Application of the matK gene sequences to grass systematics

1996 ◽  
Vol 74 (1) ◽  
pp. 125-134 ◽  
Author(s):  
Hongping Liang ◽  
Khidir W. Hilu
Keyword(s):  
Dna Sequence ◽  
Neighbor Joining ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Dna Mutations ◽  
Monophyletic Lineage ◽  
The Family ◽  
Basal Clade ◽  
Matk Gene ◽  
Insight Into

The 3′ region of the matK gene from 17 species, representing 13 tribes and six subfamilies of the Poaceae, is used to investigate the potential of the gene in addressing systematic questions in the family. The aligned sequences were analyzed by the Wagner parsimony methods using PAUP and PHYLIP and by the neighbor-joining method. Out of the 583 bp sequenced, 30% were variable and 14.9% were informative. The strict consensus tree, rooted by Joinvillea (Joinvilleaceae), showed well-resolved major clades that represent the grass subfamilies. The bambusoid Phyllostachys appeared as a basal clade in the family. Oryza diverged either before or after the Pooideae in the parsimony and neighbor-joining methods, respectively. The three members of the Pooideae grouped in a monophyletic lineage in both analyses. Arundo (Arundinoideae) was basal to the subfamilies Panicoideae and Chloridoideae. Analysis of the various types of DNA mutations underscores the potential of the matK gene in providing insight into grass systematic and evolution. Keywords: matK, Poaceae, grasses, phylogeny, chloroplast, DNA sequence.

Linguistic homoplasy and phylogeny reconstruction. The cases of Lezgian and Tsezic languages (North Caucasus)

2017 ◽  
Vol 51 (s38) ◽  
Author(s):  
Alexei S. Kassian
Keyword(s):  
Phylogeny Reconstruction ◽  
Neighbor Joining ◽  
North Caucasus ◽  
Input Matrix ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Bayesian Mcmc ◽  
Phylogenetic Methods ◽  
Network Method ◽  
Ancestral Character States

AbstractThis paper deals with the problem of linguistic homoplasy (parallel or backward development), how it can be detected, what kinds of linguistic homoplasy can be distinguished and which varieties of the phenomenon are the most deleterious for the reconstruction of language phylogeny. It is proposed that language phylogeny reconstruction should consist of two main stages. Firstly, a strict consensus tree should be built on the basis of high-quality input data elaborated with the help of the main phylogenetic methods (such as Neighbor-joining, Bayesian MCMC, and Maximum parsimony), and ancestral character states, allowing us to reveal a certain number of homoplastic characters. Secondly, after the detected instances of homoplasy are eliminated from the input matrix, the consensus tree is to be compiled again. It is expected that after homoplastic optimization it will be possible to better resolve individual “problem clades”, and generally the homoplasy-optimized phylogeny should be more robust than the tree constructed initially. The proposed procedure is tested on the 110-item Swadesh wordlists of the Lezgian and Tsezic groups. The Lezgian and Tsezic results generally support theoretical expectations. The MLN (minimal lateral network) method, currently implemented in the LingPy software, is a helpful tool for the detection of linguistic homoplasy.

scholarly journals Phylogenetic relationships within the Pylochelidae (Decapoda: Anomura: Paguroidea): A cladistic analysis based on morphological characters

Zootaxa ◽  
2009 ◽  
Vol 2022 (1) ◽  
pp. 1-14 ◽  
Author(s):  
RAFAEL LEMAITRE ◽  
PATSY A. MCLAUGHLIN ◽  
ULF SORHANNUS
Keyword(s):  
Hermit Crab ◽  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Data Matrix ◽  
Parsimony Analysis ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
The Family

Phylogenetic relationships within the “symmetrical” hermit crab family Pylochelidae were analyzed for 41 of the 45 species and subspecies currently considered valid. In the analyses, 78 morphological characters comprised the data matrix and the outgroup consisted of Thalassina anomala, a member of the Thalassinidae, and Munida quadrispina, a member of the Galatheidae. A poorly resolved strict consensus tree was obtained from a heuristic parsimony analysis of unweighted and unordered characters, which showed the family Pylochelidae and the subfamilies Pylochelinae and Pomatochelinae to be monophyletic taxa – the latter two groups had the highest Bremer support values. Additionally, while the subgenus Pylocheles (Pylocheles) was strongly supported, the subgenera Xylocheles, and Bathycheles were not. More fully resolved trees were obtained when using implied weighting, which recognized the monotypic subfamilies Parapylochelinae, Cancellochelinae and Mixtopagurinae. The subfamily Trizochelinae was found to have four distinct clades and several ambiguously placed taxa.

