scholarly journals A DNA barcode library for ground beetles of Germany: the genus Agonum Bonelli, 1810 (Insecta, Coleoptera, Carabidae)

2020 ◽  
Vol 67 (2) ◽  
pp. 197-207
Author(s):  
Michael J. Raupach ◽  
Karsten Hannig ◽  
Jérome Morinière ◽  
Lars Hendrich
Keyword(s):  
Ground Beetle ◽  
Dna Barcode ◽  
Ground Beetles ◽  
Correct Identification ◽  
Dna Barcodes ◽  
Intraspecific Variations ◽  
Species Pairs ◽  
Large Genus ◽  
Total Dna ◽  
The Given

The ground beetle genus Agonum Bonelli, 1810 is a large genus of the tribe Platynini with many species that show high amounts of intraspecific variations, making a correct identification challenging. As part of the German Barcode of Life initiative, this publication provides a comprehensive DNA barcode library for species of Agonum that are reported for Germany. In total, DNA barcodes from 258 beetles and 23 species were analysed using the Barcode of Life Data System (BOLD) workbench, including sequences from former studies and 68 newly-generated sequences. The neighbour-joining analyses, based on K2P distances, revealed distinct clustering for all studied species, with unique Barcode Index Numbers (BINs) for 15 species (65%). BIN sharing but distinct clustering was found for three species pairs: Agonum micans/Agonum scitulum, Agonum impressum/Agonum sexpunctatum and Agonum duftschmidi/Agonum emarginatum. The given dataset and its analysis represent another important step in generating a comprehensive DNA barcode library for the ground beetles of Germany and Central Europe in terms of modern biodiversity research.

scholarly journals A DNA barcode library for ground beetles of Germany: the genus Pterostichus Bonelli, 1810 and allied taxa (Insecta, Coleoptera, Carabidae)

ZooKeys ◽  
2020 ◽  
Vol 980 ◽  
pp. 93-117
Author(s):  
Michael J. Raupach ◽  
Karsten Hannig ◽  
Jérome Morinière ◽  
Lars Hendrich
Keyword(s):  
Central Europe ◽  
Related Species ◽  
Ground Beetle ◽  
Dna Barcode ◽  
Ground Beetles ◽  
Dna Barcodes ◽  
Haplotype Sharing ◽  
Closely Related Species ◽  
Biodiversity Research ◽  
Species Pairs

Species of the ground beetle genus Pterostichus Bonelli, 1810 are some of the most common carabids in Europe. This publication provides a first comprehensive DNA barcode library for this genus and allied taxa including Abax Bonelli, 1810, Molops Bonelli, 1810, Poecilus Bonelli, 1810, and Stomis Clairville, 1806 for Germany and Central Europe in general. DNA barcodes were analyzed from 609 individuals that represent 51 species, including sequences from previous studies as well as more than 198 newly generated sequences. The results showed a 1:1 correspondence between BIN and traditionally recognized species for 44 species (86%), whereas two (4%) species were characterized by two BINs. Three BINs were found for one species (2%), while one BIN for two species was revealed for two species pairs (8%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for four species pairs. Haplotype sharing was found for two closely related species pairs: Pterostichus adstrictus Eschscholtz, 1823/Pterostichus oblongopunctatus (Fabricius, 1787) and Pterostichus nigrita Paykull, 1790/Pterostichus rhaeticus Heer, 1837. In contrast to this, high intraspecific sequence divergences with values above 2.2% were shown for three species (Molops piceus (Panzer, 1793), Pterostichus panzeri (Panzer, 1805), Pterostichus strenuus (Panzer, 1793)). Summarizing the results, the present DNA barcode library does not only allow the identification of most of the analyzed species, but also provides valuable information for alpha-taxonomy as well as for ecological and evolutionary research. This library represents another step in building a comprehensive DNA barcode library of ground beetles as part of modern biodiversity research.

scholarly journals A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae)

ZooKeys ◽  
2018 ◽  
Vol 759 ◽  
pp. 57-80 ◽  
Author(s):  
Michael J. Raupach ◽  
Karsten Hannig ◽  
Jérôme Morinière ◽  
Lars Hendrich
Keyword(s):  
Dna Barcode ◽  
Ground Beetles ◽  
Dna Barcodes ◽  
Haplotype Sharing ◽  
Reference Library ◽  
Considerable Difficulty ◽  
Molecular Species Identification ◽  
Difficult Genus ◽  
Species Pairs ◽  
Extensive Reference

The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amaraalpina/Amaratorrida and Amaracommunis/Amaraconvexior/Amaramakolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.

