Phylogenetic relationships of Echeveria (Crassulaceae) and related genera from Mexico, based on three DNA barcoding loci

Phytotaxa ◽  
2019 ◽  
Vol 422 (1) ◽  
pp. 33-57 ◽  
Author(s):  
LUIS E. DE LA CRUZ-LÓPEZ ◽  
FRANCISCO VERGARA-SILVA ◽  
JERÓNIMO REYES SANTIAGO ◽  
GABRIELA ESPINO ORTEGA ◽  
PABLO CARRILLO-REYES ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Dna Barcoding ◽  
Phylogenetic Relationships ◽  
Consensus Trees ◽  
As Species ◽  
Tree Inference ◽  
Selection Of

Mexico is considered as diversification and endemism center of the genus Echeveria. Previous tree inference studies have shown the genus to be non-monophyletic in relation to other genera, but sampling for Echeveria has been poor, and has not allowed to understand the relationships within the genus. In this work, Bayesian and maximum likelihood phylogenetic analysis were performed, using a combined standard DNA barcoding loci matrix (rbcL, matK and ITS2) and GenBank ITS2 accessions for Graptopetalum, some Sedum and few Echeveria taxa. The selection of taxa encompasses all current infrageneric categories of the genus Echeveria, as well as species from genera previously associated with it. The inferred consensus trees suggested that Echeveria is paraphyletic. Instead, four main clades were retrieved within the “Echeveria group”: Clade I includes exclusively Pachyphytum species. Clade II is formed by the majority of series Urbiniae; Clade III encompasses series Chloranthae, Ciliatae, Echeveria, Mucronatae, Nudae, Racemosae, Thyrsiflorae, Pachyphytum cuicatecananum and Thompsonella; Clade IV contains series Angulatae, Gibbiflorae, Occidentales, Pruinosae, Secundae, some Urbiniae species, Valvatae. genera Cremnophila, Graptopetalum and Reidmorania. Pachyphytum and Thompsonella were retrieved as monophyletic groups, but the first outside Echeveria while the latter inside. Results of our study suggest that Echeveria and the Echeveria Group require a redefinition.

scholarly journals A BARCODE-BASED PHYLOGENETIC SCAFFOLD FOR XYSTICUS AND ITS RELATIVES (ARANEAE: THOMISIDAE: CORIARACHNINI)

2019 ◽  
Vol 20 ◽  
pp. 198-206 ◽  
Author(s):  
Rainer Breitling
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcoding ◽  
Phylogenetic Relationships ◽  
Genetic Data ◽  
Target Area ◽  
Starting Point ◽  
Main Target ◽  
Holarctic Region ◽  
Species Groups ◽  
Crab Spider

The phylogenetic relationships and taxonomy of the crab spider genus Xysticus and its closest relatives (i.e., the tribe Coriarachnini, also including, e.g., Ozyptila, Coriarachne and Bassaniana) have long been controversial, with several alternative classifications being proposed, none of which has gained universal acceptance. As Coriarachnini is largely confined to the Holarctic region, the main target area of recent DNA barcoding projects for spiders, a large amount of genetic data for the group is now publicly available. The results of a phylogenetic analysis of this sequence dataset are largely congruent with earlier morphology-based results regarding the evolutionary structure of the group. In particular, they highlight the fact that Xysticus s. lat. is a paraphyletic assembly and that several species groups need to be placed in separate genera to achieve monophyly of Xysticus s. str. Similarly, Coriarachne and Bassaniana appear as independent clades rather than a joined monophyletic Coriarachne s. lat. In contrast, further subdivision of Ozyptila is not supported by the genetic data. Importantly, the analysis also shows that anapophysate members of Xysticus s. lat. form two widely separated groups: a primarily anapophysate division, also including Coriarachne and Bassaniana, at the base of Xysticus s. lat., and a secondarily anapophysate clade deeply nested within Xysticus s. str. This might explain some of the earlier difficulties when trying to define generally accepted subgroups within Xysticus s. lat. The phylogenetic scaffold based on barcode sequences is sufficiently dense and well resolved to attempt the tentative and provisional placement of the majority of species in Xysticus s. lat. in the independent genera Xysticus s. str., Bassaniodes, Psammitis and Spiracme as a starting point for a future more formal revision of the group.

