The effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae

Designing a novel method based on multiplex PCR for detecting various meat of birds in processed ground meat products

Falsified food directly influences wildlife, fair trade, religion, and the health of society. Here, we report a multiplex polymerase chain reaction to evaluate the accurate determination of seven species of bird meat in meals on a single assay platform. To amplify segments of DNA from Columba livia, Corvus moneduloides, Gallus gallus, Coturnix japonica, Phasianus colchicus, Struthio camelus, and Meleagris gallopavo meats, respectively, a total of seven sets of species-specific primers targeting the mitochondrial and cytochrome b genes were developed. Gel photographs and electrochromatography from an Experion Bioanalyzer were used to identify all PCR products. Species specificity checks discovered no cross-species amplification. The applicability of its screening to find target species in processed food was shown in commercial and model meatballs. A validation study revealed that the test is reliable, quick, affordable, repeatable, specific, and accurate down to 50,000 mitochondrial copies. It might be used for raw meats and products involving processed and severely deteriorated food samples. The customers, the food business, and law enforcement would all benefit immensely from this suggested approach.

Variants in the mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) infected with Oryctes rhinoceros nudivirus in oil palm and coconut plantations

The CRB (coconut rhinoceros beetle) haplotype was classified into CRB-S and CRB-G, based on the presence of single nucleotide polymorphisms (SNPs) in the mitochondrial cox1 gene. Mitochondrial genomes (mitogenomes) are the most widely used genetic resources for molecular evolution, phylogenetics, and population genetics in relation to insects. This study presents the mitogenome CRB-G and CRB-S which were collected in Johor, Malaysia. The mitogenome of CRB-G collected from oil palm plantations in 2020 and 2021, and wild coconut palms in 2021 was 15,315 bp, 15,475 bp, and 17,275 bp, respectively. The CRB-S was discovered in coconut and oil palms in 2021, and its mitogenome was 15,484 bp and 17,142 bp, respectively. All the mitogenomes have 37 genes with more than 99% nucleotide sequence homology, except the CRB-G haplotype collected from oil palm in 2021 with 89.24% nucleotide sequence homology. The mitogenome of Johor CRBs was variable in the natural population due to its elevated mutation rate. Substitutions and indels in cox1, cox2, nad2 and atp6 genes were able to distinguish the Johor CRBs into two haplotypes. The mitogenome data generated in the present study may provide baseline information to study the infection and relationship between the two haplotypes of Johor CRB and OrNV in the field. This study is the first report on the mitogenomes of mixed haplotypes of CRB in the field.

Mitochondrial Genome Sequence of Salvia officinalis (Lamiales: Lamiaceae) Suggests Diverse Genome Structures in Cogeneric Species and Finds the Stop Gain of Genes through RNA Editing Events

Our previous study was the first to confirm that the predominant conformation of mitochondrial genome (mitogenome) sequence of Salvia species contains two circular chromosomes. To further understand the organization, variation, and evolution of Salvia mitogenomes, we characterized the mitogenome of Salvia officinalis. The mitogenome of S. officinalis was sequenced using Illumina short reads and Nanopore long reads and assembled using a hybrid assembly strategy. We found that the predominant conformation of the S. officinalis mitogenome also had two circular chromosomes that were 268,341 bp (MC1) and 39,827 bp (MC2) in length. The S. officinalis mitogenome encoded an angiosperm-typical set of 24 core genes, 9 variable genes, 3 rRNA genes, and 16 tRNA genes. We found many rearrangements of the Salvia mitogenome through inter- and intra-specific comparisons. A phylogenetic analysis of the coding sequences (CDs) of 26 common protein-coding genes (PCGs) of 11 Lamiales species and 2 outgroup taxa strongly indicated that the S. officinalis was a sister taxon to S. miltiorrhiza, consistent with the results obtained using concatenated CDs of common plastid genes. The mapping of RNA-seq data to the CDs of PCGs led to the identification of 451 C-to-U RNA editing sites from 31 PCGs of the S. officinalis mitogenome. Using PCR amplification and Sanger sequencing methods, we successfully validated 113 of the 126 RNA editing sites from 11 PCGs. The results of this study suggest that the predominant conformation of the S. officinalis mitogenome are two circular chromosomes, and the stop gain of rpl5 was found through RNA editing events of the Salvia mitogenome.

