Phylogenetic relationships of three families of the suborder Mononchina Kirjanova & Krall, 1969 inferred from 18S rDNA

Nematology ◽  
2015 ◽  
Vol 17 (9) ◽  
pp. 1113-1125 ◽  
Author(s):  
Mina Koohkan ◽  
Ebrahim Shokoohi ◽  
Peter Mullin
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
18S Rdna ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Nuclear Genome ◽  
Sister Group ◽  
Ssu Rdna ◽  
Rdna Analysis

Mononchida is an order of predatory nematodes and includes the suborders Bathyodontina and Mononchina. In this survey, sequences of the 18S rDNA were amplified and used to reconstruct the phylogeny of the Mononchina. Phylogenetic analyses using Neighbour Joining (NJ) and Maximum Likelihood (ML) were employed with five outgroup taxa and 65 mononch sequences including 14 new sequences from Iran. Both analyses indicated that the Anatonchus is monophyletic. Actus was placed as the sister group of Mylonchulus with weak and strong support, respectively, from the ML and NJ analyses. In both phylogenetic analyses, trees obtained from SSU rDNA alignments were subdivided into five highly- or moderately-supported clades, designated Clade I: Mylonchulus spp., Clade II: Actus salvadoricus, Clade III: Anatonchus spp., a group comprising the genera Clarkus, Coomansus, Miconchus and Prionchulus, Clade IV: Mononchus spp., and Clade V: Granonchulus sp. The 18S rDNA analysis demonstrated that this region of the nuclear genome can be used to resolve the relationships of members of this suborder.

Phylogenetic relationships in Hypomyces and allied genera, with emphasis on species growing on wood-decaying homobasidiomycetes

2000 ◽  
Vol 77 (12) ◽  
pp. 1756-1768 ◽  
Author(s):  
Kadri Põldmaa ◽  
Ellen Larsson ◽  
Urmas Kõljalg
Keyword(s):  
Maximum Likelihood ◽  
Sexual Reproduction ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Sister Group ◽  
28S Rdna ◽  
The Other ◽  
Molecular Evidence

To infer phylogenetic relationships among species of Hypomyces (Fr.) Tul and allied genera, partial sequences of the 28S rDNA were obtained for 21 strains representing 19 species. On the basis of these data and 38 sequences obtained from GenBank, phylogenetic analyses were performed using the programs PAUP and Pee-Wee. Hypomyces appears to be paraphyletic, with species having wet-conidial phialidic anamorphs more closely related to other genera. Hypomyces chrysostomus Berk & Broome is a sister group to the clade that includes species of Aphysiostroma Barrasa et al., Arachnocrea Moravec, and Hypocrea Fr. Based on morphological and molecular evidence, a new genus, Sporophagomyces, is described for Hypomyces chrysostomus and two allied species. Hypomyces broomeanus Tul. forms one clade with species of Sphaerostilbella Sacc. and is transferred to this genus. The recognition of Arachnocrea is justified. The integration of Cladobotryum Nees species that are not known to undergo sexual reproduction with Hypomyces species that possess Cladobotryum anamorphs receives strong support, but the whole complex of these species appears to be paraphyletic. However, constraint trees, which require monophyly of all these ana- and pleo-morphic species, do not appear significantly less likely than the other trees obtained under maximum likelihood or parsimony criteria. For the remaining species of Hypomyces, four distinct lineages are distinguished.

Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 719-731 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Peter J. Prentis ◽  
Hardeep S. Rai ◽  
Sean W. Graham
Keyword(s):  
Phylogenetic Relationships ◽  
Strong Support ◽  
Sister Group ◽  
Higher Order ◽  
Special Issue ◽  
Likelihood Methods ◽  
The Family ◽  
Selection Of

To characterize higher-order phylogenetic relationships among the five families of Commelinales, we surveyed multiple plastid loci from exemplar taxa sampled broadly from the order, and from other major monocot lineages. Phylogenetic inferences in Commelinales using parsimony and likelihood methods are congruent, and we find strong support for most aspects of higher-order relationship in the order. We obtain moderately strong support for the local placement of Philydraceae, a family whose position has proven particularly difficult to infer in previous studies. Commelinaceae and Hanguanaceae are sister taxa, and together they are the sister group of a clade consisting of Haemodoraceae, Philydraceae, and Pontederiaceae; Haemodoraceae and Pontederiaceae are also sister taxa. Our sampling of Philydraceae includes all three or four genera in the family; we identify Philydrella as the sister group of a Helmholtzia–Philydrum clade, a resolution that is potentially consistent with several aspects of morphology.

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.

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.

Phlebia nigrodontea sp. nov. in Meruliaceae (Polyporales) with a black hymenial surface

Phytotaxa ◽  
2020 ◽  
Vol 458 (3) ◽  
pp. 195-206
Author(s):  
RUO-XIA HUANG ◽  
KAI-YUE LUO ◽  
CHANG-LIN ZHAO
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Molecular Data ◽  
Molecular Evidence ◽  
Monophyletic Lineage ◽  
Phlebioid Clade ◽  
Thin Walled ◽  
Inference Methods

A new wood-inhabiting fungus, Phlebia nigrodontea, is proposed based on a combination of morphological features and molecular evidence. The species is characterized by a grandinioid hymenophore with vinaceous brown to black colour, a monomitic hyphal system with clamped generative hyphae and ellipsoid, colourless, thin-walled, smooth basidiospores (3.9–4.9 × 2.3–3.1 µm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses carried out using maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on the molecular data of ITS+nLSU sequences showed that P. nigrodontea nested within the phlebioid clade. A further investigation of more representative taxa from Phlebia, based on ITS+nLSU sequences, demonstrated that the species P. nigrodontea formed a monophyletic lineage with strong support (100% BS, 100% BT, 1.00 BPP) and closely grouped with P. chrysocreas.