Siamosuchus phuphokensis, a new goniopholidid from the Early Cretaceous (ante-Aptian) of northeastern Thailand

2007 ◽  
Vol 178 (3) ◽  
pp. 201-216 ◽  
Author(s):  
Komsorn Lauprasert ◽  
Gilles Cuny ◽  
Eric Buffetaut ◽  
Varavudh Suteethorn ◽  
Kumthorn Thirakhupt
Keyword(s):  
The Other ◽  
New Taxon ◽  
Postcranial Skeleton ◽  
Consensus Tree ◽  
Caudal Part ◽  
Strict Consensus Tree ◽  
The Family ◽  
The Right ◽  
High Median ◽  
Northeastern Thailand

Abstract A new taxon of a broad-snouted goniopholidid, Siamosuchus phuphokensis, gen. et sp. nov., was discovered in the Sao Khua Formation (ante-Aptian), northeastern Thailand. The specimen is described on the basis of an incomplete skeleton showing the premaxillae, maxillae, nasals, left lacrimal, frontal, left jugal, right postorbital, caudal part of the cranial table, most of the right part of the postcranial skeleton, and several heavily sculptured osteoderms. S. phuphokensis is distinguished from the other broad-snouted goniopholidids on the basis of the following characters: penetration of the nasals in the narial border; presence of a robust and high median ridge on the interorbital surface; lateral margin of the frontal forming the medial edge of the orbit; supraoccipital exhibiting a wide pentagonal shape. A phylogenetic analysis using 101 characters for 29 mesoeucrocodylian taxa and 3 outgroup taxa supports the monophyly of the family Goniopholididae. In addition, the Thai specimen forms a clade with the European Goniopholis. Based on our strict consensus tree, the generic name Goniopholis should be restricted to the European forms only.

scholarly journals Phylogenetic Systematics of the Family Pentacerotidae(Actinopterygii: Order Perciformes)

Zootaxa ◽  
2012 ◽  
Vol 3366 (1) ◽  
pp. 1 ◽  
Author(s):  
SEONG-YONG KIM
Keyword(s):  
Family Members ◽  
Monophyletic Group ◽  
Phylogenetic Systematics ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Center Of Origin ◽  
Region I ◽  
The Family ◽  
Lateral Ethmoid ◽  
Transformation Series

The osteologic and myologic characteristics of the family Pentacerotidae are described in detail. The family Pentaceroti-dae is a monophyletic group supported by 11 synapomorphies found in all family members. Of their synapomorphies, two(the second infraorbital and endopterygoid articulate with lateral ethmoid conditions) are considerably rare in percoidsand strongly support the monophyly of the family. A comparison of 44 transformation series among all species revealedfour equally parsimonious trees, and a strict consensus tree was adopted. On the basis of the inferred phylogenetic rela-tionships of the Pentacerotidae, this family was cladistically classified into two subfamilies and seven genera: Histiopter-inae (Histiopterus, Evistias, Zanclistius, Pentaceropsis, Paristiopterus, and Parazanclistius) and Pentacerotinae(Pentaceros). The center of origin of pentacerotids was inferred to be the Southern Australian region. I propose that the two families, Ostracoberycidae and Chaetodontidae, are closely related with Pentacerotidae.

scholarly journals Phylogenetic systematics of the driftwood catfishes (Siluriformes: Auchenipteridae): a combined morphological and molecular analysis

2019 ◽  
Vol 187 (3) ◽  
pp. 661-773 ◽  
Author(s):  
Bárbara B Calegari ◽  
Richard P Vari ◽  
Roberto E Reis
Keyword(s):  
Large Scale ◽  
Classification Scheme ◽  
Optimality Criteria ◽  
Valid Species ◽  
Phylogenetic Systematics ◽  
Species Relationships ◽  
New Classification ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
The Family

Abstract A comprehensive phylogeny of species relationships of the Auchenipteridae is reconstructed here with a large-scale taxon sampling based on combined morphological and molecular datasets. The hypothesized phylogeny includes most species of Auchenipteridae (97 of 124 valid species) and multiple members of siluriform families as an outgroup (32 species) to embrace the diversity of forms among related catfishes. As the first large-scale phylogeny of the Auchenipteridae, comparison between taxa included information from both morphology (264 characters) and mitochondrial and nuclear molecular markers (3490 nucleotides) from five genes: coI, 16S, rag2, myh6 and SH3PX3. Trees were generated under two different optimality criteria (Maximum Parsimony and Bayesian Inference). A new classification for the family is presented herein to bring the taxonomy more in line with the new phylogenetic hypothesis. The strict consensus tree corroborates the monophyly of superfamily Doradoidea, family Auchenipteridae and its two subfamilies, Centromochlinae and Auchenipterinae. The new classification scheme proposes nine tribes in Auchenipteridae, based on the monophyly of major groups in both subfamilies. Centromochlus, Glanidium and Tatia are each recovered as paraphyletic. To maintain a monophyletic classification, some species treated as Tatia and Centromochlus are assigned to genera not previously recognized as valid.

