scholarly journals Molecular phylogenetics of leafrollers application to DNA diagnostics

2000 ◽  
Vol 53 ◽  
pp. 157-162 ◽  
Author(s):  
D. Gleeson ◽  
P. Holder ◽  
R. Newcomb ◽  
R. Howitt ◽  
J. Dugdale
Keyword(s):  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Rapid Diagnosis ◽  
Molecular Techniques ◽  
Crucial Importance ◽  
Dna Diagnostics ◽  
Future Studies ◽  
Dna Sequence Data ◽  
Recent Developments ◽  
Diagnostic Key

Accurate and rapid diagnosis of taxa whether they be welldefined species or biotypes is of crucial importance to quarantine pest management and research Recent developments in DNA technology has resulted in a range of molecular techniques being available for use in such applications We have employed a phylogenetically focussed approach in the development of a diagnostic key to distinguish a range of leafroller species (Lepidoptera Tortricidae) using DNA sequence data derived from a 23 kb region of the mitochondrial genome containing the genes cytochrome oxidase I and II Phylogenetic analysis has revealed clear relationships between taxa although the genus Apoctena does not appear monophyletic The most appropriate diagnostic characters are either those which are phylogenetically informative either synapomorphies or autapomorphies A standardised approach to data collection is advocated for future studies

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.

scholarly journals Molecular Phylogenetics of The Tody-Tyrant and Flatbill Assemblage of Tyrant Flycatchers (Tyrannidae)

The Auk ◽  
2007 ◽  
Vol 124 (1) ◽  
pp. 134-154 ◽  
Author(s):  
Jose G. Tello ◽  
John M. Bates
Keyword(s):  
Molecular Phylogenetics ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Data Sets ◽  
Skull Morphology ◽  
Base Pairs ◽  
Dna Sequence Data ◽  
Phylogenetic Framework ◽  
Data Partitions ◽  
Tyrant Flycatchers

Abstract The tody-tyrant and flatbill assemblage, sensuLanyon (1988a), includes 12 genera of tyrant flycatchers known variously as “tody-tyrants” and “flatbills.” Lanyon supported the monophyly of the group based on similar skull morphology and nest form, and built intergeneric relationships based on syringeal characters. However, these comparisons were made without a phylogenetic framework. A more recent study assessing relationships in the tyrant flycatchers using published morphological and behavioral data failed to recover monophyly of this assemblage (Birdsley 2002). Using DNA sequence data, we test for the monophyly of the tody-tyrant and flatbill assemblage and compare and contrast phylogenetic signals from mitochondrial and nuclear DNA character systems. We discuss our results in light of results from previous studies. We include representatives of the other major tyrant flycatcher assemblages for a total of 42 individuals (representing 27 tyrannid genera and 36 species). We sequenced 3,022 base pairs (bp) of three mitochondrial genes (ND2, ND3, and cytochrome b) and one nuclear intron (FIB5). Our results resolve many of the basal relationships of the tody-tyrant and flatbill phylogeny, but separate and combined analyses of data partitions are necessary to understand the nature of conflict among data sets. The tody-tyrants constitute a monophyletic clade, but the genera Hemitriccus and Lophotriccus are not monophyletic, and the limits of Oncostoma-Lophotriccus need to be revised with more complete sampling at the species level. The flatbills as defined by Lanyon are not monophyletic (Onychorhynchus and Platyrinchus are not true flatbills). Pseudotriccus and Corythopis are sister taxa and, together with Leptopogon and Mionectes, are allied to the tody-tyrant and flatbill clade. Filogenia Molecular del Grupo de los Picochatos y Mosquiteros de la Familia Tyrannidae

Gyretes Brullé (Coleoptera: Gyrinidae) from Brazil: Morphology of eggs and early instars

Zootaxa ◽  
2018 ◽  
Vol 4526 (3) ◽  
pp. 331 ◽  
Author(s):  
DANIARA COLPANI ◽  
CÉSAR JOÃO BENETTI ◽  
NEUSA HAMADA ◽  
VANDERLY ANDRADE-SOUZA ◽  
MARIANO C. MICHAT
Keyword(s):  
Related Species ◽  
Sequence Data ◽  
Larval Survival ◽  
Molecular Techniques ◽  
Coi Gene ◽  
Immature Stages ◽  
Closely Related Species ◽  
Species Association ◽  
Dna Sequence Data ◽  
Laboratory Conditions

Taxonomic information regarding Gyrinidae is mostly based on adults, especially due to the difficulty in collecting immatures and assigning them to a particular species. Association between immatures and adults is sometimes difficult because closely related species can be found in the same habitat. To solve this problem a feasible technique is rearing under laboratory conditions. However, this method is challenging because larval survival rate is usually low, and emulation of natural conditions is difficult. Molecular techniques, especially the use of the COI gene, have been applied to identify species and to associate different life stages. However, in some species groups this marker has not been successful in distinguishing closely related species. The objectives of this study are to describe the egg and the first two instars of Gyretes nubilus Ochs, 1965 and the egg of G. minax Ochs, 1967 and to evaluate the utility of COI to associate immatures and adults. The association of these immature stages with adults was done either rearing adults under laboratory conditions or by using DNA sequence data (COI), corroborating the utility of this molecular marker to associate immature and adults in Gyretes. These immature stages are described, including chaetotaxic analysis of larvae for the first time for the genus Gyretes Brullé, 1835. The eggs are described based on scanning electron microscopy. The eggs are similar to those of other Gyrinidae genera in having a micropylar region in the anterior pole and a longitudinal fissure, and by the absence of an aeropyle, but they differ mainly in characters related to chorionic structure and reticulation. Larvae of Gyretes can be distinguished from those of the other Neotropical Gyrinidae genera by a combination of several characters, including the frontoclypeal seta FR3 short, presence of three conspicuous additional setae on lateral region of parietal (contiguous to stemmata), and posterior margin of lacinia smooth, with apex not indented. 

