scholarly journals Molecular phylogenetics of the giant genus Croton and tribe Crotoneae (Euphorbiaceae sensu stricto) using ITS and TRNL-TRNF DNA sequence data

2005 ◽  
Vol 92 (9) ◽  
pp. 1520-1534 ◽  
Author(s):  
Paul E. Berry ◽  
Andrew L. Hipp ◽  
Kenneth J. Wurdack ◽  
Benjamin Van Ee ◽  
Ricarda Riina
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Sensu Stricto ◽  
Dna Sequence Data

Molecular phylogeny and systematics of the centipede genus Ethmostigmus Pocock (Chilopoda : Scolopendromorpha) from peninsular India

2018 ◽  
Vol 32 (6) ◽  
pp. 1316 ◽  
Author(s):  
Jahnavi Joshi ◽  
Gregory D. Edgecombe
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Indian Plate ◽  
Eastern Ghats ◽  
Integrative Approach ◽  
Phylogenetic Position ◽  
Ecological Data ◽  
Peninsular India ◽  
Dna Sequence Data

Integrative taxonomy assesses the congruence between different lines of evidence for delimiting species, such as morphological, molecular or ecological data. Herein molecular phylogenetics is used to test monophyly and determine the phylogenetic position of the Old World tropical centipede genus Ethmostigmus Pocock, 1898, and to define species boundaries for Ethmostigmus in peninsular India. A phylogeny of the family Scolopendridae based on DNA sequence data for three markers from 427 specimens sampling in all major lineages (144 individuals generated in this study) recovers Ethmostigmus as a monophyletic group, but relationships among the genera in its subfamily Otostigminae are poorly supported. Two species delimitation methods for DNA sequence data and phylogeny are integrated with morphology and geographic data to propose a well-supported species hypothesis for Ethmostigmus on the peninsular Indian plate. Five species of Ethmostigmus are recognised in peninsular India, of which E. coonooranus Chamberlin, 1920 and three new species, namely, E. agasthyamalaiensis, sp. nov., E. sahyadrensis, sp. nov. and E. praveeni, sp. nov., occur in the Western Ghats, a biodiversity hotspot. The lesser-known Eastern Ghats harbour one species, E. tristis (Meinert, 1886), which has been nearly unreported for 130 years. This study highlights the value of an integrative approach to systematics, especially in underexplored, high biodiversity regions and where morphological variation is limited among closely related species.

Phylogeny, taxonomy, and zoogeography of the genus Gekko Laurenti, 1768 with the revalidation of G. reevesii Gray, 1831 (Sauria: Gekkonidae)

Zootaxa ◽  
2011 ◽  
Vol 2989 (1) ◽  
pp. 1 ◽  
Author(s):  
HERBERT RÖSLER ◽  
AARON M. BAUER ◽  
MATTHEW P. HEINICKE ◽  
ELI GREENBAUM ◽  
TODD JACKMAN ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Identification Key ◽  
Dna Sequence Data ◽  
Preliminary Identification ◽  
Specific Rank ◽  
Species Groups

A review of the taxonomy, phylogeny, and zoogeography of all currently recognized Gekko species is provided based on morphology (including size, scalation, color, and pattern) and mitochondrial and nuclear DNA sequence data. We distinguish six morphological (phenotypic) species groups within the gekkonid genus Gekko: the G. gecko, G. japonicus, G. monarchus, G. petricolus, G. porosus, and G. vittatus groups, all of which receive support from molecular phylogenetics. The taxon G. reevesii, formerly evaluated as a synonym of G. gekko, is revalidated herein at specific rank. Furthermore, a preliminary identification key of all currently recognized Gekko taxa is provided.