The complete mitochondrial genome of Attacus atlas formosanus Villiard, 1969 (Lepidoptera: Saturniidae)

The complete mitochondrial genome (mitogenome) of Attacus atlas formosanus (Villiard, 1969) is 15,280 bp in length, with the typical gene content and arrangement usually observed in Insecta. It contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one AT-rich region. The overall nucleotide composition of the mitogenome was 39.8% A, 12.9% C, 7.7% G, and 39.6% T, with an A + T bias of 79.4%. Phylogenetic analyses of 23 species in Saturniidae and 3 species in Bombycidae by Bayesian inference showed that A. atlas formosanus belonged to the Tribe Attacini, closely related to Tribe Saturniini. Besides, A. atlas formosanus is closely related to A. atlas with 99% sequence identity. This result well supported the taxonomic position of Saturniidae and their close relationship with the family Bombycidae.

Morphometric and molecular discrimination of the sugarcane aphid, Melanaphis sacchari, (Zehntner, 1897) and the sorghum aphid Melanaphis sorghi (Theobald, 1904)

Melanaphis sacchari (Zehntner, 1897) and Melanaphis sorghi (Theobald, 1904) are major worldwide crop pests causing direct feeding damage on sorghum and transmitting viruses to sugarcane. It is common in the scientific literature to consider these two species as synonyms, referred to as the 'sugarcane aphid', although no formal study has validated this synonymy. In this study, based on the comparison of samples collected from their whole distribution area, we use both morphometric and molecular data to better characterize the discrimination between M. sacchari and M. sorghi. An unsupervised multivariate analysis of morphometric data clearly confirmed the separation of the two species. The best discriminating characters separating these species were length of the antenna processus terminalis relative to length of hind tibia, siphunculus or cauda. However, those criteria sometimes do not allow an unambiguous identification. Bayesian clustering based on microsatellite data delimited two clusters, which corresponded to the morphological species separation. The DNA sequencing of three nuclear and three mitochondrial regions revealed slight divergence between species. In particular, the COI barcode region proved to be uninformative for species separation because one haplotype is shared by both species. In contrast, one SNP located on the nuclear EF1-α gene was diagnostic for species separation. Based on morphological and molecular evidence, the invasive genotype damaging to sorghum in the US, Mexico and the Caribbean since 2013 is found to be M. sorghi.

Seasonal Migration in the Aphid Genus Stomaphis (Hemiptera: Aphididae): Discovery of Host Alternation Between Woody Plants in Subfamily Lachninae

About 10% of aphid species show host alternation. These aphids migrate between primary and secondary host plant species in spring and autumn. Host alternation has not been observed in subfamily Lachninae, although it has been suggested on the basis of circumstantial evidence that Stomaphis japonica (Takahashi) may alternate its host between Quercus serrata (Murray) and Quercus acutissima (Carruth). However, a molecular phylogenetic study has indicated that the Stomaphis individuals feeding on these two plant species belong to two different lineages and aphids feeding on Q. acutissima and Pinus densiflora (Sieb. & Zucc.) belong to the same lineage. Here, we examined host alternation in Stomaphis species by comparing molecular phylogenetic identities, morphological features, and life cycles. The molecular analysis and morphological examination showed that aphids feeding on Q. acutissima were the same as those feeding on P. densiflora, whereas aphids feeding on Q. serrata were different from those feeding on Q. acutissima or on P. densiflora. Furthermore, winged aphids were observed on both Q. acutissima and P. densiflora in autumn, but we did not observe winged aphids on Q. serrata. These results indicate that Stomaphis (Walker) individuals feeding on Q. serrata and Q. acutissima belong to two species, one that feeds year-round on Q. serrata, and another, heteroecious species that feeds on P. densiflora as a primary host and on Q. acutissima as a secondary host. This study documents host alternation in subfamily Lachninae for the first time and discusses the acquisition of host alternation by Stomaphis from evolutionary and ecological perspectives.

BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae)

DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these species with conspecific populations from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from a range of plant species at sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. Sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance. These species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 49% of the species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.

