Molecular phylogeny of the genus Hylodesmum (Fabaceae)

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.

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A phylogenetic analysis and new delimitation of Crepidiastrum (Asteraceae, tribe Cichorieae)

Phytotaxa ◽

10.11646/phytotaxa.159.4.1 ◽

2014 ◽

Vol 159 (4) ◽

pp. 241 ◽

Cited By ~ 7

Author(s):

Yu-lan Peng ◽

Yu Zhang ◽

Xin-fen Gao ◽

Lin-jing Tong ◽

Liang Li ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Maximum Likelihood ◽

Chloroplast Dna ◽

Maximum Parsimony ◽

Phylogenetic Analyses ◽

Systematic Position ◽

Likelihood Inference ◽

Nuclear Its ◽

Chloroplast Dna Regions

The systematic position of Paraixeris humifusa (Asteraceae) is hard to define, because the circumscription of Paraixeris, Youngia and Crepidiastrum, three closely related genera in subtribe Crepidinae (Cichorieae), is not clear. This paper reports on the relationships between 30 species in subtribe Crepidinae, based on an analysis of nucleotides from one nuclear (ITS) and three chloroplast DNA regions ( trnL-F, rps16 and atpB-rbcL). The phylogenetic analyses used maximum parsimony with maximum likelihood inference. The monophyly of Crepidiastrum in the most recent generic classification of Shih & Kilian (2011) is explored. The results show that 12 species in Crepidiastrum constitute a monophyletic group, and that Paraixeris humifusa should be treated as Youngia humifusa.

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The Phylogenetic Relationship Revealed Three New Wood-Inhabiting Fungal Species From Genus Trechispora

Frontiers in Microbiology ◽

10.3389/fmicb.2021.650195 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wei Zhao ◽

Chang-Lin Zhao

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Maximum Parsimony ◽

Internal Transcribed Spacer ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Fungal Species ◽

Molecular Evidence ◽

Wood Degradation ◽

Inference Methods

Wood-inhabiting fungi play a significant role in wood degradation and the cycle of matter in the ecological system. In the present study, three new wood-inhabiting fungal species, Trechispora bambusicola, Trechispora fimbriata, and Trechispora fissurata spp. nov., are nested in Trechispora, which are proposed based on a combination of morphological features and molecular evidence. Sequences of internal transcribed spacer (ITS) and large subunit (nLSU) regions of the studied samples were generated, and the phylogenetic analyses were performed with maximum likelihood, maximum parsimony, and Bayesian inference methods. The phylogenetic analyses inferred from ITS showed that T. bambusicola was sister to Trechispora stevensonii, T. fimbriata grouped with Trechispora nivea, and T. fissurata grouped with Trechispora echinospora. The phylogenetic tree based on ITS + nLSU sequences demonstrated that T. bambusicola formed a single lineage and then grouped with Trechispora rigida and T. stevensonii. T. fimbriata was sister to T. nivea. T. fissurata grouped with Trechispora thelephora.

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Phylogenetic Relationships in the Salicornioideae / Suaedoideae / Salsoloideae s.l. (Chenopodiaceae) Clade and a Clarification of the Phylogenetic Position of Bienertia and Alexandra Using Multiple DNA Sequence Datasets

Systematic Botany ◽

10.1600/036364406778388674 ◽

2006 ◽

Vol 31 (3) ◽

pp. 571-585 ◽

Cited By ~ 51

Author(s):

Maxim V. Kapralov ◽

Hossein Akhani ◽

Elena V. Voznesenskaya ◽

Gerald Edwards ◽

Vincent Franceschi ◽

...

