Phylogeny, diversity, and classification of the Accipitridae based on DNA sequences of the RAG-1 exon

2007 ◽  
Vol 38 (5) ◽  
pp. 587-602 ◽  
Author(s):  
Carole S. Griffiths ◽  
George F. Barrowclough ◽  
Jeff G. Groth ◽  
Lisa A. Mertz
Keyword(s):  
Dna Sequences ◽  
Rag 1

Discovery of New Genera Challenges the Subtribal Classification of Tok-Tok Beetles (Coleoptera: Tenebrionidae: Sepidiini)

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Olivia M Gearner ◽  
Marcin J Kamiński ◽  
Kojun Kanda ◽  
Kali Swichtenberg ◽  
Aaron D Smith
Keyword(s):  
Dna Sequences ◽  
Species Group ◽  
Phylogenetic Placement ◽  
Darkling Beetles ◽  
Species Groups ◽  
Taxonomic Groups ◽  
Inference Methods ◽  
A New Species ◽  
Coleoptera Tenebrionidae

Abstract Sepidiini is a speciose tribe of desert-inhabiting darkling beetles, which contains a number of poorly defined taxonomic groups and is in need of revision at all taxonomic levels. In this study, two previously unrecognized lineages were discovered, based on morphological traits, among the extremely speciose genera Psammodes Kirby, 1819 (164 species and subspecies) and Ocnodes Fåhraeus, 1870 (144 species and subspecies), namely the Psammodes spinosus species-group and Ocnodes humeralis species-group. In order to test their phylogenetic placement, a phylogeny of the tribe was reconstructed based on analyses of DNA sequences from six nonoverlapping genetic loci (CAD, wg, COI JP, COI BC, COII, and 28S) using Bayesian and maximum likelihood inference methods. The aforementioned, morphologically defined, species-groups were recovered as distinct and well-supported lineages within Molurina + Phanerotomeina and are interpreted as independent genera, respectively, Tibiocnodes Gearner & Kamiński gen. nov. and Tuberocnodes Gearner & Kamiński gen. nov. A new species, Tuberocnodes synhimboides Gearner & Kamiński sp. nov., is also described. Furthermore, as the recovered phylogenetic placement of Tibiocnodes and Tuberocnodes undermines the monophyly of Molurina and Phanerotomeina, an analysis of the available diagnostic characters for those subtribes is also performed. As a consequence, Phanerotomeina is considered as a synonym of the newly redefined Molurina sens. nov. Finally, spectrograms of vibrations produced by substrate tapping of two Molurina species, Toktokkus vialis (Burchell, 1822) and T. synhimboides, are presented.

Towards a monophyletic classification of Lejeuneaceae III: the systematic position of Leiolejeunea

Phytotaxa ◽  
2014 ◽  
Vol 170 (3) ◽  
pp. 187 ◽  
Author(s):  
ALFONS SCHÄFER-VERWIMP ◽  
KATHRIN FELDBERG ◽  
SHANSHAN DONG ◽  
HUUB VAN MELICK ◽  
DENILSON F. PERALTA ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Its Region ◽  
Systematic Position ◽  
Leaf Cell ◽  
Oil Bodies ◽  
Sister Relationship ◽  
First Time

The derived liverwort Leiolejeunea grandiflora was recollected at the type locality in Jamaica after more than 100 years. The characteristics of its oil bodies were described for the first time based on the new collections. Each leaf cell possesses 2-4(-6) rather small, subhomogeneous to very finely segmented, subglobose to ellipsoidal, colorless oil bodies. The plants were either dioicous or autoicous. DNA sequences of two chloroplast regions (trnL-trnF, rbcL) and the nuclear ribosomal ITS region were obtained for two accessions of Leiolejeunea to enable the inference of the phylogenetic relationships of these plants. Based on Bayesian inference of phylogeny as well as maximum parsimony and maximum likelihood analyses of a dataset including 87 representatives of Lejeuneaceae, Leiolejeunea was found as the putative sister to either Echinolejeuneinae or Cheilolejeuneinae. Thus, we propose the new monogeneric subtribe Leiolejeuneinae with relationships to Cheilolejeuneinae and Echinolejeuneinae. The analyses included also one accession of the generitype of Cheilolejeunea, C. decidua [= Cheilolejeunea adnata]. This species was found in a well supported sister relationship with Cystolejeunea. To avoid nomenclatural confusion, we propose a wide genus concept for Cheilolejeunea including Aureolejeunea, Cyrtolejeunea, Cystolejeunea, Evansiolejeunea, Leucolejeunea, and Omphalanthus.

