Assessing the effects of primer specificity on eliminating numt coamplification in DNA barcoding: a case study from Orthoptera (Arthropoda: Insecta)

To Be, or Not to Be: That Is the Hamletic Question of Cryptic Evolution in the Eastern Atlantic and Mediterranean Raja miraletus Species Complex

Despite a high species diversity, skates (Rajiformes) exhibit remarkably conservative morphology and ecology. Limited trait variations occur within and between species, and cryptic species have been reported among sister and non-sister taxa, suggesting that species complexes may be subject to stabilising selection. Three sibling species are currently recognised in the Raja miraletus complex: (i) R. miraletus occurring along the Portuguese and Mediterranean coasts, (ii) R. parva in the Central-Eastern Atlantic off West Africa and (iii) R. ocellifera in the Western Indian Ocean off South Africa. In the present study, the genetic variation at mitochondrial and nuclear markers was estimated in the species complex by analysing 323 individuals sampled across most of its geographical distribution area to test the hypothesis that restricted gene flow and genetic divergence within species reflect known climate and bio-oceanographic discontinuities. Our results support previous morphological studies and confirm the known taxonomic boundaries of the three recognised species. In addition, we identified multiple weakly differentiated clades in the Northeastern Atlantic Ocean and Mediterranean, at least two additional cryptic taxa off Senegal and Angola, a pronounced differentiation of ancient South African clades. The hidden genetic structure presented here may represent a valuable support to species' conservation action plans.

A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China

Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa. Automated cluster delineation using the Barcode of Life Data System (BOLD) revealed 118 BINs (Barcodes Index Numbers). Among these 90 species-level taxa, 68 corresponded with morphospecies, while the remaining 22 were identified based on reverse taxonomy using BIN assignment. Thirteen of these morphospecies were represented by a single barcode (so-called singletons), and each of 19 morphospecies were split into more than one BIN. The consensus delimitation scheme yielded 55 Molecular Operational Taxonomic Units (MOTUs). Only four morphospecies (I _max > DNN) failed to be recovered as monophyletic clades (i.e., Elimaeaterminalis, Phyllomimusklapperichi, Sinochloraszechwanensis and Xizicushowardi), so it is speculated that these may be species complexes. Therefore, the diversity of katydids, cave crickets, and leaf-rolling crickets in Zhejiang Province is probably slightly higher than what current taxonomy would suggest.

MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments

Multi-marker metabarcoding is increasingly being used to generate biodiversity information across different domains of life from microbes to fungi to animals such as for molecular ecology and biomonitoring applications in different sectors from academic research to regulatory agencies and industry. Current popular bioinformatic pipelines support microbial and fungal marker analysis, while ad hoc methods are often used to process animal metabarcode markers from the same study. MetaWorks provides a harmonized processing environment, pipeline, and taxonomic assignment approach for demultiplexed Illumina reads for all biota using a wide range of metabarcoding markers such as 16S, ITS, and COI. A Conda environment is provided to quickly gather most of the programs and dependencies for the pipeline. Several workflows are provided such as: taxonomically assigning exact sequence variants, provides an option to generate operational taxonomic units, and facilitates single-read processing. Pipelines are automated using Snakemake to minimize user intervention and facilitate scalability. All pipelines use the RDP classifier to provide taxonomic assignments with confidence measures. We extend the functionality of the RDP classifier for taxonomically assigning 16S (bacteria), ITS (fungi), and 28S (fungi), to also support COI (eukaryotes), rbcL (eukaryotes, land plants, diatoms), 12S (fish, vertebrates), 18S (eukaryotes, diatoms) and ITS (fungi, plants). MetaWorks properly handles ITS by trimming flanking conserved rRNA gene regions as well as protein coding genes by providing two options for removing obvious pseudogenes. MetaWorks can be downloaded from https://github.com/terrimporter/MetaWorks and quickstart instructions, pipeline details, and a tutorial for new users can be found at https://terrimporter.github.io/MetaWorksSite.