A Phylogenetic Analysis and Taxonomic Revision of Bartonia (Gentianaceae: Gentianeae), Based on Molecular and Morphological Evidence

2009 ◽  
Vol 34 (1) ◽  
pp. 162-172 ◽  
Author(s):  
Katherine G. Mathews ◽  
Niall Dunne ◽  
Emily York ◽  
Lena Struwe
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Species Boundaries ◽  
Morphological Evidence ◽  
Phylogenetic Study ◽  
Sister Group Relationship ◽  
Internal Transcribed Spacer Region ◽  
Test Species

A phylogenetic study and taxonomic revision of the four currently accepted species of Bartonia (Gentianaceae, subtribe Swertiinae) were conducted in order to test species boundaries and interspecific relationships. Species boundaries were examined based on measurements of key quantitative and qualitative morphological characters as given in the original descriptions. Phylogenetic analyses were performed using molecular data from the nuclear internal transcribed spacer region and chloroplast DNA (trnL intron through the trnL-F spacer), separately and combined using parsimony and Bayesian methodologies, incorporating outgroups from subtribes Swertiinae and Gentianinae. The morphological study revealed that characters of one species, B. texana, represent a subset of the morphological variation found within B. paniculata, but that B. paniculata, B. verna, and B. virginica could all be separated from one another. The molecular phylogenetic analyses all found B. texana to nest in a clade with the two recognized subspecies of B. paniculata (subsp. paniculata and subsp. iodandra), making the latter paraphyletic. Bartonia texana is here reduced to subspecific rank, as Bartonia paniculata subsp. texana. Also, the phylogenetic analyses showed strong support for a sister group relationship between B. verna and B. virginica, as opposed to between B. paniculata and B. virginica as has been previously suggested.

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.

Molecular phylogeny of the spoonbills (Aves: Threskiornithidae) based on mitochondrial DNA

Zootaxa ◽  
2010 ◽  
Vol 2603 (1) ◽  
pp. 53 ◽  
Author(s):  
R. TERRY CHESSER ◽  
CAROL K. L. YEUNG ◽  
CHENG-TE YAO ◽  
XIU-HUA TIAN ◽  
SHOU-HSIEN LI
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Sister Group ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Bayesian Analyses ◽  
Limited Sampling

Spoonbills (genus Platalea) are a small group of wading birds, generally considered to constitute the subfamily Plataleinae (Aves: Threskiornithidae). We reconstructed phylogenetic relationships among the six species of spoonbills using variation in sequences of the mitochondrial genes ND2 and cytochrome b (total 1796 bp). Topologies of phylogenetic trees reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses were virtually identical and supported monophyly of the spoonbills. Most relationships within Platalea received strong support: P. minor and P. regia were closely related sister species, P. leucorodia was sister to the minor-regia clade, and P. alba was sister to the minor-regia-leucorodia clade. Relationships of P. flavipes and P. ajaja were less well resolved: these species either formed a clade that was sister to the four-species clade, or were successive sisters to this clade. This phylogeny is consistent with ideas of relatedness derived from spoonbill morphology. Our limited sampling of the Threskiornithinae (ibises), the putative sister group to the spoonbills, indicated that this group is paraphyletic, in agreement with previous molecular data; this suggests that separation of the Threskiornithidae into subfamilies Plataleinae and Threskiornithinae may not be warranted.

scholarly journals Comparative Mitogenomic Analysis of the Eurydema Genus in the Context of Representative Pentatomidae (Hemiptera: Heteroptera) Taxa

2019 ◽  
Vol 19 (6) ◽  
Author(s):  
Wanqing Zhao ◽  
Qing Zhao ◽  
Min Li ◽  
Jiufeng Wei ◽  
Xianhong Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Rna Structures ◽  
Protein Coding ◽  
Transfer Rnas ◽  
The Family ◽  
Maximum Likelihood Methods

Abstract The family Pentatomidae, the largest within the superfamily Pentatomoidae, comprises about 5,000 species; many of which are economically important pests. Although the phylogeny of Pentatomidae species has been studied using various molecular markers, their phylogenetic relationships remain controversial. Recently, mitochondrial genomes (mitogenomes) have been extensively employed to examine the phylogenetics and evolution of different insects, and in this study, we sequenced complete/near-complete mitochondrial genomes from five shield bug species of Eurydema to gain a better understanding of phylogenetic relationships in the Pentatomidae. The five mitogenomes ranged in length from 15,500 to 16,752 bp and comprised 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. We compared mitogenomic characteristics of the Pentatomidae and constructed phylogenetic trees using Bayesian inference and maximum likelihood methods. Our results showed that gene arrangements, base composition, start/stop codons, gene overlaps, and RNA structures were conserved within the Pentatomidae and that congeneric species shared more characteristics. Saturation and heterogeneity analyses revealed that our PCGs and PCGRNA datasets were valid for phylogenetic analysis. Phylogenetic analyses showed consistent topologies based on BI and ML methods. These analyses strongly supported that Eurydema species belong to the tribe Strachiini, and formed a sister group with Pentatomini. The relationships among Eurydema species were shown to be consistent with their morphological features. (Strachiini + Pentatomini) was found to be a stable sibling of the clade comprising Cappaeini, Graphosomini, and Carpocorini. Furthermore, our results indicated that Graphosoma rubrolineatum (Heteroptera: Pentatomidae) belongs to the Pentatominae and not the Podopinae.

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