Molecular Phylogeny of Coprophanaeus (Megaphanaeus) d’Olsoufieff, 1924 (Coleoptera: Scarabaeidae: Scarabaeinae) and the position of C. bellicosus

2020 ◽  
Vol 51 (2) ◽  
pp. 241-255 ◽  
Author(s):  
Maria E. Maldaner ◽  
Fernando Z. Vaz-de-Mello ◽  
Daniela M. Takiya ◽  
Daniela C. Ferreira
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Maximum Parsimony ◽  
Phylogenetic Inference ◽  
Sister Group ◽  
Monophyletic Group ◽  
Valid Species ◽  
Nuclear Marker

Coprophanaeus (Megaphanaeus) d’Olsoufieff, 1924 has four valid species: C. lancifer (Linné, 1767), C. ensifer (Germar, 1821), C. bonariensis (Gory, 1844) and C. bellicosus (Olivier, 1789). However, authors disagree about the placement of C. bellicosus. Thus, our aims were (I) to test if Megaphanaeus is a monophyletic group and (II) verify to which subgenus C. bellicosus belongs. We sequenced three mitochondrial and one nuclear marker for ten Phanaeini species: COI (672bp), COI-II (1326bp), 16S (527bp) and 28S (994bp). For fifteen species we sequenced two markers, COI (681pb) and 16S (532pb). Both matrices were analyzed under three methods of phylogenetic inference: Maximum Parsimony, Maximum Likelihood, and Bayesian Inference. Megaphanaeus is here considered monophyletic including C. bellicosus as sister-group to (C. bonariensis (C. lancifer + C. ensifer)). All analyses recovered the non-monophyly of both C. lancifer and C. ensifer, because of a population of C. lancifer grouped with C. ensifer specimens.

The phylogenetic relationships of Paramesotriton (Caudata: Salamandridae) based on partial mitochondrial DNA gene sequences

Zootaxa ◽  
2012 ◽  
Vol 3150 (1) ◽  
pp. 59
Author(s):  
XIAOMING GU ◽  
HUI WANG ◽  
RONGRONG CHEN ◽  
YINGZHOU TIAN ◽  
SONG LI
Keyword(s):  
Mitochondrial Dna ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
16S Rdna ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Mitochondrial Gene ◽  
Sister Group ◽  
Species Group ◽  
Close Phylogenetic Relationship

We examined phylogenetic relationships among newst of the genus Paramesotriton using partial mitochondrial gene se-quences, including the ND2-tRNATyr region (1415 bp) and the 12S rDNA-tRNAVal -16S rDNA region (1774 bp), from 42individuals of 10 recognized Paramesotriton species and outgroups by Bayesian inference (BI), Maximum likelihood(ML) and Maximum Parsimony (MP) methods. We found that, (1) Laotriton laoensis is the sister group of Paramesotri-ton, (2) the genus Paramesotriton is monophyletic, composed of either the P. caudopunctatus species group and the P.chinensis species group, or the subgenera Allomesotriton and Paramesotriton (3) P. longliensis and P. zhijinensis shouldbe placed in the P. caudopunctatus species group or subgenus Allomesotriton; (4) P. fuzhongensis is not a junior synonym of P. chinensis, and there is a close phylogenetic relationship between P. fuzhongensis and P. guangxiensis.

Molecular phylogeny of the genus Hylodesmum (Fabaceae)

Phytotaxa ◽  
2019 ◽  
Vol 403 (3) ◽  
pp. 221
Author(s):  
HUAI-CHENG LI ◽  
XUE-LI ZHAO ◽  
XIN-FEN GAO ◽  
BO XU
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Nuclear Marker ◽  
Bayesian Analyses ◽  
Chloroplast Dna Regions ◽  
Taxonomic System

