scholarly journals Characterizing Billbug (Sphenophorus spp.) Seasonal Biology Using DNA Barcodes and a Simple Morphometric Analysis

Insects ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 930
Author(s):  
Marian M. Rodriguez-Soto ◽  
Douglas S. Richmond ◽  
Ricardo A. Ramirez ◽  
Xi Xiong ◽  
Laramy S. Enders
Keyword(s):  
Dna Barcoding ◽  
Growing Season ◽  
Head Capsule ◽  
Clear Understanding ◽  
Dna Barcodes ◽  
Reference Library ◽  
Cytochrome Oxidase Subunit ◽  
Species Identity ◽  
Coi Sequences ◽  
The Aesthetic

Billbugs (Sphenophorus spp.) are a complex of grass-feeding weevil species that reduce the aesthetic and functional qualities of turfgrass. Effective billbug monitoring and management programs rely on a clear understanding of their seasonal biology. However, our limited understanding of regional variation in the species compositions and seasonal biology of billbugs, stemming primarily from our inability to identify the damaging larval stage to species level, has hindered efforts to articulate efficient IPM strategies to growers. We used a combination of DNA barcoding methods and morphometric measures to begin filling critical gaps in our understanding of the seasonal biology of the billbug species complex across a broad geographic range. First, we developed a DNA barcoding reference library using cytochrome oxidase subunit 1 (COI) sequences from morphologically identified adult billbugs collected across Indiana, Missouri, Utah and Arizona. Next, we used our reference library for comparison and identification of unknown larval specimens collected across the growing season in Utah and Indiana. Finally, we combined our DNA barcoding approach with larval head capsule diameter, a proxy for developmental instar, to develop larval phenology charts. Adult COI sequences varied among billbug species, but variation was not influenced by geography, indicating that this locus alone was useful for resolving larval species identity. Overlaid with head capsule diameter data from specimens collected across the growing season, a better visualization of billbug species composition and seasonal biology emerged. This approach will provide researchers with the tools necessary to fill critical gaps in our understanding of billbug biology and facilitate the development of turfgrass pest management programs.

Prospects on the Application of DNA Barcoding on Soil-Transmitted Helminths in Children

2017 ◽  
Vol 12 (04) ◽  
pp. 256-263
Author(s):  
Romano Ngui ◽  
Veeranoot Nissapatorn ◽  
Guo-Jie Brandon-Mong
Keyword(s):  
Dna Barcoding ◽  
Epidemiological Data ◽  
Special Focus ◽  
Dna Barcodes ◽  
Future Prospects ◽  
Reference Library ◽  
Cytochrome Oxidase Subunit ◽  
Mtdna Sequences ◽  
Soil Transmitted Helminths ◽  
Ancylostoma Duodenale

AbstractSince more than a decade, DNA barcoding has been widely used to examine biological samples and differentiate species, as well as employed in ecological and conservational studies. There is a growing interest of DNA barcoding, particularly in medical parasitology, but its potential utility in soil-transmitted helminths (STHs) remains unclear. Therefore, in this article, we review the studies using DNA barcoding and its applications in medical parasitology with special focus on STHs such as Ascaris lumbricoides, Ancylostoma duodenale, Necator americanus, and Trichuris trichiura. DNA barcoding is reliable for identifying STH species as well as its cryptic species. In addition, epidemiological data and the impacts of STH infections on children are discussed. This article further discusses the paucity of STH DNA barcodes (partial cytochrome oxidase subunit 1 [COI] mitochondrial DNA [mtDNA] sequences) in two gene banks; National Center for Biotechnology Information (NCBI) and Barcode of Life Data (BOLD) Systems. It also highlights the future prospects of DNA barcoding including primer designing and reference library on STHs.

scholarly journals COI-based barcoding of Chinese vipers (Reptilia: Squamata: Viperidae)

2015 ◽  
Vol 36 (4) ◽  
pp. 361-372 ◽  
Author(s):  
Qin Liu ◽  
Fei Zhu ◽  
Guanghui Zhong ◽  
Yunyu Wang ◽  
Min Fang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Intraspecific Variability ◽  
Gene Fragment ◽  
Reference Library ◽  
Threshold Method ◽  
Cytochrome Oxidase Subunit ◽  
Barcoding Gap ◽  
Putative Species ◽  
Interspecific Divergence ◽  
Identification Of Species

DNA barcoding seeks to assemble a standardized reference library for rapid and unambiguous identification of species, and can be used to screen for potentially cryptic species. The 5′ region of cytochrome oxidase subunit I (COI), which is a mitochondrial DNA (mtDNA) gene fragment, has been proposed as a universal marker for this purpose among animals. However, DNA barcoding of reptiles is still supported only by few datasets compared with other groups. We investigated the utilization of COI to discriminate 34 putative species of vipers, representing almost 92% of the recorded species in China. Based on a total of 241 sequences, our results indicated that the average degree of intraspecific variability (0.0198) tends to be one-sixth the average of interspecific divergence (0.0931), but no barcoding gap was detected between them. The threshold method, BLOG analyses and tree-based methods all can identify species with a high success rate. These results consistently suggested the usefulness and reliability of the DNA barcoding approach in Chinese vipers.