Molecular phylogenetics of the Onobrychis genus (Fabaceae: Papilionoideae) using ITS and trnL–trnF DNA sequence data

2014 ◽  
Vol 62 (3) ◽  
pp. 235 ◽  
Author(s):  
S. Safaei Chaei Kar ◽  
F. Ghanavati ◽  
M. R. Naghavi ◽  
H. Amirabadi-zade ◽  
R. Rabiee
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Sequence Data ◽  
Group I ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Cultivated Species ◽  
Relationship Of

Onobrychis, comprising more than 130 species, is a genus of the family Fabaceae. At this time, the interspecies relationship of this biologically important genus is still a subject of great discussion and debate. To help resolve this disagreement, we used molecular phylogeny to analyse internal transcribed spacer (ITS) and trnL–trnF sequences of 76 species of Onobrychis. Bayesian interference, maximum parsimony and maximum likelihood analyses of nuclear ITS and plastid trnL–trnF DNA sequence data generated trees with strong posterior probability for two groups: Onobrychis subgen. Sisyrosema (including: Heliobrychis, Hymenobrychis, Afghanicae and Anthyllium sections) along with Laxiflorae section in Group I and Onobrychis subgen. Onobrychis (except Laxiflorae section) in the other (Group II). The Laxiflorae section roots back to the ancestral node for Sisyrosema subgen. O. viciifolia (cultivated species), which is closely associated with O. cyri var. cyri, suggesting that the latter may be a wild progenitor of O. viciifolia. The present study supported the paraphyly of subgenera Onobrychis and Sisyrosema. The study proposed the paraphyletic nature of the sections Onobrychis, Dendrobrychis, Heliobrychis and Hymenobrychis. Together with our molecular phylogenetic analyses we present a review of Onobrychis morphology and discuss and compare our results with those of earlier morphological and molecular phylogenetic analyses.

Taxonomy and DNA sequence databases: A perfect match?

2011 ◽  
Vol 4 (3) ◽  
pp. 221-236 ◽  
Author(s):  
John James Wilson
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Perfect Match ◽  
Dna Sequence Data ◽  
Online Databases ◽  
Sequence Databases ◽  
Diversity Of Life

AbstractDespite the declining number of traditional taxonomists, our knowledge of Earth's biodiversity continues to grow in the form of DNA sequence data. Freely available through online databases, analyses of sequence datasets are increasingly used as an alternative for the traditional taxonomic process. Species identifications have become “DNA barcoding,” new species discoveries are characterised by genetic divergences, and traditional classification has been supplanted by molecular phylogenetics. These developments are illustrated through a case study investigating the identities of Taygetis butterflies of Costa Rica. Here I review prospects and problems with the molecularization of taxonomy and the key role of publicly available nucleotide sequence databases in efforts to catalogue diversity of life.

A New Species of Physeterostemon (Melastomataceae) from Bahia, Brazil, with Notes on the Phylogeny of the Genus

2009 ◽  
Vol 34 (2) ◽  
pp. 324-329 ◽  
Author(s):  
André M. Amorim ◽  
Renato Goldenberg ◽  
Fabián A. Michelangeli
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Dna Sequence ◽  
Atlantic Forest ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Sensu Stricto ◽  
The Other ◽  
Dna Sequence Data ◽  
A New Species

Physeterostemon thomasii is described from the southern Bahian Atlantic forest of Brazil. It differs from the other two species of the genus by the paleaceous trichomes on young stems and petioles, and by the strongly bullate/foveolate leaves. A phylogenetic analysis with all three species, based on rbcL and ndhF DNA sequence data, showed that Physeterostemon forms a monophyletic group, sister to Eriocnema fulva, and this clade is placed in a polytomy at the base of the tribe Miconieae sensu stricto. However, there is no resolution within Physeterostemon, thus the phylogenetic relationships of the three species cannot be established.

scholarly journals Molecular Phylogenetics of Bromus (Poaceae: Pooideae) Based on Chloroplast and Nuclear DNA Sequence Data

Aliso ◽  
2007 ◽  
Vol 23 (1) ◽  
pp. 450-467 ◽  
Author(s):  
Jeffery Saarela ◽  
Paul Peterson ◽  
Ryan Keane ◽  
Jacques Cayouette ◽  
Sean Graham
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Dna Sequence Data

scholarly journals DNA sonification for public engagement in bioinformatics

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Heleen Plaisier ◽  
Thomas R. Meagher ◽  
Daniel Barker
Keyword(s):  
Dna Sequence ◽  
Public Engagement ◽  
Sequence Data ◽  
Sensory Perception ◽  
Data Representation ◽  
Sequence Information ◽  
Dna Sequence Data ◽  
Public Events ◽  
Dna Base ◽  
Alternative Means

Abstract Objective Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification. Results We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education.

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