From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes

With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future. The existing data also opens new questions regarding the causes of observed low inter- and high intraspecific genetic variation and furthermore highlight the necessity of taxonomic revisions for various taxa, combining both molecular and morphological data.

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Congruence between morphology-based species and Barcode Index Numbers (BINs) in Neotropical Eumaeini (Lycaenidae)

PeerJ ◽

10.7717/peerj.11843 ◽

2021 ◽

Vol 9 ◽

pp. e11843

Author(s):

Carlos Prieto ◽

Christophe Faynel ◽

Robert Robbins ◽

Axel Hausmann

Keyword(s):

Incomplete Lineage Sorting ◽

Dna Barcode ◽

Morphological Data ◽

Biological Assessment ◽

Index Number ◽

High Mountain ◽

Lineage Sorting ◽

Data Set ◽

Index Numbers ◽

The Mean

Background With about 1,000 species in the Neotropics, the Eumaeini (Theclinae) are one of the most diverse butterfly tribes. Correct morphology-based identifications are challenging in many genera due to relatively little interspecific differences in wing patterns. Geographic infraspecific variation is sometimes more substantial than variation between species. In this paper we present a large DNA barcode dataset of South American Lycaenidae. We analyze how well DNA barcode BINs match morphologically delimited species. Methods We compare morphology-based species identifications with the clustering of molecular operational taxonomic units (MOTUs) delimitated by the RESL algorithm in BOLD, which assigns Barcode Index Numbers (BINs). We examine intra- and interspecific divergences for genera represented by at least four morphospecies. We discuss the existence of local barcode gaps in a genus by genus analysis. We also note differences in the percentage of species with barcode gaps in groups of lowland and high mountain genera. Results We identified 2,213 specimens and obtained 1,839 sequences of 512 species in 90 genera. Overall, the mean intraspecific divergence value of CO1 sequences was 1.20%, while the mean interspecific divergence between nearest congeneric neighbors was 4.89%, demonstrating the presence of a barcode gap. However, the gap seemed to disappear from the entire set when comparing the maximum intraspecific distance (8.40%) with the minimum interspecific distance (0.40%). Clear barcode gaps are present in many genera but absent in others. From the set of specimens that yielded COI fragment lengths of at least 650 bp, 75% of the a priori morphology-based identifications were unambiguously assigned to a single Barcode Index Number (BIN). However, after a taxonomic a posteriori review, the percentage of matched identifications rose to 85%. BIN splitting was observed for 17% of the species and BIN sharing for 9%. We found that genera that contain primarily lowland species show higher percentages of local barcode gaps and congruence between BINs and morphology than genera that contain exclusively high montane species. The divergence values to the nearest neighbors were significantly lower in high Andean species while the intra-specific divergence values were significantly lower in the lowland species. These results raise questions regarding the causes of observed low inter and high intraspecific genetic variation. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the montane species concerned are relatively young and hybridization is probable. The release of our data set represents an essential baseline for a reference library for biological assessment studies of butterflies in mega diverse countries using modern high-throughput technologies an highlights the necessity of taxonomic revisions for various genera combining both molecular and morphological data.

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

Genes ◽

10.3390/genes9120637 ◽

2018 ◽

Vol 9 (12) ◽

pp. 637 ◽

Cited By ~ 9

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.

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The genus Cystoseira s.l. (Ochrophyta, Fucales, Sargassaceae) in the Black Sea: morphological variability and molecular taxonomy of Gongolaria barbata and endemic Ericaria crinita f. bosphorica comb. nov.

Phytotaxa ◽

10.11646/phytotaxa.480.1.1 ◽

2021 ◽

Vol 480 (1) ◽

pp. 1-21

Author(s):

SOFIA S. SADOGURSKA ◽

JOÃO NEIVA ◽

ANNALISA FALACE ◽

ESTER A. SERRÃO ◽

ÁLVARO ISRAEL

Keyword(s):