Molecular phylogeny of the butterfly tribe Baorini Doherty, 1886 (Hesperiidae, Hesperiinae) in China

Zootaxa ◽  
2019 ◽  
Vol 4565 (1) ◽  
pp. 108 ◽  
Author(s):  
WEIBIN JIANG ◽  
HAIYAN HE ◽  
YUANYUAN LI ◽  
YING WANG ◽  
CHEN GE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Species Diversity ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Mitochondrial Genes ◽  
Nuclear Genes ◽  
Large Group ◽  
The Status

The butterfly tribe Baorini Doherty, 1886 is a large group of skippers. In this study, a total of 8 genera and 41 species of putative members of this tribe, which represent most of the generic diversity and nearly all the species diversity of the group in China, were sequenced for two mitochondrial genes and three nuclear genes (2084 bp). Phylogenetic relationships and subdivision of this tribe were investigated and the status of the genera are discussed. Partitioned maximum likelihood analyses were performed based on the combined dataset. Our results suggest that the data are split into two well-supported clades in the phylogeny tree. This analysis also represents the most complete phylogenetic analysis of the tribe Baorini in China to date, and includes several genera and species that have been previously excluded from published phylogenies of this group. 

scholarly journals Phylogenetic Analysis of Mandarin Landraces, Wild Mandarins, and Related Species in China Using Nuclear LEAFY Second Intron and Plastid trnL-trnF Sequence

2007 ◽  
Vol 132 (6) ◽  
pp. 796-806 ◽  
Author(s):  
Li Yingzhi ◽  
Cheng Yunjiang ◽  
Tao Nengguo ◽  
Deng Xiuxin
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Related Species ◽  
Phylogenetic Relationships ◽  
Average Length ◽  
Hybrid Origin ◽  
Data Sets ◽  
Citrus Reticulata ◽  
F Region ◽  
Plausible Hypothesis

Nucleotide sequences of the second intron of the nuclear LEAFY gene (FLint2) and trnL-trnF region of the chloroplast genome were used to analyze the phylogenetic relationships among eight wild mandarins (Citrus reticulata Blanco), 19 mandarin landraces, and 19 related species of Citrus L. Forty-six trnL-trnF sequences and 111 FLint2 sequences were obtained from 46 ingroup accessions, with an average length of 1059.7 and 776.7 bp respectively. Phylogeny reconstructions were conducted separately for these two data sets using maximum parsimony and maximum likelihood criteria. Monophyly of mandarins was supported by both of these data sets, and in this clade, most mandarin landraces formed an unresolved polytomy, whereas ‘Jiangyong 1’, ‘Chongyi A2’, ‘Chongyi A1’ (or ‘Jiangyong 4’ in FLint2 data), and ‘Daoxian 1’ wild mandarins formed a subclade. ‘Mangshan A1’ and ‘Daoxian 5’ wild mandarins were sisters to this mandarin clade. A hybrid origin of five mandarin landraces and several mandarin-related species was suggested as a plausible hypothesis to explain the incongruence between the FLint2 and trnL-trnF data sets.

scholarly journals Phylogenetic analysis of lysine, threonine and butanol strain-producers

1970 ◽  
Vol 21 ◽  
pp. 288-292
Author(s):  
O. O. Tigunova ◽  
G. S. Andriiash ◽  
N. Ye. Beiko ◽  
S. M. Shulha
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
Phylogenetic Relationships ◽  
Clostridium Acetobutylicum ◽  
Genomic Dna ◽  
Agarose Gel ◽  
Brevibacterium Flavum ◽  
Mutant Strains