The phylogeny of cockroach families: a cladistic appraisal of morpho-anatomical data

1996 ◽  
Vol 74 (3) ◽  
pp. 508-527 ◽  
Author(s):  
Philippe Grandcolas
Keyword(s):  
Sister Group ◽  
Reproductive Behaviour ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Anatomical Data ◽  
The Family ◽  
Life Habits ◽  
Anatomical Characters ◽  
Test Current

Seventy-two morpho-anatomical characters were examined in 221 genera belonging to the families Blattidae, Polyphagidae, Blattellidae, and Blaberidae. They were cladistically analyzed and polarized using two mantids and two termites. As no autapomorphies of the family Blattellidae were found, the constituent subfamilies were used as terminal taxa together with other families. Three trees were found (CI = 0.81 and RI = 0.88, without autapomorphies) that differed only by the position of Nyctiborinae relative to Blattellinae and Ectobiinae. The strict consensus tree was [Blattidae [Polyphagidae [Anaplectinae [[Pseudophyllodromiidae, Blaberidae] [Nyctiborinae, Blattellinae, Ectobiinae]]]]]. The main discrepancies with McKittrick's tree were the monophyly of Polyphagidae (instead of paraphyly) and that the Blaberidae is the sister-group of Pseudophyllodromiinae (instead of the sister-group of Blattellinae, Ectobiinae, and Nyctiborinae). These results made it necessary to elevate the Anaplectinae and Pseudophyllodromiinae to familial status, and to give a new sense to the family Blattellidae, which includes only the subfamilies Blattellinae, Ectobiinae, and Nyctiborinae. This phylogeny was used to test current evolutionary hypotheses concerning sociality and reproductive behaviour; many traits were assumed to be ancestral to all cockroaches (protozoan symbionts and familial life habits) or preadaptive (progressing from advanced oviparity in Blattellidae to ovoviviparity in Blaberidae) that must actually be considered homoplasic.

Phylogeny of the family Spongicolidae (Crustacea: Stenopodidea): evolutionary trend from shallow-water free-living to deep-water sponge-associated habitat

2003 ◽  
Vol 83 (1) ◽  
pp. 119-131 ◽  
Author(s):  
Tomomi Saito ◽  
Masatsune Takeda
Keyword(s):  
Deep Water ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Evolutionary Trend ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Free Living ◽  
The Family ◽  
Outgroup Species ◽  
Hexactinellid Sponges

The phylogenetic relationships within the family Spongicolidae were examined based on a cladistic analysis of 38 adult morphological characters with reference to two outgroup species of the family Stenopodidae. The strict consensus tree identified Microprosthema as the most basal genus, followed by Paraspongicola, Spongicola and the remaining genera. The Spongicoloides represents the most derived genus among spongicolids. The genera Spongicola, Spongicoloides and Spongiocaris should be redefined, because they formed paraphyletic clades. The cladogram indicates that symbiosis with the hexactinellid sponges is coincident with the loss of gills, exopods on maxillipeds 2 and 3, and with the loss of spination on carapace, pereopods, abdomen, tail fan etc. These losses in the spongicolids are thought to be secondarily derived in relation to their sponge-associated habitat.

scholarly journals Phylogeny of Galium L. (Rubiaceae) from Korea and Japan based on chloroplast DNA sequence

2016 ◽  
Vol 23 (2) ◽  
pp. 237-246 ◽  
Author(s):  
Keum Seon Jeong ◽  
Jae Kwon Shin ◽  
Masayuki Maki ◽  
Jae-Hong Pak
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Bayesian Analyses ◽  
Plant Taxon ◽  
Chloroplast Dna Sequences