A molecular study of Neophyllaphisvaricolor (Hemiptera, Aphididae) in Costa Rica

The genus Neophyllaphis (Takahashi) (Aphididae: Neophyllaphidinae) is composed of 18 species; however, in the Americas only nine species have been reported previously. A new species, Neophyllaphisvaricolor Miller & Halbert, was described in 2014 in USA. Colonies resembling those of this new species have been observed in Costa Rica on Podocarpus spp. In order to determine if N.varicolor is also present in Costa Rica, we sampled Neophyllaphis colonies from Podocarpusfalcatus and P.chinensis. Additionally, we sampled individuals from Podocarpus sp. in Spain and Vietnam. DNA of each sample was extracted and used to amplify and sequence the cytochrome c oxidase subunit I (COI) and elongation factor I (EF-1α) partial regions. According to morphological characteristics, sequences comparisons done in GenBank and BOLD, and phylogenetic analyses, the colonies collected from Podocarpus spp. in Costa Rica and the colony from Vietnam corresponded to the species N.varicolor. To the best of our knowledge this is the first report of the presence of N.varicolor in Central America and Vietnam.

The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications

Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light-strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA-Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination-associated sequence, six conserved sequence blocks (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E, CSB-F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.

Rapid identification of common medicinal snakes and their adulterants using the Bar-HRM analysis method

Effective identification methods for snake species are lacking, exacerbating the extermination of medicinal and commercially valuable snake species. Hence, it is imperative to find fast and reliable methods to distinguish snake samples available on the market. Seventy-three samples from four families belonging to 13 genera were collected in China and found to contain common medicinal snakes and their adulterants. Cytochrome oxidase I (COI) was utilized as a DNA barcode to analyse these common snakes, and a DNA mini-barcode was employed for fast detection. Then, the DNA mini-barcode assays were coupled with a high-resolution melting (HRM) analysis (Bar-HRM) to realize the rapid discrimination of these snake species. The results showed the power of DNA barcoding with COI, which was capable of distinguishing all collected snake samples, and the combined Bar-HRM method can successfully identify the adulterants and different snake species. In particular, Bar-HRM revealed Bungarus fasciatus adulterants in B. multicinctus at concentrations as low as 1.6%. Moreover, the results of the study confirmed the effectiveness of the technique in terms of the rapid identification of snakes, which has great potential for ensuring the safety of commercially valuable snake species.

Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view of M. challengeri diet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta; however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of M. challengeri identified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctata), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitzai), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

DNA barcoding and a precise morphological comparison revealed a cryptic species in the Nippolachnus piri complex (Hemiptera: Aphididae: Lachninae)

Nippolachnus is a small Palaearctic-Oriental genus of very characteristic aphids that live on the leaves of woody Rosaceae. One species, N. piri, has hitherto been regarded to be widely distributed and relatively polyphagous. Members of this genus are considered to be easy to recognize due to the absence of the ocular tubercle and triommatidia on the head. We conducted research on the morphology and generic characters of Nippolachnus piri complex using scanning electron microscopy (for the first time) and DNA barcoding. We analyzed N. piri populations on Pyrus and other plants (Eriobotrya, Rhaphiolepis and Sorbus) in Japan and the Republic of Korea. Specifically, a high genetic divergence value was found between the N. piri populations associated with different host plants. SEM investigation of the head capsule revealed that a triommatidium is present under the compound eye, despite their lack of an ocular tubercle. We propose Nippolachnus micromeli Shinji, 1924 stat. nov. as a cryptic species in the N. piri complex based on a morphological comparison, DNA barcoding and different host-plant associations. Illustrations and descriptions of studied species are given. Morphological keys to the apterae and alatae of all known species of the genus Nippolachnus are also provided.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for comparative phylogenetic analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

DNA barcoding evaluation and implications for phylogenetic relationships in ladybird beetles (Coleoptera: Coccinellidae)