Species delimitation of Lachlania Hagen (Ephemeroptera: Oligoneuriidae) with description of two new species from Brazil

Zoosymposia ◽  
2016 ◽  
Vol 11 ◽  
pp. 121-134 ◽  
Author(s):  
FABIANA CRISTE MASSARIOL ◽  
ROBERTA PARESQUE ◽  
FREDERICO FALCÃO SALLES
Keyword(s):  
New Species ◽  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Body Length ◽  
Species Delimitation ◽  
Immature Stages ◽  
Dna Barcodes ◽  
Cytochrome Oxidase Subunit ◽  
Male And Female ◽  
Two New Species

Based on DNA barcodes (cytochrome oxidase subunit I sequences) of Lachlania specimens from Atlantic Forest and Cerrado of Brazil, eight lineages were delimited through DNA barcoding and imagoes and immature stages were associated. Among these lineages, two new species are described, Lachlania alcidesi sp. nov. and Lachlania aldinae sp. nov., from State of Espírito Santo. The former species based on nymph, male, and female imagoes, and the latter based on nymph and female imagoes. The main characteristics used to distinguish female imagoes of the new species from those of known species of the genus are: 1) body length; 2) head coloration; 3) number of cross veins on forewing; 4) coloration of caudal filaments; 5) relation between length from point of origin of IMP to margin and total length of MA2- MP1 of forewing.

scholarly journals Identification of Nepeta olgae Regel and phylogenetic status of some genera in subtribe Nepetinae (Lamiaceae) using DNA markers

2021 ◽  
Vol 38 ◽  
pp. 00087
Author(s):  
Elena Nikitina ◽  
Abdurashid Rakhmatov
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Biodiversity Monitoring ◽  
Reference Library ◽  
Accurate Identification ◽  
Unknown Species ◽  
Phylogenetic Status ◽  
Nuclear Its

The species level diversity is the reference unit for biodiversity accounting, should be systematized and include full information about the species. Reliable identification of any species is critical for a large-scale biodiversity monitoring and conservation. A DNA barcode is a DNA sequence that identifies a species by comparing the sequence of an unknown species with barcodes of a known species sequence database. Accurate identification of important plants is essential for their conservation, inventory. The species diversity assessing exampled on the subtribe Nepetinae (Lamiaceae) representatives, growing in Uzbekistan is given, using DNA barcoding method. The study was aimed to identify indigenous important plants with the nuclear (ITS) and plastid (matK, rbcL, trnL-F) genomes. This work demonstrates the phylogenetic relationships of some genera within the subtribe Nepetinae Coss. & Germ. (Lamiaceae), based on ITS locus gene. All results indicate that the DNA barcoding tool can be successfully used to reliably identify important plants, to inventory the botanical resources of Uzbekistan and to create a reference library of DNA barcodes. So, the combination of three-four locus gene is a good candidate for this approach.

scholarly journals New records of water mites from the Balkans revealed by DNA barcoding (Acari, Hydrachnidia)

2021 ◽  
Vol 49 ◽  
pp. 20-34
Author(s):  
Vladimir Pešić ◽  
Milica Jovanović ◽  
Ana Manović ◽  
Ioannis Karaouzas ◽  
Harry Smit
Keyword(s):  
Dna Barcoding ◽  
New Records ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Water Mites ◽  
Water Mite ◽  
The Balkans ◽  
Coi Sequences ◽  
First Time

New records of water mites from Serbia, North Macedonia and Greece revealed by DNA barcoding are presented. DNA barcodes were recovered from 63 water mite specimens morphologically assigned to 32 species. One species Lebertia algeriensis Lundblad, 1942, is reported for the first time for the Balkans; four species, i.e. Lebertia fimbriata Thor, 1899, L. rivulorum K. Viets, 1933, Atractides stankovici Pešić & Gerecke, 2010, and Wettina lacustris Pešić & Smit, 2018 are new for North Macedonia; Monatractides madritensis (K. Viets, 1930) and Mideopsis roztoczensis Biesiadka & Kowalik, 1979 are new for Serbia; and Hygrobates mediterraneus Pešić, 2020 is new for Greece. Comparing sequences of our study with the available COI sequences we recognized five possible cases of cryptic diversity involving species clusters with more than 5% divergence indicating that these species need further study.

scholarly journals DNA barcoding of marine fish species from Rongcheng Bay, China

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5013 ◽  
Author(s):  
Lijuan Wang ◽  
Zhihao Wu ◽  
Mengxia Liu ◽  
Wei Liu ◽  
Wenxi Zhao ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Dna Barcode ◽  
Gc Content ◽  
Genetic Distances ◽  
Dna Barcodes ◽  
Reference Library ◽  
Fish Species Identification ◽  
Northern Yellow Sea ◽  
Coastal Bay

