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.

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.

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 Application of PCR-DGGE method for identification of nematode communities in pepper growing soil

2016 ◽  
Vol 7 (1) ◽  
pp. 9-14
Author(s):  
Duong Duc Hieu
Keyword(s):  
Maximum Likelihood ◽  
Community Sample ◽  
Nematode Species ◽  
Viet Nam ◽  
Soil Nematode ◽  
Nematode Communities ◽  
Maximum Likelihood Tree ◽  
Relationship Of ◽  
First Time ◽  
Soil Nematode Communities

Soil nematodes play an important role in indication for assessing soil environments and ecosystems. Previous studies of nematode community analyses based on molecular identification have shown to be useful for assessing soil environments. Here we applied PCR-DGGE method for molecular analysisoffive soil nematode communities (designed as S1 to S5) collected from four provinces in Southeastern Vietnam (Binh Duong, Ba Ria Vung Tau, Binh Phuoc and Dong Nai) based on SSU gene. By sequencing DNA bands derived from S5 community sample, our data show 15 species containing soil nematode, other nematode and non-nematode (fungi) species. Genus Meloidogyne was found as abundant one. The genetic relationship of soil nematode species in S5 community were determined by Maximum Likelihood tree re-construction based on SSU gene. This molecular approach is applied for the first time in Vietnam for identification of soil nematode communities. Tuyến trùng đất đóng vai trò chỉ thị quan trọng trong công tác đánh giá môi trường và hệ sinh thái đất. Các nghiên cứu trước đây đã cho thấy lợi ích của việc phân tích cộng đồng tuyến trùng đất bằng định danh sinh học phân tử đối với việc đánh giá môi trường đất. Ở đây, chúng tôi ứng dụng phương pháp PCR-DGGE dựa trên gene SSU để phân tích năm (ký hiệu từ S1 đến S5) cộng đồng tuyến trùng đất thuộc các vùng trồng chuyên canh cây hồ tiêu ở miền nam Việt Nam (Bình Dương, Bà Rịa Vũng Tàu, Bình Phước và Đồng Nai). Bằng cách giải trình tự các vạch của mẫu tuyến trùng S5, kết quả cho thấy cộng đồng tuyến trùng này có 15 loài gồm nhóm tuyến trùng đất, nhóm các loại tuyến trùng khác và nhóm không phải tuyến trùng (nấm) và trong đó Meloidogyne là giống ưu thế. Mối quan hệ di truyền của các các loài tuyến trùng đất thuộc cộng đồng S5 được xác định bằng việc thiết lập cây phát sinh loài Maximum Likelihood dựa trên gene SSU. Đây là nghiên cứu đầu tiên ở Việt Nam sử dụng kỹ thuật PCR-DGGE để phân tích các cộng đồng tuyến trùng đất trồng hồ tiêu.

A contribution towards the systematics of Magneuptychia Forster, 1964: Caeruleuptychia francisca (Butler, 1870), n. comb. (Lepidoptera: Nymphalidae: Satyrinae)

2020 ◽  
pp. 1-11
Author(s):  
Shinichi Nakahara ◽  
Kaylin Kleckner ◽  
Gerardo Lamas ◽  
Blanca Huertas ◽  
Keith R. Willmott
Keyword(s):  
Maximum Likelihood ◽  
Molecular Data ◽  
Maximum Likelihood Analysis ◽  
Maximum Likelihood Tree ◽  
Likelihood Analysis ◽  
First Time

We here transfer an euptychiine taxon hitherto placed in the polyphyletic genus Magneuptychia Forster, 1964, to Caeruleuptychia Forster, 1964. Caeruleuptychia francisca (Butler, 1870), n. comb. is reclassified based on a morphology-based maximum likelihood analysis, which is consistent with ongoing analyses of molecular data. Two putative synapomorphic characters are identified for the “Caeruleuptychia umbrosa clade”, one of which appears to be an unusual characteristic of euptychiine butterflies and is tested by optimizing onto the maximum likelihood tree. We also discuss the systematic placement of three additional enigmatic Caeruleuptychia species. A lectotype is designated for Euptychia francisca, and the genitalia of this species are illustrated here for the first time.