scholarly journals A DNA barcode-based survey of wild urban bees in the Loire Valley, France

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Irene Villalta ◽  
Romain Ledet ◽  
Mathilde Baude ◽  
David Genoud ◽  
Christophe Bouget ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Morphological Differentiation ◽  
Mass Trapping ◽  
Dna Barcodes ◽  
Wild Bees ◽  
Wild Bee ◽  
Species Pairs ◽  
Trapping Methods ◽  
Bee Decline ◽  
Loire Valley

AbstractThe current decline of wild bees puts important ecosystem services such as pollination at risk. Both inventory and monitoring programs are needed to understand the causes of wild bee decline. Effective insect monitoring relies on both mass-trapping methods coupled with rapid and accurate identifications. Identifying wild bees using only morphology can be challenging, in particular, specimens from mass-trapped samples which are often in poor condition. We generated DNA barcodes for 2931 specimens representing 157 species (156 named and one unnamed species) and 28 genera. Automated cluster delineation reveals 172 BINs (Barcodes Index Numbers). A total of 36 species (22.93%) were found in highly urbanized areas. The majority of specimens, representing 96.17% of the species barcoded form reciprocally exclusive groups, allowing their unambiguous identification. This includes several closely related species notoriously difficult to identify. A total of 137 species (87.26%) show a “one-to-one” match between a named species and the BIN assignment. Fourteen species (8.92%) show deep conspecific lineages with no apparent morphological differentiation. Only two species pairs shared the same BIN making their identification with DNA barcodes alone uncertain. Therefore, our DNA barcoding reference library allows reliable identification by non-experts for the vast majority of wild bee species in the Loire Valley.

DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

2021 ◽  
pp. 1-8
Author(s):  
J.-C. Huang ◽  
X.-Y. Li ◽  
Y.-P. Li ◽  
R.-S. Zhang ◽  
D.-B. Chen ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

scholarly journals A Systematic Study on DNA Barcoding of Medicinally Important Genus Epimedium L. (Berberidaceae)

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 637 ◽  
Author(s):  
Mengyue Guo ◽  
Yanqin Xu ◽  
Li Ren ◽  
Shunzhi He ◽  
and Xiaohui Pang
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Identification Accuracy ◽  
Dna Barcodes ◽  
Success Rates ◽  
Data Set ◽  
Herba Epimedii ◽  
Potential Risks ◽  
Medicinal Properties ◽  
Species Being

Genus Epimedium consists of approximately 50 species in China, and more than half of them possess medicinal properties. The high similarity of species’ morphological characteristics complicates the identification accuracy, leading to potential risks in herbal efficacy and medical safety. In this study, we tested the applicability of four single loci, namely, rbcL, psbA-trnH, internal transcribed spacer (ITS), and ITS2, and their combinations as DNA barcodes to identify 37 Epimedium species on the basis of the analyses, including the success rates of PCR amplifications and sequencing, specific genetic divergence, distance-based method, and character-based method. Among them, character-based method showed the best applicability for identifying Epimedium species. As for the DNA barcodes, psbA-trnH showed the best performance among the four single loci with nine species being correctly differentiated. Moreover, psbA-trnH + ITS and psbA-trnH + ITS + rbcL exhibited the highest identification ability among all the multilocus combinations, and 17 species, of which 12 are medicinally used, could be efficiently discriminated. The DNA barcode data set developed in our study contributes valuable information to Chinese resources of Epimedium. It provides a new means for discrimination of the species within this medicinally important genus, thus guaranteeing correct and safe usage of Herba Epimedii.

scholarly journals Ground beetles (Carabidae) of field margin habitats

Biologia ◽  
2020 ◽  
Vol 75 (10) ◽  
pp. 1631-1641
Author(s):  
Janina Bennewicz ◽  
Tadeusz Barczak
Keyword(s):  
Conservation Status ◽  
Ground Beetle ◽  
Abundant Species ◽  
Ground Beetles ◽  
Field Margin ◽  
Poecilus Cupreus ◽  
The Status ◽  
Beetle Assemblages ◽  
Anchomenus Dorsalis ◽  
Pterostichus Melanarius