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Dna Sequence ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Phylogenetic Position ◽

Kranz Anatomy ◽

Statistical Support ◽

Chloroplast Dna Regions

The Chenopodiaceae includes taxa with both C3 and C4 photosynthesis with diverse kinds of Kranz anatomy and single-celled C4 species without Kranz anatomy; thus, it is of key importance for understanding evolution of C4 photosynthesis. All of the C4 genera except Atriplex, which belongs to Chenopodioideae, are in the Salicornioideae / Suaedoideae / Salsoloideae s.l. (including Camphorosmeae and Sclerolaeneae) clade. Our study focused on the relationships of the main lineages within this clade with an emphasis on the placement of the single cell functioning C4 genus Bienertia using maximum parsimony, maximum likelihood, and Bayesian inference phylogenetic analyses of the nuclear ribosomal ITS and five chloroplast DNA regions (atpB-rbcL, matK, psbB-psbH, rbcL, and trnL-trnF). Further we provide a detailed phylogeny of Alexandra and Suaeda based on ITS, atpB-rbcL, and psbB-psbH. Our molecular data provide strong statistical support for the monophyly of: (1) a Salicornioideae / Suaedoideae / Salsoloideae s.l. clade; (2) a Salicornioideae / Suaedoideae clade; (3) the subfamilies Salicornioideae, Suaedoideae (including Bienertia) and Salsoloideae s.l.; (4) the tribes Suaedeae, Salsoleae, and Camphorosmeae; (5) the Salicornieae if Halopeplideae is included; and (6) Suaeda if Alexandra is included. Alexandra lehmannii is therefore reclassified as Suaeda lehmannii and a new section of Suaeda is created, section Alexandra. There are four independent origins of C4 photosynthesis within the Suaedoideae including two parallel origins of Kranz C4 anatomy (in Suaeda sections Salsina s.l. and Schoberia) and two independent origins of C4 systems without Kranz anatomy (in Bienertia and in Suaeda section Borszczowia).

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Phylogeny and taxonomy of the genus Hyphodontia (Hymenochaetales, Basidiomycota) in China

Phytotaxa ◽

10.11646/phytotaxa.309.1.4 ◽

2017 ◽

Vol 309 (1) ◽

pp. 45 ◽

Cited By ~ 5

Author(s):

MIN WANG ◽

YUAN-YUAN CHEN

Keyword(s):

New Species ◽

Maximum Likelihood ◽

Maximum Parsimony ◽

Internal Transcribed Spacer ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Hyphal System ◽

Two New Species ◽

Its Regions

In this paper, two new species in Hyphodontia, H. bubalina and H. mongolica, are reported as new to science based on morphological characteristics and phylogenetic analyses. Detailed descriptions and illustrations are provided with comparisons among allied taxa. Hyphodontia bubalina has thin cream basidiomata, a monomitic hyphal system with thin- to slightly thick-walled generative hyphae, hyphoid or subulate cystidioles, ellipsoid to subglobose basidiospores measuring as 4–5.3 × 3–4.2 µm. Hyphodontia mongolica is characterized by the partly confluent or branched aculei, a monomitic hyphal system with thick-walled generative hyphae, clavate and tubular cystidia, and ellipsoid basidiospores measuring as 4.9–6.6 × 2.5–3.2 µm. Phylogenetic analyses based on the internal transcribed spacer (ITS) regions which performed by Bayesian (BI), maximum likelihood (ML) and maximum parsimony (MP) methods confirm to place the two species in the genus Hyphodontia.

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Phylogenetic relationships in the tribe Alysseae (Brassicaceae) based on nuclear ribosomal ITS DNA sequences

Botany ◽

10.1139/b08-013 ◽

2008 ◽

Vol 86 (4) ◽

pp. 315-336 ◽

Cited By ~ 45

Author(s):

Suzanne I. Warwick ◽

Connie A. Sauder ◽

Ihsan A. Al-Shehbaz

Keyword(s):

Maximum Likelihood ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Maximum Parsimony ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Its Region ◽