Crow-ENN

2020 ◽  
pp. 173-213
Author(s):  
Rehan Ullah ◽  
Abdullah Khan ◽  
Syed Bakhtawar Shah Abid ◽  
Siyab Khan ◽  
Said Khalid Shah ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Search Algorithm ◽  
Heuristic Model ◽  
Classification Problems ◽  
Elman Neural Network ◽  
Main Research ◽  
Research Activities ◽  
Proposed Model ◽  
Simulation Results

DNA sequence classification is one of the main research activities in bioinformatics on which, many researchers have worked and are working on it. In bioinformatics, machine learning can be applied for the analysis of genomic sequences like the classification of DNA sequences, comparison of DNA sequences. This article proposes a new hybrid meta-heuristic model called Crow-ENN for leukemia DNA sequences classification. The proposed algorithm is the combination of the Crow Search Algorithm (CSA) and the Elman Neural Network (ENN). DNA sequences of Leukemia are used to train and test the proposed hybrid model. Five other comparable models i.e. Crow-ANN, Crow-BPNN, ANN, BPNN and ENN are also trained and tested on these DNA sequences. The performance of models is evaluated in terms of accuracy and MSE. The overall simulation results show that the proposed model has outperformed all the other five comparable models by attaining the highest accuracy of over 99%. This model may also be used for other classification problems in different fields because it can achieve promising results.

Higher-order Markov models for metagenomic sequence classification

2020 ◽  
Vol 36 (14) ◽  
pp. 4130-4136
Author(s):  
David J Burks ◽  
Rajeev K Azad
Keyword(s):  
Dna Sequences ◽  
Markov Models ◽  
Fragment Size ◽  
Higher Order ◽  
Training Data ◽  
Supplementary Information ◽  
Local Alignment ◽  
Metagenomic Sequence ◽  
Higher Order Models

Abstract Motivation Alignment-free, stochastic models derived from k-mer distributions representing reference genome sequences have a rich history in the classification of DNA sequences. In particular, the variants of Markov models have previously been used extensively. Higher-order Markov models have been used with caution, perhaps sparingly, primarily because of the lack of enough training data and computational power. Advances in sequencing technology and computation have enabled exploitation of the predictive power of higher-order models. We, therefore, revisited higher-order Markov models and assessed their performance in classifying metagenomic sequences. Results Comparative assessment of higher-order models (HOMs, 9th order or higher) with interpolated Markov model, interpolated context model and lower-order models (8th order or lower) was performed on metagenomic datasets constructed using sequenced prokaryotic genomes. Our results show that HOMs outperform other models in classifying metagenomic fragments as short as 100 nt at all taxonomic ranks, and at lower ranks when the fragment size was increased to 250 nt. HOMs were also found to be significantly more accurate than local alignment which is widely relied upon for taxonomic classification of metagenomic sequences. A novel software implementation written in C++ performs classification faster than the existing Markovian metagenomic classifiers and can therefore be used as a standalone classifier or in conjunction with existing taxonomic classifiers for more robust classification of metagenomic sequences. Availability and implementation The software has been made available at https://github.com/djburks/SMM. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
F. A. Bastiaan von Meijenfeldt ◽  
Ksenia Arkhipova ◽  
Diego D. Cambuy ◽  
Felipe H. Coutinho ◽  
Bas E. Dutilh
Keyword(s):  
Dna Sequences ◽  
De Novo ◽  
Taxonomic Classification ◽  
Classification Method ◽  
Reference Database ◽  
Annotation Tool ◽  
Multiple Signals

Abstract Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent novel deep lineages. We present a classification method that integrates multiple signals to classify sequences (Contig Annotation Tool, CAT) and metagenome-assembled genomes (Bin Annotation Tool, BAT). Classifications are automatically made at low taxonomic ranks if closely related organisms are present in the reference database and at higher ranks otherwise. The result is a high classification precision even for sequences from considerably unknown organisms.