Morphology and molecular analysis ofOncicola venezuelensis(Acanthocephala: Oligacanthorhynchidae) from the ocelotLeopardus pardalisin Brazil

2016 ◽  
Vol 91 (5) ◽  
pp. 605-612 ◽  
Author(s):  
E.G.N. Santos ◽  
M. Chame ◽  
V.A. Chagas-Moutinho ◽  
C.P. Santos
Keyword(s):  
Maximum Likelihood ◽  
Genetic Analysis ◽  
National Park ◽  
Genetic Data ◽  
Genetic Profile ◽  
28S Rrna ◽  
Leopardus Pardalis ◽  
Ultrastructural Studies ◽  
Maximum Likelihood Tree ◽  
Geographical Locality

AbstractOncicola venezuelensisMarteau, 1977 was found parasitizing adults ofLeopardus pardalis(Linnaeus) found dead in Serra da Capivara National Park, Piauí state, Brazil, a new geographical locality reported for the species. The diversity ofOncicolaTravassos, 1916 species is large, but genetic data are scarce. This article presents the results of genetic, morphological and ultrastructural studies carried out for taxonomic purposes. The first ultrastructural view showed a globular, short proboscis with 36 hooks, divided into six longitudinal rows of six hooks each. Hooks differ in size and shape: hooks I, II and III have a ‘chisel-shaped’ tip. The genetic profile included new sequences of ribosomal DNA ITS1, 5.8S and ITS2, and partial 28S rRNA regions. The results of maximum-likelihood tree analyses for each region showed Oligacanthorhynchidae Southwell et Macfie, 1925 close to Gigantorhynchidae Hamann, 1892 (supported >91%). Both use mammals and birds as definitive hosts. Morphological and ultrastructural studies combined with genetic analysis shed more light on the diversity ofOncicolaspecies.

scholarly journals A fast and memory-efficient implementation of the transfer bootstrap

2019 ◽  
Vol 36 (7) ◽  
pp. 2280-2281 ◽  
Author(s):  
Sarah Lutteropp ◽  
Alexey M Kozlov ◽  
Alexandros Stamatakis
Keyword(s):  
General Public ◽  
Efficient Implementation ◽  
Supplementary Information ◽  
Bootstrap Support ◽  
Supplementary Data ◽  
Original Algorithm ◽  
Parallel Version ◽  
Branch Support ◽  
General Public License ◽  
Memory Efficient

Abstract Motivation Recently, Lemoine et al. suggested the transfer bootstrap expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support for taxon-rich datasets. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Results We developed a fast and memory-efficient TBE implementation. We improve upon the original algorithm by Lemoine et al. via several algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10× to 40× memory savings compared with booster. Availability and implementation Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallel version that also computes additional TBE-related statistics is available at: https://github.com/lutteropp/raxml-ng/tree/tbe. Supplementary information Supplementary data are available at Bioinformatics online.

Molecular evidence for the systematic positions of two enigmatic mosses: Pterogonidium pulchellum (Sematophyllaceae, Musci) and Piloecium pseudorufescens (Myuriaceae, Musci)

2006 ◽  
Vol 84 (3) ◽  
pp. 501-507
Author(s):  
Ying Chang ◽  
Chan Woon Khiong ◽  
Sean W. Graham ◽  
Benito C. Tan
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Molecular Evidence ◽  
Rbcl Gene ◽  
Branch Support ◽  
New Evidence ◽  
Rbcl Gene Sequences

The systematic position of Pterogonidium pulchellum (W.J. Hooker) Muell. Hal. in the Sematophyllaceae and Piloecium pseudorufescens (Hampe) Muell. Hal. in the Myuriaceae is reexamined with new evidence derived from rbcL gene sequences. A total of 18 taxa from Sematophyllaceae, Hypnaceae, Myuriaceae, and Hookeriaceae were included, 11 of which were newly sequenced for the rbcL gene. Analyses were done using maximum parsimony, maximum likelihood (TrN + Γ + I model and GTR + Γ + I model), and Bayesian inference (GTR + Γ + I model). The results show that Pterogonidium pulchellum has a closer relationship with members of Hypnaceae than with Sematophyllaceae, while Piloecium pseudorufescens forms a clade with the Sematophyllaceae in all phylogenetic analyses, with robust branch support. Two SOWH tests were carried out and the results show that it is not appropriate to classify Pterogonidium pulchellum in Sematophyllaceae and it is also not appropriate to classify Piloecium pseudorufescens in Myuriaceae.

Sign in / Sign up

Export Citation Format

Share Document