Ladybird beetles (Coleoptera: Coccinellidae), with broad morphological diversity, wide geographic distribution and substantial agricultural significance, are a challenging group for taxonomists and phylogenetics. As a promising tool to identify and discover new species, DNA barcoding might offer significant potential for identification, taxonomy and phylogeny of ladybird beetles. In the present study, a total of 1364 COI (cytochrome C oxidase subunit I) sequences representing 128 species from 52 genera of ladybird beetles were screened for barcoding evaluation and phylogenetic analysis. Our results from the barcoding analysis revealed that COI displays a similar level of species identification efficiency (nearly 90%) either based on Kimura two-parameter (K2P) distances calculation or on simplified neighbour-joining (NJ) tree construction. The phylogenetic relationships within the family Coccinellidae was analyzed by Bayesian-inference (BI) method. The phylogenetic results confirmed the monophyly of the subfamilies Microweisinae and Coccinellinae sensu Ślipiński (2007), and suggested that the subfamilies Coccidulinae, Chilocorinae and Scymninae are paraphyletic. However, the phylogenetic relationships among different subfamilies are not clearly defined and thus remain to be thoroughly studied. Overall, our study confirmed the usefulness of DNA barcoding for coccinellid species identification and phylogenetic inference.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Assessing the effectiveness of mitochondrial COI and 16S rRNA genes for DNA barcoding of farmland spiders in China

DNA barcoding has been widely used to identify and discover new species in a wide range of taxa. In order to assess the effectiveness of COI (cytochrome C oxidase subunit I) and 16S (16S ribosomal RNA) in the discrimination of spiders, we have generated 289 barcodes for a total of 56 farmland spider species from 14 different families for the first time in China. Our results reveal that the standard barcoding marker COI can be used to distinguish the farmland spiders both in species and family level by NJ tree-based method, despite the absence of a barcode gap between the intra- and inter-specific genetic divergences. 16S has a lower species identification success as compared with COI. However, almost 98% of the species can be correctly distinguished for both COI and 16S when a threshold of 3% nucleotide divergence was used for species discrimination. Our study significantly improves the barcode reference sequence library for Chinese farmland spiders, and will be very useful in pest management and eco-environmental monitoring and protection.

EF-1α DNA Sequences Indicate Multiple Origins of Introduced Populations of Essigella californica (Hemiptera: Aphididae)

Aphids in the pine-feeding Nearctic genus Essigella (Sternorrhyncha, Aphididae, Lachninae) have been introduced in Europe, North Africa, Oceania, and South America. Mitochondrial, nuclear, and endosymbiont DNA sequences of 12 introduced populations from three continents confirm they all belong to Essigella californica (Essig, 1909). Intron sequence variation of the nuclear gene EF-1α has revealed the existence of four distinct groups. Group I gathers one population from China, where the species is newly reported, and several from Europe (France and Italy); Group II is represented by one population from Argentina; Group III includes two populations from Southern Australia with one from New Zealand; and Group IV corresponds to five populations from Eastern and South-Eastern Australia. These results indicate that introduced populations of E. californica have at least four source populations. They also show that intron variation of EF-1α can be a method to discriminate populations of asexually reproducing aphids.

Cryptic diversity of the subfamily Calaphidinae (Hemiptera: Aphididae) revealed by comprehensive DNA barcoding

Aphids are a species rich group comprising many important pests. However, species identification can be very difficult for aphids due to their morphological ambiguity. DNA barcoding has been widely adopted for rapid and reliable species identification as well as cryptic species detection. In this study, we investigated cryptic diversity in the subfamily Calaphidinae (Hemiptera: Aphididae) based on 899 sequences of cytochrome c oxidase I (COI) for 115 morphospecies (78 species collected in this study and sequences of 73 species downloaded from Genbank). Among these 115 morphospecies, DNA barcoding results of 90 (78.3%) species were identical to results of morphological identification. However, 25 (21.7%) morphospecies showed discrepancies between DNA barcoding and traditional taxonomy. Among these 25 discordances, a total of 15 cryptic species were identified from 12 morphospecies. We also found three morphologically distinct species pairs that sharing DNA barcoding. Based on molecular operational taxonomic unit (MOTU) estimation, we discussed on species delimitation threshold value for these taxa. Our findings confirm that Calaphidinae has high cryptic diversity even though aphids are relatively well-studied.

DNA barcoding and species delimitation of Chaitophorinae (Hemiptera, Aphididae)

Chaitophorinae aphids are widespread across Eurasia and North America, and include some important agricultural and horticultural pests. So, accurate rapid species identification is very important. Here, we used three mitochondrial genes and one endosymbiont gene to calculate and analyze the genetic distances within different datasets. For species delimitation, two distance-based methods were employed, threshold with NJ (neighbor-joining) and ABGD (Automatic Barcode Gap Discovery), and two tree-based approaches, GMYC (General Mixed Yule Coalescent) and PTP (Poisson Tree Process). The genetic interspecific divergence was clearly larger than the intraspecific divergence for four molecular markers. COI and COII genes were found to be more suitable for Chaitophorinae DNA barcoding. For species delimitation, at least one distance-based method combined with one tree-based method would be preferable. Based on the data for Chaitophorussaliniger and Laingiapsammae, DNA barcoding may also reveal geographical variation.