Mediterranean Sea ◽

Black Sea ◽

Molecular Taxonomy ◽

Morphological Variability ◽

Morphological Characteristics ◽

Molecular Data ◽

Morphological Data ◽

The Black Sea ◽

Morphological Identification ◽

Additional Tool

Brown algae of the genus Cystoseira sensu lato form the most diverse and productive marine ecosystems throughout the Mediterranean Sea and have equal roles also in the Black Sea where they have been decreasing in the recent years. The taxonomy of Cystoseira s.l. taxa from the Black Sea is still not well understood, and questions arise when related taxa have to be delimited. In addition to morphological descriptions, this study provides for the first time molecular data of the Black Sea Cystoseira s.l. distinct morphologies as an additional tool to clarify their identities and phylogenetic affinities. The analysis of two mitochondrial markers (cytochrome oxidase subunit 1—COI, and 23S-tRNAVal intergenic spacer—mt-spacer) showed that Cystoseira s.l. specimens from the Black Sea belong to two recently resurrected genera, namely Gongolaria and Ericaria. Molecular data confirm the morphological identification of G. barbata, which is characterized by high morphological plasticity in the Black Sea. The morphological data presented in this study support the transition of G. barbata to the genus Gongolaria, which was previously proposed based solely on genetic data. For the Black Sea endemic taxon C. bosphorica, sequence divergence suggests conspecificity with Mediterranean Sea species E. crinita and E. barbatula. However, considering original morphological characteristics of the taxon, its geographical isolation, and endemism, the new combination Ericaria crinita f. bosphorica comb. nov. is proposed.

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DNA Barcoding: Mixed results for big-headed flies (Diptera: Pipunculidae)

Zootaxa ◽

10.11646/zootaxa.1423.1.1 ◽

2007 ◽

Vol 1423 (1) ◽

pp. 1-26 ◽

Cited By ~ 20

Author(s):

JEFFREY H. SKEVINGTON ◽

CHRISTIAN KEHLMAIER ◽

GUNILLA STÅHLS

Keyword(s):

Dna Barcoding ◽

Sequence Data ◽

Phylogenetic Signal ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Base Pairs ◽

Data Set ◽

Taxonomic Decision ◽

Morphological Species

Sequence data from 658 base pairs of mitochondrial cytochrome c oxidase I (cox1) were analysed for 28 described species of Pipunculidae (Diptera) in an effort to test the concept of DNA Barcoding on this family. Two recently revised but distantly related pipunculid lineages with presumed different evolutionary histories were used for the test (Clistoabdominalis Skevington, 2001 and Nephrocerus Zetterstedt, 1838). An effort was made to test the concept using sister taxa and morphologically similar sibling species swarms in these two genera. Morphological species concepts for Clistoabdominalis taxa were either supported by cox1 data or found to be too broad. Most of the discordance could be accounted for after reassessing morphological characters. In these cases, the molecular data were invaluable in assisting taxonomic decision-making. The radiation of Nearctic species of Nephrocerus could not be diagnosed using cox1. The ability of cox1 to recover phylogenetic signal was also tested on Clistoabdominalis. Morphological data for Clistoabdominalis were combined with the molecular data set. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology. Partitioned Bremer support is used to localize areas of conflict between the datasets.

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The phylogenetic conundrum of Lutzia (Diptera: Culicidae: Culicini): a cautionary account of conflict and support

Insect Systematics & Evolution ◽

10.1163/1876312x-45032119 ◽

2015 ◽

Vol 46 (3) ◽

pp. 269-290 ◽

Cited By ~ 6

Author(s):

Ian J. Kitching ◽

C. Lorna Culverwell ◽

Ralph E. Harbach

Keyword(s):

Dna Sequences ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Data Set ◽

Generic Status ◽

Strong Signal ◽

Phylogenetic Studies ◽

Data Support

Lutzia Theobald was reduced to a subgenus of Culex in 1932 and was treated as such until it was restored to its original generic status in 2003, based mainly on modifications of the larvae for predation. Previous phylogenetic studies based on morphological and molecular data have provided conflicting support for the generic status of Lutzia: analyses of morphological data support the generic status whereas analyses based on DNA sequences do not. Our previous phylogenetic analyses of Culicini (based on 169 morphological characters and 86 species representing the four genera and 26 subgenera of Culicini, most informal group taxa of subgenus Culex and five outgroup species from other tribes) seemed to indicate a conflict between adult and larval morphological data. Hence, we conducted a series of comparative and data exclusion analyses to determine whether the alternative positions of Lutzia are due to conflicting signal or to a lack of strong signal. We found that separate and combined analyses of adult and larval data support different patterns of relationships between Lutzia and other Culicini. However, the majority of conflicting clades are poorly supported and once these are removed from consideration, most of the topological disparity disappears, along with much of the resolution, suggesting that morphology alone does not have sufficiently strong signal to resolve the position of Lutzia. We critically examine the results of other phylogenetic studies of culicinine relationships and conclude that no morphological or molecular data set analysed in any study conducted to date has adequate signal to place Lutzia unequivocally with regard to other taxa in Culicini. Phylogenetic relationships observed thus far suggest that Lutzia is placed within Culex but further data and extended taxon sampling are required to confirm its position relative to Culex.