Abstract The aim of this study was to identify the role of field margin habitats in preserving the diversity and abundance of ground beetle assemblages, including potentially entomophagous species and those with conservation status in Poland. Research material was collected in 2006–2007 in four types of margin habitats – a forest, bushes, ditches and in two arable fields. Insects were captured into pitfalls, without preservation liquid or bait added to the traps. Traps were inspected twice a week, between May and August, and one sample was a weekly capture. In field margin habitats the most abundant species were Limodromus assimilis, Anchomenus dorsalis, Pterostichus melanarius and Carabus auratus. A lower abundance of species was noted on fields, with dominant Poecilus cupreus and P. melanarius. The group of zoophagous carabids found in our study includes 30 species from field margin habitats, i.e. 37.5% of all captured Carabidae taxa and 58.3% of all specimens. The share of aphidophagous species was 84.9% among bushes, 86.7% near ditches, and 88.0% in the forest habitat. Several species captured during the study are under protection in Poland. These include the partly protected Carabus convexus, which also has the status of near threatened species, the partly protected Calosoma auropunctatum, and Broscus cephalotes. Considering all the investigated field margin habitats, ground beetles were most numerous in the oak-hornbeam habitat, defined as bushes, formed predominantly by Prunus spinosa, Crataegus leavigata, Sambucus nigra and Rosa canina. Thus, this habitat was the most important reservoir/refugium for the ground beetles.

scholarly journals Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

NeoBiota ◽  
2021 ◽  
Vol 70 ◽  
pp. 151-165
Author(s):  
Francesco Zangaro ◽  
Benedetta Saccomanno ◽  
Eftychia Tzafesta ◽  
Fabio Bozzeda ◽  
Valeria Specchia ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Special Focus ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
The Mediterranean ◽  
Taxonomic Groups ◽  
Non Indigenous Species

The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

scholarly journals DNA barcodes and morphology of P. krempfi, P. mekongensis, and P. elongatus

2016 ◽  
Vol 14 (1) ◽  
pp. 29-37 ◽  
Author(s):  
Dương Thúy Yên ◽  
Nguyễn Kiệt ◽  
Bùi Sơn Nên ◽  
Nguyễn Văn Thường ◽  
Nguyễn Bạch Loan ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Mekong Delta ◽  
Genetic Distances ◽  
Dna Barcodes ◽  
Gill Rakers ◽  
Coi Sequences ◽  
Relationship Of ◽  
Metric Traits ◽  
I Gene

Three Pangasius species including P. krempfi, P. elongatus and P. mekongensis, are economically important. They can be mis-identified due to similar external appreance at small sizes. This study aimed to distinguish these species based on their differences in DNA barcode, COI (cytochrome c oxidase subunit I) gene, and morphological characteristics. Fish with various sizes (>90 samples/species) were sampled at the lower Mekong delta region. Kimura-2 parameter genetic distances based on COI sequences of three species (15 samples, in which, 4 unique sequences were assigned Genbank accession numbers from KT289877 to KT289880) are relatively high, ranging 9.33 – 12.10 %. Morphological measurements show that coutanble traits including numbers of fin rays and the first gill rakers vary in similar ranges but ratios of metric traits are significantly different among three species (P<0.01). Principle component analysis using metric traits sets three species apart. P. elongatus is characterized by elongated body, long caudal preduncle, large eyes, and retangle palatine tooth plates. P. krempfi differs from P. mekongesis in characteristics on their head. The number of sections, shape and length of barbel are different among three species. Phylogenetic relationship of three species based on morphology and COI sequences indicate that P. krempfi is closer to P. mekongenis rather than P. elongatus, and that the distance between P. mekongenis and P. elongatus is the largest.

scholarly journals Gene Sequence Analysis of Mitochondrial COI in Genus Saperda (Coleoptera: Cerambycidae: Lamiinae)

2021 ◽  
Author(s):  
Wei XU ◽  
Qinhua Gan ◽  
Jian Pu ◽  
Yingwen Pan ◽  
Bo Cai ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Detection Rate ◽  
Gene Sequence ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Nuclear Gene ◽  
Rapid Identification ◽  
Mitochondrial Coi ◽  
Gene Sequence Analysis ◽  
Total Dna

In this study, the total DNA of nine species of Saperda (Lopezcolonia) octopunctata (Scopoli, 1772), Saperda (Lopezcolonia) scalaris (Linnaeus, 1758), Saperda interrupta Gebler, Saperda Alberti (Plavilstshikov), Saperda (Saperda) similis Laicharting, 1784, Saperda (Compsidia) populnea (Linnaeus, 1758), Saperda (Saperda) carcharias (Linnaeus, 1758), Saperda (Lopezcolonia) perforata Pallas, 1773 and Saperda ohbayashi were extracted. Two partial sequences of mitochondrial gene and one partial sequence of nuclear gene were amplified. Comparing the COI sequence with the DNA barcode data in GenBank can effectively identify the related species of Saperda. It will be applied to the rapid identification of some species of Saperda in imported wood at ports, and improve the detection rate of plant quarantine.

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