Novel Rickettsia and emergent tick-borne pathogens: A molecular survey of ticks and tick-borne pathogens in Shimba Hills National Reserve, Kenya

Ticks are important vectors of emerging and re-emerging zoonoses, the majority of which originate from wildlife. In recent times, this has become a global public health concern that necessitates surveillance of both known and unknown tick-borne pathogens likely to be future disease threats, as well as their tick vectors. We carried out a survey of the diversity of ticks and tick-borne pathogens in Kenya's Shimba Hills National Reserve (SHNR), an area with intensified human-livestock-wildlife interactions, where we collected 4297 questing ticks (209 adult ticks, 586 nymphs and 3502 larvae). We identified four tick species of two genera (Amblyomma eburneum, Amblyomma tholloni, Rhipicephalus maculatus and a novel Rhipicephalus sp.) based on both morphological characteristics and molecular analysis of 16S rRNA, internal transcribed spacer 2 (ITS 2) and cytochrome oxidase subunit 1 (CO1) genes. We pooled the ticks (3-8 adults, 8-15 nymphs or 30 larvae) depending on species and life-cycle stages, and screened for bacterial, arboviral and protozoal pathogens using PCR with high-resolution melting analysis and sequencing of unique melt profiles. We report the first molecular detection of Anaplasma phagocytophilum, a novel Rickettsia-like and Ehrlichia-like species, in Rh. maculatus ticks. We also detected Ehrlichia chaffeensis, Coxiella sp., Rickettsia africae and Theileria velifera in Am. eburneum ticks for the first time. Our findings demonstrate previously unidentified tick-pathogen relationships and a unique tick diversity in the SHNR that may contribute to livestock, and possibly human, morbidity in the region. This study highlights the importance of routine surveillance in similar areas to elucidate disease transmission dynamics, as a critical component to inform the development of better tick-borne disease diagnosis, prevention and control measures.

DNA barcoding reveals a mysterious high species diversity of conifer-feeding aphids in the mountains of southwest China

The mountains of southwest China are one of the hot spots of biodiversity in the world. However, the high-altitude fauna that inhabit these mountains remain a mystery. In this study, the species diversity of the aphids of the genus Cinara from the high-altitude coniferous forests was first assessed, and then the processes and the mechanisms of speciation were discussed. Three hundreds and four aphid samples that contained 3040 individuals were collected during fourteen field surveys. The molecular clusters derived from the DNA barcodes were used to explore the species diversity. Notably, the aphid alpha-diversity was high, with as many as 94 candidate species, and furthermore, 86.2% of the species collected had not been previously recorded. The centers of aphid species richness corresponded to the distributional pattern of the diversity of the host conifer plant species. The divergence time revealed that following the uplift of the Qinghai-Tibetan Plateau during the Pleistocene, the changes in the climate, ecology and host habitats were likely the most important factors that drove the rapid process of evolutionary radiation in the aphids. Our findings revealed the high species diversity of the aphids with DNA barcoding.

A new species of Docosia Winnertz from Central Europe, with DNA barcoding based on four gene markers (Diptera, Mycetophilidae)

A new species of Docosia Winnertz, Docosia dentata sp. n., is described and illustrated, based on a single male specimen collected in Muránska planina National Park in Central Slovakia. DNA sequences (COI, COII, CytB, and ITS2) are included and compared for 13 species of Docosia. There was found only little congruence between the molecular results and previous scarce data about interspecific relationships based on morphology. The COI and CytB gene markers showed the highest interspecific gene distances while ITS2 showed the lowest ones. An updated key to the 23 Central European species of Docosia is also presented.

A Checklist of Iranian Cockroaches (Blattodea) with Description of Polyphaga sp as a New Species in Iran

BACKGROUND

Cockroaches are of vital importance medically and hygienically. They are able to contaminate foods and act as vectors of pathogenic agents such as bacteria, protozoa, and parasites to human environment either mechanically or through their digestive system. Cockroaches belong to the phylum Arthropoda, class Insecta, and order Blattodea or Blattaria. To date, over 4,500 cockroach species have been reported from different parts of the world. We overviewed the documents involved Iranian cockroaches to up-to-date checklist of cockroach species distributed in various provinces of Iran.