Morphological Characters ◽

Data Support ◽

Its Dna Sequences

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 85 species (131 accessions) were used to determine the tribal limits, monophyly status, and phylogenetic intra-tribal relationships of genera within the tribe Alysseae (Brassicaceae). Both maximum parsimony and maximum likelihood analyses support the recognition of the tribe Alysseae s. str. (12 genera: Alyssoides , Alyssum , Aurinia , Berteroa , Bornmuellera , Clastopus , Clypeola , Degenia , Fibigia , Galitzkya , Hormathophylla , and Physoptychis ). Six well-supported clades were recognized within the Alysseae clade, including two Alyssum clades (one of which includes Clypeola ), an Alyssoides and allies clade (includes Alyssoides , Bornmuellera , Clastopus , Degenia , Fibigia , Hormathophylla , and Physoptychis ), a Berteroa and allies clade (includes Aurinia , Berteroa , and Galitzkya ), a Bornmuellera clade, and a Hormathophylla clade. Morphological and cytological support for these clades is reviewed. The ITS data support the exclusion of the following taxa from the Alysseae, with appropriate tribal assignment given in parentheses: Alyssum klimesii Al-Shehbaz (Camelineae), Asperuginoides (unresolved), Athysanus (Arabideae), Botschantzevia (Arabideae), Didymophysa (unresolved), Farsetia (Malcolmieae), Lobularia (Malcolmieae), and Ptilotrichum (Arabideae). Farsetia and Lobularia are inferred to be monophyletic, and based on molecular and morphological characters they are assigned to Malcolmieae, a recently described tribe.

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A new species and a new record of Clitopilus and a description of C. orientalis from India based on morphology and molecular phylogeny

Phytotaxa ◽

10.11646/phytotaxa.343.1.4 ◽

2018 ◽

Vol 343 (1) ◽

pp. 47 ◽

Cited By ~ 4

Author(s):

K. N. ANIL RAJ ◽

PATINJAREVEETTIL MANIMOHAN

Keyword(s):

New Species ◽

Maximum Likelihood ◽

Molecular Phylogeny ◽

Rna Polymerase Ii ◽

Internal Transcribed Spacer ◽

New Record ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Kerala State ◽

A New Species

Three species of Clitopilus, C. albidus sp. nov., C. subscyphoides and C. orientalis, are described from Kerala State, India, based on morphology and molecular phylogeny. Comprehensive descriptions, photographs, and comparisons with phenetically similar and phylogenetically related species are provided. The RNA polymerase II genes (rpb2) of the three species were sequenced and analyzed. In addition, the nuclear ribosomal internal transcribed spacer regions (ITS) and the nuclear ribosomal large subunit (nLSU) genes were sequenced and used in BLAST searches to find similar sequences. Phylogenetic analyses based on rpb2 sequences performed using both Maximum Likelihood (ML) and Bayesian Analysis (BA) methods supported the novelty of C. albidus and its placement within the genus Clitopilus. C. subscyphoides and C. orientalis are the first and second record respectively of these species from India.

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MOLECULAR PHYLOGENY OF MAIDENHAIR FERN GENUS ADIANTUM (PTERIDACEAE) FROM LESSER SUNDA ISLANDS INDONESIA BASED ON RBCL AND TRNL-F

REINWARDTIA ◽

10.14203/reinwardtia.v14i1.409 ◽

2014 ◽

Vol 14 (1) ◽

pp. 143

Author(s):

Wenni Setyo Lestari ◽

Bayu Adjie ◽

Tassanai Jaruwatanaphan ◽

Yasuyuki Watano ◽

Made Pharmawati

Keyword(s):

