data

2016 ◽  
Vol 29 (5) ◽  
pp. 265 ◽  
Author(s):  
Paul M. Musili ◽  
Adele K. Gibbs ◽  
Karen L. Wilson ◽  
Jeremy J. Bruhl
Keyword(s):  
Bayesian Inference ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Bootstrap Support ◽  
Nuclear Rdna ◽  
Its Nrdna ◽  
Rdna Sequence Data ◽  
Strong Bootstrap Support ◽  
Lines Of Evidence

We used nuclear rDNA-sequence data from the internal transcribed spacer (ITS) region to test the monophyly of Schoenus by using maximum parsimony and Bayesian inference. Schoenus is not monophyletic, with strong bootstrap support for most branches and congruence across analyses. nrITS does not resolve terminal taxa fully and, therefore, needs to be used in combination with other lines of evidence to address questions of species limits.

scholarly journals Figs S1-S3

2021 ◽  
Author(s):  
E. Karlsen-Ayala
Keyword(s):  
Maximum Likelihood ◽  
Bootstrap Support ◽  
Posterior Probabilities ◽  
Maximum Likelihood Tree ◽  
Branch Support

Fig. S1. Maximum likelihood tree based on ITS dataset. Branch support values >75 % and Bayesian posterior probabilities > 0.90 are indicated. Symbols with closed circles represent gasteroid taxa, symbols with half circles represent secotoid taxa, and all other taxa are agaricoid. Limacella glioderma was used as an outgroup.Fig. S2. Maximum likelihood tree based on LSU dataset. Branch support values >75 % and Bayesian posterior probabilities > 0.90 are indicated. Symbols with closed circles represent gasteroid taxa, symbols with half circles represent secotoid taxa, and all other taxa are agaricoid. Limacella glioderma was used as an outgroup. Fig. S3. Maximum likelihood tree based on concatenated LSU, rpb2, and tef1 dataset with ambiguously aligned regions excluded. Branch bootstrap support values >75 % and Bayesian posterior probabilities > 0.90 are indicated. Limacella delicata, Limacella glioderma and Limacella guttata were used as an outgroup.

A molecular phylogeny of the Rhigonematomorpha De Ley & Blaxter, 2002 as inferred from SSU and LSU rDNA sequences

Nematology ◽  
2018 ◽  
Vol 20 (6) ◽  
pp. 547-565
Author(s):  
Hugo H. Mejia-Madrid
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Bootstrap Support ◽  
Lsu Rdna ◽  
Posterior Probabilities ◽  
Monophyletic Clade ◽  
Bayesian Analyses ◽  
Rdna Sequences ◽  
The Future ◽  
Combined Matrix

Summary A molecular hypothesis of the Infraorder Rhigonematomorpha is presented. The phylogeny recovered using combined SSU and LSU markers suggests that the Rhigonematomorpha is nested within a larger clade that includes Ascaridomorpha, Spiruromorpha and Oxyuridomorpha and is strongly supported by maximum likelihood (ML) bootstrap support values (BS) and Bayesian posterior probabilities (BPP). SSU and LSU ML and Bayesian analyses recovered Rhigonematomorpha as a paraphyletic clade. In the ML and Bayesian analyses of a combined matrix of complete to partial sequences of SSU and LSU, respectively, Rhigonematomorpha is recovered as a monophyletic clade with moderate BPP but low BS. Highly supported BS and BPP of a combined SSU and LSU matrix support a hypothesis of a monophyletic Superfamily Ransomnematoidea that includes the families Carnoyidae, Hethidae, Ransomnematidae plus a Brumptaemilius, Cattiena, Insulanema clade, and a monophyletic Superfamily Rhigonematoidea that probably includes the paraphyletic families Rhigonematidae and Ichthyocephalidae. It is suggested that the future inclusion of more families and genera might help resolve the monophyly of the Infraorder Rhigonematomorpha as advanced here.

scholarly journals Sanghuangporus toxicodendri sp. nov. (Hymenochaetales, Basidiomycota) from China

MycoKeys ◽  
2019 ◽  
Vol 57 ◽  
pp. 101-111 ◽  
Author(s):  
Sheng-Hua Wu ◽  
Chiung-Chih Chang ◽  
Chia-Ling Wei ◽  
Guo-Zheng Jiang ◽  
Bao-Kai Cui
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Hubei Province ◽  
Monophyletic Group ◽  
Pore Surface ◽  
Monophyletic Clade ◽  
Brownish Yellow