Rongcheng Bay is a coastal bay of the Northern Yellow Sea, China. To investigate and monitor the fish resources in Rongcheng Bay, 187 specimens from 41 different species belonging to 28 families in nine orders were DNA-barcoded using the mitochondrial cytochrome c oxidase subunit I gene (COI). Most of the fish species could be discriminated using this COI sequence with the exception of Cynoglossus joyneri and Cynoglossus lighti. The average GC% content of the 41 fish species was 47.3%. The average Kimura 2-parameter genetic distances within the species, genera, families, and orders were 0.21%, 5.28%, 21.30%, and 23.63%, respectively. Our results confirmed that the use of combined morphological and DNA barcoding identification methods facilitated fish species identification in Rongcheng Bay, and also established a reliable DNA barcode reference library for these fish. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in this area.

A new melanistic variant of the caterpillar hunter Calosoma wilcoxi LeConte, 1848 from Texas, United States of America and a preliminary phylogeny of the genus Calosoma Weber, 1801 (Coleoptera: Carabidae)

2016 ◽  
Vol 149 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Jesse W. Ray ◽  
Matthias Seidel ◽  
Martin Husemann
Keyword(s):  
United States ◽  
United States Of America ◽  
Phylogenetic Analyses ◽  
Ground Beetle ◽  
Abundant Species ◽  
Cytochrome Oxidase Subunit ◽  
New Variant ◽  
Central Texas ◽  
Coi Sequences ◽  
Dark Blue

AbstractTwo aberrant ground beetle (Coleoptera: Carabidae) specimens from the genus Calosoma Weber, 1801 were collected in Waco, Texas, United States of America, in 2012–2013. The specimens, which are morphologically most similar to Calosoma wilcoxi LeConte, 1848, but are dark blue-black instead of the typical metallic green. We employed DNA barcoding and phylogenetic methods to confirm the identities of the aberrant specimens. Preliminary phylogenetic analyses of cytochrome oxidase subunit 1 (COI) sequences of central Texas and southwestern species place the aberrant specimens with 100% confidence as C. wilcoxi. The new variant of C. wilcoxi presumably occurs at low densities. Frequent collecting from 2011 to 2014 resulted in the discovery of only two of the aberrant coloured individuals among hundreds of typical green specimens. These specimens (to our knowledge) represent the first published record of melanistic Calosoma from North America. While the majority of North American species in the genus are naturally black, two of the most widely distributed and abundant species, C. scrutator (Fabricius, 1775) and C. wilcoxi, are typically green. We sequenced the aberrant form as well as all species co-occurring with the new colour morph at the collection locality and used records from GenBank and the Barcode of Life Data System to generate a preliminary phylogeny of the genus, which suggested that some of the currently established subgenera are likely not monophyletic.

scholarly journals Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 851-854 ◽  
Author(s):  
Mehrdad Hajibabaei ◽  
Gregory AC Singer ◽  
Donal A Hickey
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Primate Species ◽  
Dna Barcodes ◽  
Global Biodiversity ◽  
Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

New species and findings of Pagastia Oliver (Diptera: Chironomidae: Diamesinae) from Central Asia, with DNA barcoding of known species of the genus

Zootaxa ◽  
2021 ◽  
Vol 4951 (3) ◽  
pp. 559-570
Author(s):  
EUGENYI A.  MAKARCHENKO ◽  
ALEXANDER A. SEMENCHENKO ◽  
DMITRY M. PALATOV
Keyword(s):  
New Species ◽  
Central Asia ◽  
Cytochrome Oxidase ◽  
Phylogenetic Trees ◽  
Morphological Characters ◽  
Molecular Data ◽  
Adult Males ◽  
Cytochrome Oxidase Subunit ◽  
Oxidase Subunit ◽  
Coi Sequences

Chironomids of the genus Pagastia Oliver (Diamesinae, Diamesini) from the mountains of Central Asia are revised using both morphological characters and molecular data. Illustrated descriptions of the adult male Pagastia (P.) caelestomontana sp. nov. from Kirgizstan and Tajikistan, P. (P.) hanseni sp. nov. from Tajikistan, and record of a finding apparently a new species P. (P.) aff. lanceolata (Tokunaga) from Tajikistan as well as an updated a key to the determination of the adult males of all known species of Pagastia are provided. A phylogenetic framework is reconstructed based on two mitochondrial genes cytochrome oxidase subunit I (COI) sequences of 34 samples belonging to 7 species of the genus Pagastia and cytochrome oxidase subunit II (COII) available for most samples. Phylogenetic trees of some known species of the genus Pagastia were reconstructed using the combined dataset and Bayesian inference (BI) and Maximum Likelihood (ML) methods. The interspecific K2P distances between seven Pagastia species including P. (P.) caelestomontana sp. nov., P. (P.) hanseni sp. nov. and undescribed P. (P.) aff. lanceolata (Tokunaga) are 6.3–13.2 which corresponding to species level. 

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