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The greenhouse thrips, Heliothrips haemorrhoidalis, and its generic relationships within the subfamily Panchaetothripinae (Thysanoptera: Thripidae)

Insect Systematics & Evolution ◽

10.1163/187631201x00164 ◽

2001 ◽

Vol 32 (2) ◽

pp. 205-216 ◽

Cited By ~ 2

Author(s):

John W.H. Trueman ◽

Rita Marullo ◽

Laurence A. Mound

Keyword(s):

Sister Group ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Sister Group Relationship ◽

Pest Species ◽

Data Set ◽

Weak Support ◽

Heliothrips Haemorrhoidalis ◽

Generic Relationships

AbstractThe subfamily Panchaetothripinae, comprising 35 genera and 98 species, includes several pest species of which the most notorious is the greenhouse thrips, Heliothrips haemorrhoidalis. In an attempt to establish the sister-group of Heliothrips, the relationships of this genus to 31 of the other genera in the subfamily were examined cladistically, using 35 parsimony-informative morphological characters. The analysis indicated that there was no support for two of the three tribes into which this subfamily is customarily arranged, the Monilothripini and the Panchaetothripini, but weak support for the tribe Tryphactothripini. No clear sister-group relationship could be identified for the New World genus Heliothrips, although it grouped with three old world genera Australothrips, Retithrips and Rhipiphorothrips. It is concluded that a morphological data set is not capable of producing a robust phylogeny of the Panchaetothripinae, and that the subject requires re-examination using molecular data.

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Preliminary Study on the Solanum nigrum L. (Solanaceae) Complex in the Democratic Republic of the Congo

European Journal of Biology and Biotechnology ◽

10.24018/ejbio.2021.2.5.256 ◽

2021 ◽

Vol 2 (5) ◽

pp. 9-18

Author(s):

Blaise Bikandu Kapesa ◽

Marc Sosef ◽

Steven Janssens ◽

Timothée Le Péchon ◽

Félicien Lukoki Luyeye

Keyword(s):

Democratic Republic ◽

Democratic Republic Of Congo ◽

Morphological Variability ◽

Central Africa ◽

Molecular Study ◽

Molecular Data ◽

Solanum Nigrum ◽

High Rate ◽

Data Set ◽

Solanum Nigrum Complex

Black nightshade, or the Solanum nigrum complex, includes a number of species that botanists consider problematic due to their morphological resemblance and the high rate of hybridization. As part of the revision of the family Solanaceae for the Flora central Africa,we realized a molecular study of the Solanum nigrum complex in the western part of the Democratic Republic of Congo. A total of 21 samples of this complex were collected and identified using the recent revision by [11]. The DNA of each specimen was extracted and then amplified by PCR for 4 molecular markers: the two nuclear regions waxy and ITS, and the two chloroplastics markers trnL-F and trnH-psbA. Additional sequences of specimens reliably identified were obtained from GenBank. The combined molecular data set allowed for the identification of two distinct groups. The first we conclude that in the western part of D.R. Congo, two species of the Solanum nigrum complex occur, both showing high morphological variability, while the true Solanum nigrum is absent from that region. The two species are Solanum americanum Mill. and Solanum scabrum Mill. The results confirm the taxonomic decisions of [11]. The generally low resolution in the analyses did not allow to visualize a geographical signal in the variation.

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Linking karyotypes with DNA barcodes: proposal for a new standard in chromosomal analysis with an example based on the study of Neotropical Nymphalidae (Lepidoptera)

Comparative Cytogenetics ◽

10.3897/compcytogen.v13i4.48368 ◽

2019 ◽

Vol 13 (4) ◽

pp. 435-449 ◽

Cited By ~ 2

Author(s):

Vladimir A. Lukhtanov ◽

Yaroslavna Iashenkova

Keyword(s):

Chromosome Number ◽

Chromosome Numbers ◽

Species Complex ◽

Dna Barcode ◽

Molecular Data ◽

Published Data ◽

Dna Barcodes ◽

Undescribed Species ◽

Species Identity ◽

Chromosomal Data

Chromosomal data are important for taxonomists, cytogeneticists and evolutionary biologists; however, the value of these data decreases sharply if they are obtained for individuals with inaccurate species identification or unclear species identity. To avoid this problem, here we suggest linking each karyotyped sample with its DNA barcode, photograph and precise geographic data, providing an opportunity for unambiguous identification of described taxa and for delimitation of undescribed species. Using this approach, we present new data on chromosome number diversity in neotropical butterflies of the subfamily Biblidinae (genus Vila Kirby, 1871) and the tribe Ithomiini (genera Oleria Hübner, 1816, Ithomia Hübner, 1816, Godyris Boisduval, 1870, Hypothyris Hübner, 1821, Napeogenes Bates, 1862, Pseudoscada Godman et Salvin, 1879 and Hyposcada Godman et Salvin, 1879). Combining new and previously published data we show that the species complex Oleria onega (Hewitson, [1852]) includes three discrete chromosomal clusters (with haploid chromosome numbers n = 15, n = 22 and n = 30) and at least four DNA barcode clusters. Then we discuss how the incomplete connection between these chromosomal and molecular data (karyotypes and DNA barcodes were obtained for different sets of individuals) complicates the taxonomic interpretation of the discovered clusters.