The efficiency of the COI gene as a DNA barcode and an overview of Orthoptera (Caelifera and Ensifera) sequences in the BOLD System

Orthoptera, among the oldest and most numerous insect lineages, is an excellent model for evolutionary studies but has numerous taxonomic problems. To mitigate these issues, the cytochrome c oxidase subunit I (COI), standardized with the DNA barcode for Metazoa, is increasingly used for specimen identification and species delimitation. We tested the performance of COI as a DNA barcode in Orthoptera, using two analyses based on intra- and interspecific distances, barcode gap and Probability of Correct Identification (PCI); and estimated species richness through Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP). We filtered all sequences of Orthoptera available in Barcode of Life Data System (BOLD) and used 11,605 COI sequences, covering 1,132 species, 226 genera, and 18 families. The overall average PCI was 73.86%. For 82.2% of genera the barcode gap boxplots were classified as good or intermediate, indicating that COI can be effective as a DNA barcode in Orthoptera, although with varying efficiency depending on the need for more information. ABGD and ASAP inferred species richness similar to labels informed by BOLD for the suborders Caelifera and Ensifera. The representation of Orthoptera in the BOLD database and the results of these analyses are discussed.

Phylogeny and Integrative Taxonomy of the Genera Gymnaetoides and Pseudotachycines (Orthoptera: Rhaphidophoridae)

The genera Gymnaetoides and Pseudotachycines are endemic to China and are morphologically homogeneous. The few available diagnostic characters make species identification particularly challenging. Species cannot be classified according to the given generic diagnosis, and phylogenetic analyses have not been reported. Here, we reconstruct the phylogeny using Bayesian inference and maximum likelihood and employ four approaches to delimit species. The results suggest that both Gymnaetoides and Pseudotachycines are paraphyletic. Therefore, we revise their taxonomy based on the combination of morphological characters and molecular data. A new genus Homotachycines Zhu & Shi gen. nov. is erected, and six new combinations are proposed. Species delimitation identifies 15 new species and one new subspecies: Gymnaetoides huangshanensis, G. petalus, G. yangmingensis, G. lushanensis, Pseudotachycines procerus, P. procerus guizhouensis, P. zhengi, P. nephrus, P. sagittus, P. fengyangshanensis, Homotachycines triangulus, H. quadratus, H. baokangensis, H. fusus, H. concavus, and H. qinlingensis sp. nov. Moreover, we find that the shapes of the dorsal lateral lobes and the dorsal median lobe of the male genitalia are also important characters for identifying these genera and that the shapes of the dorsal and lateral sclerites of the male genitalia are suitable for the classifications of species.

Translocation of mitochondrial DNA into the nuclear genome blurs phylogeographic and conservation genetic studies in seabirds

Mitochondrial DNA (mtDNA) translocated into the nuclear genome (numt), when co-analysed with genuine mtDNA, could plague phylogeographic studies. To evaluate numt-related biases in population genetics parameters in birds, which are prone to accumulating numts, we targeted the mitochondrial mt-cytb gene. We looked at 13 populations of Audubon's shearwater (Puffinus lherminieri), including five mitochondrial lineages. mt-cytb homologue and paralogue (numt) sequences were determined by Sanger sequencing with and without prior exonuclease digestion of nuclear DNA. Numts formed monophyletic clades corresponding to three of the five mitochondrial lineages tested (the remaining two forming a paraphyletic group). Nineteen percent of numt alleles fell outside of their expected mitochondrial clade, a pattern consistent with multiple translocation events, incomplete lineage sorting (ILS), and/or introgression. When co-analysing mt-cytb paralogues and homologues, excluding individuals with ambiguities underestimates genetic diversity (4%) and differentiation (11%) among least-sampled populations. Removing ambiguous sites drops the proportion of inter-lineage genetic variance by 63%. While co-analysing numts with mitochondrial sequences can lead to severe bias and information loss in bird phylogeographic studies, the separate analysis of genuine mitochondrial loci and their nuclear paralogues can shed light on numt molecular evolution, as well as evolutionary processes such as ILS and introgression.

Extensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus Stenopelmatus (Orthoptera: Stenopelmatidae: Stenopelmatinae) revealed by mitochondrial and nuclear 3RAD data