Molecular Phylogeny ◽

Phylogenetic Relationships ◽

Maximum Parsimony ◽

Phylogenetic Analyses ◽

Small Islands ◽

Tree Topologies

The Lesser Sunda Islands of Indonesia are composed of small islands scattered from Bali to Timor Island. We analyzed a molecular phylogeny of Adiantum collected from Lesser Sunda Islands to reveal its phylogenetic relationships. A total of 12 species of Adiantum from this region and seven species from Java Island were collected and used in this study. Two cpDNA regions (rbcL and trnL-F) were chosen as markers and phylogenetic analyses were conducted using Neighbour-Joining (NJ) and Maximum Parsimony (MP) methods. The tree topologies reconstructed by NJ and MP from specimens used in this study and other species downloaded from GenBank are congruent in which trees are divided into five major clades. Adiantum species of Lesser Sunda Islands are not monophyletic and comprises three clades, i. e. Clade I composed of A. hispidulum group, Clade III composed of A. peruvianum group and Clade IV or A. caudatum group, each together with extra-Lesser Sunda samples. No sample from Lesser Sunda Islands examined is located in Clade II (A. tenerum group) and V (A. capillus-veneris group).

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A Re-analysis of the phylogeny of the genus Protobothrops (Reptilia: Viperidae), with particular reference to the systematic position of P. xiangchengensis

Amphibia-Reptilia ◽

10.1163/156853806778189954 ◽

2006 ◽

Vol 27 (3) ◽

pp. 433-439 ◽

Cited By ~ 4

Author(s):

Peng Guo ◽

Ermi Zhao ◽

Yaping Zhang ◽

Junfeng Pang

Keyword(s):

Maximum Likelihood ◽

16S Rrna ◽

Cytochrome B ◽

Phylogenetic Relationships ◽

Maximum Parsimony ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Systematic Position ◽

Valid Species ◽

12S Rrna

AbstractBased on three mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b), the phylogeny of Protobothrops is re-analyzed using Maximum-parsimony (MP), Maximum-likelihood (ML), and Bayesian (BI) approaches. All phylogenetic analyses indicate that all putative Protobothrops species examined formed a monophyletic group; however, the intrageneric relationships are still unresolved. The phylogenetic relationships further confirm that P. xiangchengensis is a valid species distinct from P. mucrosquamatus and that it is closely related to P. jerdonii.

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Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters

Phytotaxa ◽

10.11646/phytotaxa.376.1.1 ◽

2018 ◽

Vol 376 (1) ◽

pp. 1 ◽

Cited By ~ 5

Author(s):

XIAN LIN GUO ◽

CHANG BAO WANG ◽

JUN WEN ◽

SONGDONG ZHOU ◽

XING JIN HE

Keyword(s):

Phylogenetic Relationships ◽

Maximum Parsimony ◽

Internal Transcribed Spacer ◽

Leaf Blade ◽

Southwest China ◽

Morphological Characters ◽

Identification Key ◽

Bayesian Analyses ◽

Pinnate Leaf ◽

First Time

Chamaesium (Apiaceae) is a morphologically specific genus distributed mainly at high altitudes from East Himalaya to Southwest China. China is an important diversity center of Chamaesium, where most of its species occur. It differs from most Apiaceae taxa by 1- pinnate leaf blade, and fruit with primary and secondary ribs all prominent to narrowly winged. The objective of the present study is to contribute to the phylogenetic relationships within Chamaesium, using the nuclear internal transcribed spacer (ITS) and three plastid makers (rpl16, rps16 and trnT-trnL). Nine species involving 28 populations of Chamaesium, three species of Bupleurum were collected this time and seven sequences of Pleurospermeae clade were obtained from the NCBI, to infer their phylogeny using Maximum parsimony and Bayesian analyses for the first time. The monophyly of Chamaesium is supported, proved that each species belongs to an individual clade, and the differentiation between species is obvious. Some new characteristics such as morphology in fruit and basal leaves, are used in the identification key, and new geographical distribution of Chamaesium species in China were provided. The taxonomic treatments for six species (not include the previously described species) in China including type materials, synonyms, distribution, habitats and specimens examined were carried out comprehensively referring to previous studies and our own fieldwork. A new identification key for the Chinese species of Chamaesium is reported.

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

Insect Systematics & Evolution ◽

10.1163/1876312x-00002198 ◽

2020 ◽

Vol 51 (2) ◽

pp. 241-255 ◽

Cited By ~ 2

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.

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