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Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data

ZooKeys ◽

10.3897/zookeys.1046.57052 ◽

2021 ◽

Vol 1046 ◽

pp. 1-141

Author(s):

Kurt Jordaens ◽

Georg Goergen ◽

Jeffrey H. Skevington ◽

Scott Kelso ◽

Marc De Meyer

Keyword(s):

Dna Barcode ◽

Molecular Data ◽

Junior Synonym ◽

Dna Barcodes ◽

Identification Keys ◽

Males And Females ◽

Morphological And Molecular Data ◽

First Time

The Afrotropical representatives of the hover fly genus Mesembrius Rondani, 1857 (Diptera) are divided into two subgenera, namely Mesembrius s.s. and Vadonimyia Séguy, 1951 and, in this present work, the subgenus Mesembrius s.s. is revised. A total of 23 Mesembrius s.s. species are recognised for the Afrotropics. Known species are re-described and six species new to science are described: Mesembrius arcuatussp. nov., M. copelandisp. nov., M. longipilosussp. nov., M. sulcussp. nov., M. tibialissp. nov. and M. vockerothisp. nov. Mesembrius africanus (Verrall, 1898) is considered a junior synonym of M. senegalensis (Macquart, 1842), M. ctenifer Hull, 1941 a junior synonym of M. caffer (Loew, 1858), M. lagopus (Loew, 1869) a junior synonym of M. capensis (Macquart, 1842) and M. platytarsis Curran, 1929 a junior synonym of M. simplicipes Curran, 1929. The females of Mesembrius chapini Curran, 1939, M. rex Curran, 1927 and M. regulus (Hull, 1937) are described for the first time. Lectotypes are designated for Mesembrius caffer, M. capensis, M. cyanipennis (Bezzi, 1915), M. minor (Bezzi, 1915), M. senegalensis, M. strigilatus (Bezzi, 1912) and M. tarsatus (Bigot, 1883). Separate identification keys for males and females are presented. We obtained 236 DNA barcodes for 18 species. The relationships amongst the different Mesembrius species are briefly discussed, based on morphological and DNA barcode data.

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Molecular identification and DNA barcode screening of Acaroid mites in ground flour dust

Genome ◽

10.1139/gen-2020-0099 ◽

2021 ◽

Author(s):

Wanyu Zhang ◽

Juan Cheng ◽

Yae Zhao ◽

Dongling Niu ◽

Hongsong Guo

Keyword(s):

Molecular Identification ◽

Dna Barcode ◽

Molecular Data ◽

Universal Primers ◽

Dna Barcodes ◽

Dermatophagoides Farinae ◽

Tyrophagus Putrescentiae ◽

Multiple Target ◽

Morphological Classification ◽

Flour Dust

Molecular identification of acaroid mites is difficult because of the scarcity of molecular data in GenBank. Here, acaroid mites collected from ground flour dust in Xi'an China were preliminarily morphologically classified/grouped. Universal primers were then designed to amplify and screen suitable DNA barcodes for identifying these mites. Sixty mite samples were morphologically classified into six groups. Groups 1–2 were identified to Dermatophagoides farinae, and Tyrophagus putrescentiae; while Groups 3–6 were not identified to the species level. ITS2 exhibited higher efficiency in molecular identification in comparison with COI, 12S, and 16S. Groups 1–6 were identified as D. farinae, T. putrescentiae, Suidasia nesbitti, Chortoglyphus arcuatus, Lepidoglyphus destructor, and Gohieria sp., respectively. The phylogenetic results were consistent with the morphological classification. Group 6 was further identified as G. fusca according to the morphology of reproductive foramen. We conclude that the use of ITS2 and the availability of universal primers provides an ideal DNA barcode for molecular identification of acaroid mites. The use of multiple target genetic markers in conjunction with morphological approaches will improve the accuracy of Acaridida identification. Key words: acaroid mites, Taxonomy, universal primers, molecular identification, DNA barcode.

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