Aim. Identify and confirm the taxonomic position of the obtained mutant strains Brevibacterium sp. IMB B-7447, Brevibacterium flavum IMB B-7446 and Clostridium acetobutylicum IMB B-7407 (IFBG C6H). Methods. A fragment of genomic DNA from agarose gel using «Macherey-Nagel NucleoSpin Extract» was isolated according to the instructions of the producer and sequenced. Comparative analysis using the program «BLAST-online» was done. Phylogenetic dendrograms using methods Neighbour joining and Maximum likelihood were created. Results. Dendrograms of phylogenetic relationships of studied strains and related strains of databases «GenBank» were constructed. Conclusions. Found that homology of Brevibacterium sp. 90 and Brevibacterium sp. IMB B-7447 is 98 %, and stains B. flavum TH7 and B. flavum IMB B-7446 classified to species C. glutamicum. Strain C. acetobutylicum IMB B-7407 (IFBG C6H) been reclassified to C. pasteurianum IFBG C6H. Keywords: genes 16S rRNA, dendrogram, stains-produsers.

Guasuctenus gen. nov., a new Neotropical spider genus of Ctenidae (Araneae)

Zootaxa ◽  
2019 ◽  
Vol 4624 (4) ◽  
pp. 539-550
Author(s):  
DANIELE POLOTOW ◽  
ANTONIO D. BRESCOVIT
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Monophyletic Group ◽  
New Genera ◽  
Southern Brazil ◽  
As Species

The new genus Guasuctenus gen. nov. is described based on the results of a recent phylogenetic analysis. This phylogeny, which included representatives of all Ctenidae subfamilies, showed that the genus Ctenus as currently defined, does not comprise a monophyletic group. The results indicated that several species are misplaced in Ctenus and should be transferred to new genera. Aiming to correct the placement of two species originally described in Ctenus, we propose the new genus Guasuctenus to accommodate those species and better represent their phylogenetic relationships. Guasuctenus is supported by the presence of a dorsal cymbial projection in the male palp. Previously regarded as a subspecies, Ctenus longipes vittatissimus Strand, 1916 is here ranked as species, and Guasuctenus longipes (Keyserling, 1891) new comb. and G. vittatissimus (Strand, 1916) new rank, new comb. are redescribed. Ctenus griseus Keyserling, 1891 is recognized as a junior synyonym of Ctenus longipes Keyserling, 1891. Lectotypes and paralectotypes of Guasuctenus vittatissimus (Strand, 1016) are designated for stability. The species of the genus are distributed in southern Brazil and Uruguay. 

scholarly journals Molecular identification of stone loaches of Choman River system, Tigris Basin, based on the Cytochrome b gene with an overview of the Cobitoidea Superfamily

2017 ◽  
Author(s):  
Edris Ghaderi ◽  
Hamid Farahmand ◽  
Barzan Bahrami Kamangar ◽  
Mohammad A. Nematollahi
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Maximum Likelihood ◽  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
River System ◽  
Distinct Species ◽  
Molecular Data ◽  
Genetic Distances ◽  
Molecular Phylogenetic

AbstractMolecular data and phylogenetic relationships of four Choman loaches species (Oxynoemacheilus chomanicus, O. zagrosensis, O. kurdistanicus and Turcinoemacheilus kosswigi) recently morphologically described from western Iran were evaluated with 64 species from the Cobitoidea superfamily based on their cytochrome b sequences to exhibit the placement of the Choman loaches species within the Cobitoidea superfamily. A comparative analysis of Kimura-2-parameter (K2P) distances was accomplished using sequence divergences of Cobitoidea to calculate intra and interspecific in superfamily, family and genus taxa. The average intraspecific K2P genetic distances of Choman loaches species was 0.005 whereas this value was 0.016 for the Cobitoidea superfamily. Molecular phylogenetic relationships were assessed using Maximum likelihood and Bayesian methods. Dendrograms obtained by these methods revealed all four Choman loaches species as distinct species among other reported Nemacheilidae Spp. These species were clustered with Oxynoemacheilus and Turcinoemacheilus genera within other species in the Nemacheilidae family. The phylogenetic analysis revealed that Cobitoidea superfamily consists of nine families ((Gyrinocheilidae + Botiidae) + ((Catostomidae + Vaillentellidae) + ((Nemacheilidae + Cobitidae) + ((Ellopostomidae + Gastromyzontidae) + Balitoridae)))) and indicated Nemacheilidae is a valid and distinct family from Balitoridae.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

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