Sanghuangporus toxicodendri (Hymenochaetales) is described as new based on collections made from Shennongjia Forestry District, Hubei Province, China. All studied basidiocarps grew on living trunks of Toxicodendron sp. This new species is characterized by having perennial, effused-reflexed to pileate basidiocarps; pore surface brownish yellow or yellowish brown, pores 7–9 per mm; context 1–5 mm thick or almost invisible; setae ventricose, dark brown, 26–42 × 7–10 μm; basidia 4-sterigmate or occasionally 2-sterigmate; basidiospores broadly ellipsoid, smooth, brownish yellow, slightly thick-walled, mostly 3.5–4 × 2.8–3 μm. Maximum likelihood and Bayesian inference phylogenies inferred from internal transcribed spacer (ITS) region of rDNA indicated that Sanghuangporus spp. formed a monophyletic clade and resolved as a sister to Tropicoporus spp., and six strains of S. toxicodendri formed a monophyletic group which is sister to S. quercicola. An identification key to known species of Sanghuangporus is provided.

scholarly journals Phylogenetics of native conifer species in Vietnam based on two chloroplast gene regions rbcL and matK

2021 ◽  
Vol 57 (No. 2) ◽  
pp. 58-66
Author(s):  
Mai Phuong Pham ◽  
Viet Ha Tran ◽  
Dinh Duy Vu ◽  
Quoc Khanh Nguyen ◽  
Syed Noor Muhammad Shah
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Genetic Distance ◽  
Related Species ◽  
Phylogenetic Analyses ◽  
Chloroplast Gene ◽  
Posterior Probabilities ◽  
Conifer Species ◽  
Closely Related Species ◽  
Matk Gene

We used two chloroplast gene regions (matK and rbcL) as a tool for the identification of 33 local conifer species. All 136 sequences, 101 newly generated (14 species for gene matK; 16 species for gene rbcL) and 35 retrieved from the GenBank, were used in the analysis. The highest genetic distance (matK region) was recorded between the species in Cupressaceae with an average of 5% (0.1–8.5), Podocarpaceae with an average of 6% (0–8.5), Taxaceae with an average of 5% (0.2–0.5) and Pinaceae with an average of 20.4% (0.8–54.1). The rbcL region showed a low genetic distance between the species in Cupressaceae 2% (0–3.3), Podocarpaceae 3% (0.6–3.4), Taxaceae 1% (0–2.1) and Pinaceae 1.2% (0–5.82). The phylogenetic analyses using the Maximum likelihood (ML) and Bayesian inference (BI) bootstrap values obtained at the branching nodes of each species ranged from 62 to 100% (Maximum likelihood bootstrap – MLBS and Bayesian posterior probabilities – BPP) for the matK gene; from 66 to 100% (MLBS) and 60 to 100% (BPP) for the rbcL region. The rbcL region was not identified between the species of Taxaceae and Cephalotaxaceae. The matK gene region was very clear in the different species among the families (Cupressaceae, Podocarpaceae, and Cephalotaxaceae) and unsuitable for identifying closely related species in Amentotaxus (Taxaceae) and Pinus (Pinaceae). The gene (matK) is a useful tool as a barcode in the identification of conifer species of Cupressaceae, Podocarpaceae, and Cephalotaxaceae in Vietnam.

scholarly journals PathFinder: Bayesian inference of clone migration histories in cancer

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i675-i683
Author(s):  
Sudhir Kumar ◽  
Antonia Chroni ◽  
Koichiro Tamura ◽  
Maxwell Sanderford ◽  
Olumide Oladeinde ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Cancer Cells ◽  
Bayesian Approach ◽  
Genetic Variants ◽  
Cancer Development ◽  
Posterior Probabilities ◽  
Migration Routes ◽  
Primary Tumors ◽  
History Of ◽  
The Web

Abstract Summary Metastases cause a vast majority of cancer morbidity and mortality. Metastatic clones are formed by dispersal of cancer cells to secondary tissues, and are not medically detected or visible until later stages of cancer development. Clone phylogenies within patients provide a means of tracing the otherwise inaccessible dynamic history of migrations of cancer cells. Here, we present a new Bayesian approach, PathFinder, for reconstructing the routes of cancer cell migrations. PathFinder uses the clone phylogeny, the number of mutational differences among clones, and the information on the presence and absence of observed clones in primary and metastatic tumors. By analyzing simulated datasets, we found that PathFinder performes well in reconstructing clone migrations from the primary tumor to new metastases as well as between metastases. It was more challenging to trace migrations from metastases back to primary tumors. We found that a vast majority of errors can be corrected by sampling more clones per tumor, and by increasing the number of genetic variants assayed per clone. We also identified situations in which phylogenetic approaches alone are not sufficient to reconstruct migration routes. In conclusion, we anticipate that the use of PathFinder will enable a more reliable inference of migration histories and their posterior probabilities, which is required to assess the relative preponderance of seeding of new metastasis by clones from primary tumors and/or existing metastases. Availability and implementation PathFinder is available on the web at https://github.com/SayakaMiura/PathFinder.

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