The present paper deals with the phylogeny and inter-and intragenic relationships using four chloroplast DNA sequences within 19 Galium L. species from Korea and Japan. Maximum parsimony and Bayesian analyses were conducted to clarify the relationships among the section and species. The strict consensus tree had three main clades. Clade I comprises of the only individuals of G. paradoxum Maximowicz (sect. Cymogalia), which is distinguished by opposite leaves in the genus, supported by the 100% bootstrap value (PP: 0.98); Clade II consists of members of eight sections (sect. Galium, sect. Hylaea, sect. Kolgyda, sect. Trachygalium, sect. Leptogalium, sect. Orientigalium, sect. Aparine, and sect. Leiogalium); Clade III comprises members of eight sections (sect. Baccogalium, sect. Lophogalium, sect. Platygalium, sect. Relbunium, sect. Depauperata, sect. Aparinoides, sect. Leiogalium and Trachygalium). The sect. Leptogalium which includes two taxa namely G. tokyoense Makino and G. dahuricum var. lasiocarpum (Makino) Nakai is paraphyletic. Four taxa of Trachygalium group (G. trachyspermum A. Gray, G. gracilens (A. Gray) Makino, G. pogonanthum Franch. & Sav., G. koreanum Nakai) were placed from sect. Cymogalia to sect. Platygalium based on molecular and morphological data.Bangladesh J. Plant Taxon. 23(2): 237-246, 2016 (December)

The basal phylogeny of Scarabaeoidea (Insecta : Coleoptera) inferred from larval morphology

2004 ◽  
Vol 18 (3) ◽  
pp. 321 ◽  
Author(s):  
Vasily V. Grebennikov ◽  
Clarke H. Scholtz
Keyword(s):  
Morphological Characters ◽  
Total Evidence ◽  
Larval Morphology ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
The Family ◽  
Evidence Analysis

Larvae of 60 genera representing the following families and subfamilies of Scarabaeoidea were studied and analysed phylogenetically: Lucanidae (Aesalinae, Nicaginae, Syndesinae, Lampriminae, Lucaninae), Passalidae (Passalinae, Aulacocyclinae), Trogidae, Pleocomidae, Geotrupidae (Taurocerastinae, Lethrinae, Geotrupinae), Bolboceratidae, Ceratocanthidae, Hybosoridae, Glaphyridae, Scarabaeidae (Aphodiinae, Scarabaeinae, Melolonthinae, Dynastinae, Cetoniinae). Seventy-eight larval morphological characters were employed in the analysis. Our data confirm that Dascillidae are not closely related to Scarabaeoidea. The monophyly of the superfamily is supported by 20 apomorphic character states, 18 of them unique. Monophyly of the following scarabaeoid clades is supported (with the number of larval synapomorphies followed by the bootstrap value in parentheses): Scarabaeoidea without Passalidae (6/67), Passalidae (9/100), Pleocomidae (11/93), Trogidae (8/93), Glaphyridae (10/96), Lucanidae (9/95), Ceratocanthidae + Hybosoridae (5/74), Scarabaeinae (9/98). The family Ceratocanthidae was found to be paraphyletic with respect to Hybosoridae. Monophyly of the family Scarabaeidae is not supported. The resolution of the basal parts of the strict consensus tree is higher when using Dascillidae + Eulichadidae v. Agyrtidae + Helophoridae as an outgroup, but the differences in topology become insignificant after bootstrapping. It is suggested that larval morphology alone is not an adequate tool to address basal relationships of Scarabaeoidea and a total evidence analysis should be performed.

A Review of Phytochemical and Pharmacological Studies of Inula Species

2020 ◽  
Vol 16 (5) ◽  
pp. 557-567
Author(s):  
Aparoop Das ◽  
Anshul Shakya ◽  
Surajit Kumar Ghosh ◽  
Udaya P. Singh ◽  
Hans R. Bhat
Keyword(s):  
Bacterial Infections ◽  
Chemical Constituents ◽  
Valuable Insight ◽  
Important Ingredient ◽  
Pharmacological Activities ◽  
Medicinal Uses ◽  
The Family ◽  
Pharmacological Studies ◽  
Perennial Herbs ◽  
Insight Into

Background: Plants of the genus Inula are perennial herbs of the family Asteraceae. This genus includes more than 100 species, widely distributed throughout Europe, Africa and Asia including India. Many of them are indicated in traditional medicine, e.g., in Ayurveda. This review explores chemical constituents, medicinal uses and pharmacological actions of Inula species. Methods: Major databases and research and review articles retrieved through Scopus, Web of Science, and Medline were consulted to obtain information on the pharmacological activities of the genus Inula published from 1994 to 2017. Results: Inula species are used either alone or as an important ingredient of various formulations to cure dysfunctions of the cardiovascular system, respiratory system, urinary system, central nervous system and digestive system, and for the treatment of asthma, diabetes, cancers, skin disorders, hepatic disease, fungal and bacterial infections. A range of phytochemicals including alkaloids, essential and volatile oils, flavonoids, terpenes, and lactones has been isolated from herbs of the genus Inula, which might possibly explain traditional uses of these plants. Conclusion: The present review is focused on chemical constituents, medicinal uses and pharmacological actions of Inula species and provides valuable insight into its medicinal potential.

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