METHODS

An extensive literature review was performed in 2013 on Iranian handbooks, reports and published data available since 1986 to obtain a comprehensive list of Iranian cockroaches. Furthermore, in an entomological survey in Tehran, cockroach specimens were collected and identified based on morphological and the DNA sequences of the mitochondrial cytochrome oxidase subunit II (COII) gene (mt-DNA COII) characteristics.

RESULTS

Morphological characterization revealed presence of an un-described species very similar to Polyphaga aegyptiaca, P. indica and somehow to Pycnoscelus surinamensis, however, supplementary molecular analysis revealed the species was associated with Polyphaga of Corydiidae (Polyphagidae). With regards to the report of the un-described species, the cockroach fauna of Iran includes three families, 14 genera, and 26 species.

CONCLUSION

Some species has not been collected or reported recently and also many geographical regions of the country have not been studied yet, hence a systematic research is required to reveal the real cockroach list of the country. Geographical distributions, nomination changes, and synonyms of cockroach species are presented.

Molecular characterization, biological forms and sporozoite rate of Anopheles stephensi in southern Iran

OBJECTIVE

To identify the biological forms, sporozoite rate and molecular characterization of the Anopheles stephensi (An. stephensi) in Hormozgan and Sistan-Baluchistan provinces, the most important malarious areas in Iran.

METHODS

Wild live An. stephensi samples were collected from different malarious areas in southern Iran. The biological forms were identified based on number of egg-ridges. Molecular characterization of biological forms was verified by analysis of the mitochondrial cytochrome oxidase subunit I and II (mtDNA-COI/COII). The Plasmodium infection was examined in the wild female specimens by species-specific nested-PCR method.

RESULTS

Results showed that all three biological forms including mysorensis, intermediate and type are present in the study areas. Molecular investigations revealed no genetic variation between mtDNA COI/COII sequences of the biological forms and no Plasmodium parasites was detected in the collected mosquito samples.

CONCLUSIONS

Presence of three biological forms with identical sequences showed that the known biological forms belong to a single taxon and the various vectorial capacities reported for these forms are more likely corresponded to other epidemiological factors than to the morphotype of the populations. Lack of malaria parasite infection in An. stephensi, the most important vector of malaria, may be partly due to the success and achievement of ongoing active malaria control program in the region.

DNA barcoding and the associated PhylAphidB@se website for the identification of European aphids (Insecta: Hemiptera: Aphididae)

Aphids constitute a diverse group of plant-feeding insects and are among the most important crop pests in temperate regions. Their morphological identification is time-consuming and requires specific knowledge, training and skills that may take years to acquire. We assessed the advantages and limits of DNA barcoding with the standard COI barcode fragment for the identification of European aphids. We constructed a large reference dataset of barcodes from 1020 specimens belonging to 274 species and 87 genera sampled throughout Europe and set up a database-driven website allowing species identification from query sequences.

RESULTS

In this unbiased sampling of the taxonomic diversity of European aphids, intraspecific divergence ranged from 0.0% to 3.9%, with a mean value of 0.29%, whereas mean congeneric divergence was 6.4%, ranging from 0.0% to 15%. Neighbor-joining analysis generated a tree in which most species clustered in distinct genetic units. Most of the species with undifferentiated or overlapping barcodes belonged to the genus Aphis or, to a lesser extent, the genera Brachycaudus, Dysaphis and Macrosiphum. The taxa involved were always morphologically similar or closely related and belonged to species groups known to present taxonomic difficulties.

CONCLUSIONS

These data confirm that COI barcoding is a useful identification tool for aphids. Barcode identification is straightforward and reliable for 80% of species, including some difficult to distinguish on the basis of morphological characters alone. Unsurprisingly, barcodes often failed to distinguish between species from groups for which classical taxonomy has also reached its limits, leading to endless revisions and discussions about species and subspecies definitions. In such cases, the development of an effective procedure for the accurate identification of aphid specimens continues to pose a difficult challenge.