Two new species of Oobius (Hymenoptera: Encyrtidae) and their phylogenetic relationship with other congeners from northeastern Asia

2018 ◽  
Vol 150 (3) ◽  
pp. 303-316 ◽  
Author(s):  
Yan-Xia Yao ◽  
Jian J. Duan ◽  
Jason L. Mottern ◽  
Xiao-Yi Wang ◽  
Zhong-Qi Yang ◽  
...  
Keyword(s):  
New Species ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Emerald Ash Borer ◽  
Distinct Species ◽  
Agrilus Planipennis ◽  
Morphological Data ◽  
Dna Sequence Data ◽  
Two New Species ◽  
Phloem Feeding

AbstractTwo new species of egg parasitoids, Oobius saimaensis Yao and Mottern new species and Oobius fleischeri Yao and Duan new species (Hymenoptera: Encyrtidae), are described from eggs of Agrilus fleischeri Obenberger, 1925 (Coleoptera: Buprestidae). Agrilus fleischeri is a phloem-feeding woodborer of poplar (Populus Linnaeus; Salicaceae) in northeastern China. These two species can be distinguished morphologically as O. fleischeri has five tarsomeres and O. saimaensis has four tarsomeres. Although O. saimaensis is morphologically similar to its sympatric congener O. agrili Zhang and Hang, 2005, an important natural enemy of the invasive emerald ash borer, Agrilus planipennis Fairmaire, 1888, molecular phylogenetics and morphological data indicate that they are distinct species. Phylogenetic relationships among the new species and other closely related species are also inferred by using DNA sequence data from several ribosomal and mitochondrial genes. In addition, we expand the known distribution of Oobius primorskyensis Yao and Duan, 2016 to include South Korea.

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 novel phylogeny for the genus Echinococcus, based on nuclear data, challenges relationships based on mitochondrial evidence

Parasitology ◽  
2009 ◽  
Vol 136 (3) ◽  
pp. 317-328 ◽  
Author(s):  
U. SAARMA ◽  
I. JÕGISALU ◽  
E. MOKS ◽  
A. VARCASIA ◽  
A. LAVIKAINEN ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Evolutionary History ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Nuclear Data ◽  
Sole Source ◽  
Phenotypic Analysis ◽  
Future Studies ◽  
Dna Sequence Data

SUMMARYThe taxonomic status of Echinococcus, an important zoonotic cestode genus, has remained controversial, despite numerous attempts to revise it. Although mitochondrial DNA (mtDNA) has been the source of markers of choice for reconstructing the phylogeny of the genus, results derived from mtDNA have led to significant inconsistencies with earlier species classifications based on phenotypic analysis. Here, we used nuclear DNA markers to test the phylogenic relationships of members of the genus Echinococcus. The analysis of sequence data for 5 nuclear genes revealed a significantly different phylogeny for Echinococcus from that proposed on the basis of mitochondrial DNA sequence data, but was in agreement with earlier species classifications. The most notable results from the nuclear phylogeny were (1) E. multilocularis was placed as basal taxon, (2) all genotypes of Echinococcus granulosus grouped as a monophyletic entity, and (3) genotypes G8 and G10 clustered together. We conclude that the analysis of nuclear DNA data provides a more reliable means of inferring phylogenetic relationships within Echinococcus than mtDNA and suggest that mtDNA should not be used as the sole source of markers in future studies where the goal is to reconstruct a phylogeny that does not only reflect a maternal lineage, but aims to describe the evolutionary history at species level or higher.

Phylogeny of the Crepidula plana (Gastropoda: Calyptraeidae) cryptic species complex in North America

2000 ◽  
Vol 78 (8) ◽  
pp. 1500-1514 ◽  
Author(s):  
Rachel Collin
Keyword(s):  
North Carolina ◽  
North America ◽  
Species Complex ◽  
East Coast ◽  
Sequence Data ◽  
Single Species ◽  
The United States ◽  
Molecular Techniques ◽  
Dna Sequence Data ◽  
Cryptic Species Complex

The taxonomy of Crepidula species with flat white shells is particularly difficult. These animals from the east coast of North America have generally been classified as a single species, Crepidula plana Say, 1822. Based on allozyme and developmental data, however, Hoagland (K.E. Hoagland. 1984. Malacologia, 25: 607-628; K.E. Hoagland. 1986. Am. Malacol. Bull. 4: 173-183) concluded that two species of flat white-shelled Crepidula live along the east coast of the United States, but she did not apply any name to the second species. Herein I use molecular techniques to characterize populations of flat white-shelled Crepidula species from Texas, Florida, Georgia, North Carolina, and |Massachusetts, and describe their morphology and development. DNA-sequence data support the existence of three species. One species is readily distinguished on the basis of morphology and development, but the other two are very similar. To clarify the nomenclature of these species, I designate neotypes for C. plana Say, 1822 and Crepidula depressa Say, 1822, and describe Crepidula atrasolea sp.nov.

Sign in / Sign up

Export Citation Format

Share Document