The phylogenetic relationships of 12 Hylodesmum species and closely related genera were reconstructed using maximum parsimony, maximum likelihood, and Bayesian analyses based on two chloroplast DNA regions (rps16-trnQ and trnL-F) and one nuclear marker (internal transcribed spacer, ITS). All analyses yielded reliable relationships among the major lineages within Hylodesmum, suggesting that Hylodesmum is monophyletic. Neither the traditionally defined Desmodium sect. Podocarpium nor D. sect. Repanda within the genus was supported as being monophyletic based on the ITS analyses and the combined ITS and chloroplast dataset analyses. The phylogenetic topologies indicated that the three species included in D. sect. Repanda were separated into different clades, which suggested that D. sect. Repanda is paraphyletic. Generally, the clades retrieved by phylogenetic analyses within D. sect. Podocarpium were consistent with traditionally defined groups except for the American group. The molecular analysis provides information regarding the revision of the traditional taxonomic system of Hylodesmum and for the evaluation of the systematic positions of each species within the genus Hylodesmum.

Systematic relationships of the Taeniapterini (Diptera: Micropezidae, Taeniapterinae)

Zootaxa ◽  
2021 ◽  
Vol 5004 (2) ◽  
pp. 370-384
Author(s):  
GUSTAVO BORGES FERRO ◽  
JEFFREY H. SKEVINGTON ◽  
STEPHEN A. MARSHALL ◽  
SCOTT KELSO
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Cytochrome C ◽  
16S Rrna ◽  
Molecular Phylogeny ◽  
Cytochrome C Oxidase ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
Oxidase Subunit ◽  
Systematic Relationships

A molecular phylogeny for the Taeniapterinae is presented based on mitochondrial (cytochrome c oxidase subunit I, COI), ribosomal (16S rRNA and 28S rRNA) and nuclear (EF-1α and CAD) genes of 48 specimens including 40 species. Maximum likelihood and Bayesian inference were used to analyze the total concatenated dataset of 8769 bp. The results confirm that tribal classifications in Taeniapterinae are artificial and support the separation of Paragrallomyia Hendel and Taeniaptera sensu Ferro & Marshall (2020).

scholarly journals Molecular phylogeny of the Taeniapterini (Diptera: Micropezidae) using nuclear and mitochondrial DNA, with a reclassification of the genus Taeniaptera Macquart

2015 ◽  
Vol 46 (5) ◽  
pp. 411-430 ◽  
Author(s):  
Morgan D. Jackson ◽  
Stephen A. Marshall ◽  
Jeffrey H. Skevington
Keyword(s):  
Mitochondrial Dna ◽  
Bayesian Inference ◽  
Molecular Phylogeny ◽  
Maximum Parsimony ◽  
New World ◽  
Molecular Data ◽  
Species Group ◽  
Mitochondrial Genes ◽  
Paraphyletic Group ◽  
Total Dna

DNA molecular data are used to generate a phylogeny for the micropezid subfamily Taeniapterinae. Thirty-two taeniapterine species were sampled, including 10 of the 20 New World genera recognized by Steyskal, as well as one genus formerly treated as a synonym of Poecilotylus Hennig (Hemichaeta Steyskal). Five species from the Micropezinae were included as outgroups. A total DNA dataset of 4705 bp, including mitochondrial genes (12S and cytochrome c oxidase I (COI)) and nuclear coding genes (wingless and CAD), was analysed using maximum parsimony and Bayesian inference. The genus Taeniaptera Macquart was found to be non-monophyletic with respect to the remainder of the Taeniapterini analysed here. Taeniaptera is restricted to the Taeniaptera trivittata Macquart species group, Mitromyia Cresson is resurrected to contain the Taeniaptera grata (Wulp) species group, and Paragrallomyia Hendel is resurrected to contain most species previously considered Taeniaptera. Poecilotylus is recognized as a paraphyletic group awaiting further research.