Assessment of four DNA fragments (COI, 16S rDNA, ITS2, 12S rDNA) for species identification of the Ixodida (Acari: Ixodida)

Background

The 5’ region of cytochrome oxidase I (COI) is the standard marker for DNA barcoding. However, COI has proved to be of limited use in identifying some species, and for some taxa, the coding sequence is not efficiently amplified by PCR. These deficiencies lead to uncertainty as to whether COI is the most suitable barcoding fragment for species identification of ticks.

Methods

In this study, we directly compared the relative effectiveness of COI, 16S ribosomal DNA (rDNA), nuclear ribosomal internal transcribed spacer 2 (ITS2) and 12S rDNA for tick species identification. A total of 307 sequences from 84 specimens representing eight tick species were acquired by PCR. Besides the 1,834 published sequences of 189 tick species from GenBank and the Barcode of Life Database, 430 unpublished sequences representing 59 tick species were also successfully screened by Bayesian analyses. Thereafter, the performance of the four DNA markers to identify tick species was evaluated by identification success rates given by these markers using nearest neighbour (NN), BLASTn, liberal tree-based or liberal tree-based (+threshold) methods.

Results

Genetic divergence analyses showed that the intra-specific divergence of each marker was much lower than the inter-specific divergence. Our results indicated that the rates of correct sequence identification for all four markers (COI, 16S rDNA, ITS2, 12S rDNA) were very high (> 96%) when using the NN methodology. We also found that COI was not significantly better than the other markers in terms of its rate of correct sequence identification. Overall, BLASTn and NN methods produced higher rates of correct species identification than that produced by the liberal tree-based methods (+threshold or otherwise).

Conclusions

As the standard DNA barcode, COI should be the first choice for tick species identification, while 16S rDNA, ITS2, and 12S rDNA could be used when COI does not produce reliable results. Besides, NN and BLASTn are efficient methods for species identification of ticks.

Relationships within aphids Cinara (Cupressobium) (Hemiptera) based on mitochondrial and nuclear DNA sequences

The relationships between Cinara (Cupressobium) aphids inhabiting woody parts and leaves of conifers belonging to Cupressaceae have been studied using a mitochondrial gene (COI) and a nuclear gene (EF1-α). Based on the COI sequences, genetic distances between species ranged from 5.6 % between Cinara (C.) tujafilina (del Guercio) and Cinara (C.) juniperi (De Geer) to 10.5 % between C. (C.) tujafilina and Cinara (C.) mordvilkoi (Pašek). Genetic distances among EF1-α sequences were lower and showed from 0.1 % between C. cupressi and C. juniperi to 2.3 % between C. tujafilina and C. mordvilkoi. Molecular phylogenetic trees were constructed using the Bayesian inference (BI) phylogenetic analysis and maximum parsimony (MP) criterion. Phylogenetic trees obtained based on COI and EF1-α marker genes created two sister clades. Our results indicate that Cinara (Cupressobium) are a monophyletic group of aphids. Phylogenetic relationships amongst Cupressobium aphids do not result from the association with the host plant, but from the feeding site on the host plant or an ability to change the microhabitat on the plant. As closely related species inhabit similar microhabitats on different host plants, it suggests that the host switching is the main mode of speciation in this subgenus.

DNA barcoding of Greenideinae (Hemiptera : Aphididae) with resolving taxonomy problems

Species of the Greenideinae are distributed mainly throughout South-east Asia and include some important agricultural and horticultural pests. Rapid and accurate species circumscription and identification in this subfamily are very difficult because similar morphological traits are shared among congeneric species. Here, we test the efficiency of DNA barcoding in the Greenideinae by analysing 214 samples covering 42 species belonging to nine genera using two mitochondrial gene fragments (COI barcode fragment and Cytb gene fragment). The results show that DNA barcoding is a useful species identification method in this subfamily. Both genes can correctly identify most species using neighbour-joining tree analyses and distance-based analyses. Based on the molecular and morphological evidence, we question the validity of two species, Mollitrichosiphum rhusae Ghosh, 1917 and Schoutedenia emblica (Patel & Kulkarni, 1953). Further analysis of the COI barcode fragment shows that Greenidea psidii van der Goot, 1917, an invasive species in Hawaii, is possibly from China. This is a preliminary DNA barcoding study in Greenideinae, and comprehensive sampling is needed to rigorously test the usefulness of DNA barcoding in this subfamily.