Phylogenetic relationships and a new sectional classification of Croton (Euphorbiaceae) in Australia

2015 ◽  
Vol 28 (4) ◽  
pp. 219 ◽  
Author(s):  
Benjamin W. van Ee ◽  
Paul I. Forster ◽  
Paul E. Berry
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Pacific Islands ◽  
Australian Species ◽  
Molecular Phylogenetic ◽  
Species Lists ◽  
Nuclear Its ◽  
Australian Flora ◽  
Sectional Classification

A molecular phylogeny, morphological descriptions, species lists and a key to the sections of Croton L. (Euphorbiaceae) recognised for Australia are presented. The molecular phylogenetic results supported the recognition of six sections, to account for the 29 native Australian species. The monophyly of each of these sections was highly supported in the Bayesian and maximum-likelihood analyses of nuclear ITS and plastid trnL–F DNA sequences, whereas their relationships to each other and to other groups were less well resolved. Croton may represent one, two or three separate arrivals to Australia, with support for hypotheses of subsequent dispersals from Australia to Pacific islands and to Asia. Croton sections Argyrati, Arnhemici, Caudati, Dockrilliorum and Insulares are newly described. Croton section Gymnocroton Baill., previously placed in synonymy, is again recognised. Croton armstrongii S.Moore is excluded from the Australian flora.

Bagging Approach for Medical Plants Recognition Based on Their DNA Sequences

2018 ◽  
Vol 9 (4) ◽  
pp. 45-60
Author(s):  
Mohamed Elhadi Rahmani ◽  
Abdelmalek Amine ◽  
Reda Mohamed Hamou
Keyword(s):  
Dna Sequences ◽  
Majority Vote ◽  
Data Sets ◽  
Data Set ◽  
Drug Production ◽  
Medical Plants

Many drugs in modern medicines originate from plants and the first step in drug production, is the recognition of plants needed for this purpose. This article presents a bagging approach for medical plants recognition based on their DNA sequences. In this work, the authors have developed a system that recognize DNA sequences of 14 medical plants, first they divided the 14-class data set into bi class sub-data sets, then instead of using an algorithm to classify the 14-class data set, they used the same algorithm to classify the sub-data sets. By doing so, they have simplified the problem of classification of 14 plants into sub-problems of bi class classification. To construct the subsets, the authors extracted all possible pairs of the 14 classes, so they gave each class more chances to be well predicted. This approach allows the study of the similarity between DNA sequences of a plant with each other plants. In terms of results, the authors have obtained very good results in which the accuracy has been doubled (from 45% to almost 80%). Classification of a new sequence was completed according to majority vote.

scholarly journals Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1014 ◽  
Author(s):  
Ana Paço ◽  
Renata Freitas ◽  
Ana Vieira-da-Silva
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Evolutionary Relationship ◽  
Repetitive Dna Sequences ◽  
Dna Remodeling ◽  
Eukaryotic Genomes ◽  
Similar Organization ◽  
Dispersed Repeats

Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a “DNA remodeling mechanism”. The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.

Towards a new classification of tribe Stachydeae (Lamiaceae): naming clades using molecular evidence

2019 ◽  
Vol 190 (4) ◽  
pp. 345-358 ◽  
Author(s):  
Yasaman Salmaki ◽  
Günther Heubl ◽  
Maximilian Weigend
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Ribosomal Dna ◽  
Molecular Evidence ◽  
New Classification ◽  
Formal Classification ◽  
Phylogenetic Nomenclature

AbstractStachydeae, comprising c. 470 species, are one of the most diverse and taxonomically puzzling groups in Lamioideae. In the present study, the phylogenetic relationships in the Eurystachys clade (a phylogenetic name for all genera attributed to Stachydeae except Melittis) were reconstructed utilizing nuclear ribosomal DNA sequences (nrETS, 5S-NTS) from 148 accessions in 12 genera. Our phylogenetic results recovered Stachys as paraphyletic with numerous traditionally recognized genera nested in it. A broadly defined Eurystachys clade, however, was monophyletic. Unlike previous studies, the present study was able to resolve the group into 12 well-supported clades, named here as (1) Eriostomum, (2) Stachys, (3) Prasium, (4) Setifolia, (5) Distantes, (6) Burgsdorfia, (7) Hesiodia, (8) Empedoclia, (9) Sideritis, (10) Marrubiastrum, (11) Swainsoniana and (12) Olisia. These 12 clades were formally named in a phylogenetic nomenclature for the Eurystachys clade. Several infrageneric units were retrieved as monophyletic, namely Sideritis sections Burgsdorfia, Empedoclia and Hesiodia, Sideritis subgenus Marrubiastrum and Stachys sections Eriostomum (including Stachys section Mucronata) and Setifolia. The findings of this study also provide the basis for a future formal classification, with two options: (1) splitting of the Eurystachys clade into 12 monophyletic genera, all of them based on pre-existing genus names and redefined to encompass additional taxa, but without clear morphological apomorphies; or (2) lumping of all segregates into a broadly defined Stachys, including widely recognized and well-defined segregates such as Prasium and Sideritis.

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