Gloeodontia yunnanensis sp. nov. (Russulales, Basidiomycota) from China, evidenced by morphological characters and phylogenetic analyses

Phytotaxa ◽  
2020 ◽  
Vol 432 (2) ◽  
pp. 111-118
Author(s):  
LU CHEN ◽  
ZHENG-JUN SHI ◽  
CHUN-HUA WU ◽  
CHANG-LIN ZHAO
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Morphological Characters ◽  
Fungal Species ◽  
Monophyletic Lineage ◽  
Thin Walled ◽  
Inference Methods

A new wood-inhabiting fungal species, Gloeodontia yunnanensis, is proposed based on a combination of morphological features and DNA data. The species is characterized by an annual, resupinate basidiomata with smooth hymenial surface, a monomitic hyphal system with thin-walled, clamped generative hyphae and obclavate cystidia and subglobose to globose, hyaline, thick-walled, asperulate, strongly amyloid, acyanophilous basidiospores measuring 3.3–4.3 × 2.5–3.5 µm. Sequences of ITS and 28S gene regions of the studied samples were generated and phylogenetic analyses were performed with Maximum Likelihood, Maximum Parsimony and Bayesian Inference methods. The analyses based on ITS+28S sequences showed that G. yunnanensis nested in the Gloeodontia clade and formed a monophyletic lineage with strong support (100% BS, 100% BP, 1.00 BPP).

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.

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.

Phylogeny and reclassification of Laelius (Hymenoptera: Bethylidae) and description of four new species

2011 ◽  
Vol 42 (3) ◽  
pp. 237-275 ◽  
Author(s):  
Celso Azevedo ◽  
Diego Barbosa
Keyword(s):  
New Species ◽  
Sister Group ◽  
Monophyletic Group ◽  
Valid Species ◽  
New Combinations ◽  
Data Set ◽  
Initial Analysis ◽  
Single Clade ◽  
Cladistic Analyses

AbstractAs currently recognised, Laelius Ashmead contains 47 known species worldwide and is found on all continents except Australia (until this study). In this paper, we examined the taxonomic limits of this genus and tested whether species of the genera Laelius and Prolaelius Kieffer constitute a monophyletic group. We also tested whether the junior synonyms Allepyris Kieffer and Paralaelius Kieffer are supported by cladistic analyses. Our initial analysis indicated that these genera form a single clade. Cladistic analyses were based on 108 female structural characters. The data set was analyzed under equal-weights parsimony and implied weighting. In both analyses, Laelius was retrieved as a polyphyletic group because Prolaelius Kieffer was always nested within Laelius and Allepyris berlandi Benoit always remained in the outgroup and was retrieved as the sister group of Disepyris sp. Based on our analyses, we propose nine nomenclatural acts and recognise 52 valid species of Laelius. The following four new species are described: Laelius haplos sp.n. and L. quadrangulus sp.n. from Australia and L. ogmos sp.n. and L. titanokkos sp.n. from ailand. The following new generic synonym is proposed: Prolaelius Kieffer syn.n. of Laelius Ashmead. The following three new combinations are proposed: Disepyris berlandi (Benoit) comb.n. from Laelius, Laelius firmipennis (Cameron) comb.n. and Laelius glossinae (Turner & Waterston) comb.n. from Prolaelius. Additionally, a lectotype is designated for Laelius fulvipes Kieffer.

Phylogeny of the Micareaceae inferred from nrSSU DNA sequences

2004 ◽  
Vol 36 (1) ◽  
pp. 27-35 ◽  
Author(s):  
Heidi L. ANDERSEN ◽  
Stefan EKMAN
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Small Subunit ◽  
Sensu Stricto ◽  
Confidence Set ◽  
Tree Topologies ◽  
Small Subunit Ribosomal Dna

The phylogeny of the Micareaceae and the genus Micarea Fr. was studied using 39 nuclear small subunit ribosomal DNA sequences. Phylogenetic analyses were carried out using maximum parsimony, maximum likelihood, and Bayesian inference. A confidence set of trees was estimated using expected likelihood weights to investigate a series of hypotheses of monophyly. Tree topologies were very similar between methods and differed only in the placement of a few poorly supported branches. The results indicate that the Micareaceae in its current circumscription belongs in the Lecanorales, but that it is not monophyletic. Psilolechia, Micarea with a ‘non-micareoid’ photobiont, Micarea sensu stricto and Byssoloma form a paraphyletic grade in this study. Micarea sensu stricto and Byssoloma (Pilocarpaceae) form a strongly supported monophyletic group, which constitutes the sister group to the Bacidiaceae. Scoliciosporum A. Massal has sometimes been considered close to Micarea, but no support was found for that hypothesis.

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