The Jerusalem cricket subfamily Stenopelmatinae is distributed from south-western Canada through the western half of the United States to as far south as Ecuador. Recently, the generic classification of this subfamily was updated to contain two genera, the western North American Ammopelmatus, and the Mexican, and central and northern South American Stenopelmatus. The taxonomy of the latter genus was also revised, with 5, 13 and 14 species being respectively validated, declared as nomen dubium and described as new. Despite this effort, the systematics of Stenopelmatus is still far from complete. Here, we generated sequences of the mitochondrial DNA barcoding locus and performed two distinct DNA sequence-based approaches to assess the species’ limits among several populations of Stenopelmatus, with emphasis on populations from central and south-east Mexico. We reconstructed the phylogenetic relationships among representative species of the main clades within the genus using nuclear 3RAD data and carried out a molecular clock analysis to investigate its biogeographic history. The two DNA sequence-based approaches consistently recovered 34 putative species, several of which are apparently undescribed. Our estimates of phylogeny confirmed the recent generic update of Stenopelmatinae and revealed a marked phylogeographic structure within Stenopelmatus. Based on our results, we propose the existence of four species-groups within the genus (the faulkneri, talpa, Central America and piceiventris species-groups). The geographic distribution of these species-groups and our molecular clock estimates are congruent with the geological processes that took place in mountain ranges along central and southern Mexico, particularly since the Neogene. Our study emphasises the necessity to continue performing more taxonomic and phylogenetic studies on Stenopelmatus to clarify its actual species richness and evolutionary history in Mesoamerica.

Phylogeography of Hyalomma (Euhyalomma) lusitanicum (Acarina, Parasitiformes, Ixodidae) in Andalusia based on mitochondrial cytochrome oxidase I gene

The genetic population structure relationships of Hyalomma (Euhyalomma) lusitanicum in Andalusia (the south of the Iberian Peninsula) were examined using mtDNA sequence data from 887 bp of cytochrome oxidase subunit I (COI) gene. The sequence for the COI region was determined for 84 individuals collected in several localities of Andalusia, and 10 for other localities (i.e., five from Toledo, central Iberian Peninsula, four from Sicily (Italy) and one from Canary Island). Seventeen haplotypes were detected, including 27 polymorphic sites. The number of amino acid substitutions per site from mean diversity calculations for the entire population was 0.017. AMOVA analysis revealed a low gene flow that characterises the genetic population structure of this species in South Iberian Peninsula, with a haplotype diversity (h) value of 0.815. No geographically induced differentiation was observed, and separate evolutionary units were not detected. Our results indicate low genetic diversity across the geographical range of H. lusitanicum tick in Andalusia. Our data do not show any genetic discontinuity between the tick populations studied, including specimens from Canary Island and Sicily (Italy).

Molecular Taxonomy and Diversification of Atlantic Skates (Chondrichthyes, Rajiformes): Adding More Pieces to the Puzzle of Their Evolutionary History

Conservation and long-term management plans of marine species need to be based upon the universally recognized key-feature of species identity. This important assignment is particularly challenging in skates (Rajiformes) in which the phenotypic similarity between some taxa and the individual variability in others, hampers accurate species identification. Here, 432 individual skate samples collected from four major ocean areas of the Atlantic were barcoded and taxonomically analysed. A BOLD project ELASMO ATL was implemented with the aim of establishing a new fully available and well curated barcode library containing both biological and molecular information. The evolutionary histories of the 38 skate taxa were estimated with two concatenated mitochondrial markers (COI and NADH2) through Maximum Likelihood and Bayesian inference. New evolutionary lineages within the genus Raja were discovered off Angola, where paleogeographic history coupled with oceanographic discontinuities could have contributed to the establishment of isolated refugia, playing a fundamental role among skates' speciation events. These data successfully resolved many taxonomic ambiguities, identified cryptic diversity within valid species and demonstrated a highly cohesive monophyletic clustering among the order, laying the background for further inference of evolutionary patterns suitable for addressing management and conservation issues.

Overview of the Genetic Diversity of African Macrotermes (Termitidae: Macrotermitinae) and Implications for Taxonomy, Ecology and Food Science

Simple Summary

Macrotermes are fungus-growing termites known as ecosystem engineers for their role in cellulose recycling and soil conditioning. Macrotermes termites are also important as edible insects and are widely consumed throughout Africa. Accurate identification of Macrotermes species is challenging because of few and unreliable morphological differences among taxonomic groups. Due to this limitation, the diversity of African Macrotermes is incompletely described. Genetic data has provided new insights, but vast geographic regions remain unsurveyed. We generated COI data for specimens collected in Limpopo, South Africa, where Macrotermes termites are commonly consumed by local populations, and assessed their diversity in the context of publicly available sequences. We identified 17 genetic groups that most likely represented distinct species, in contrast with the 13 Macrotermes species currently described in Africa. The specimens collected in Limpopo belonged to four genetic groups, suggesting a high diversity of Macrotermes in the region. Our results also showed that Macrotermes species names and genetic groups do not match in most cases, likely due to inaccurate identification of specimens. We propose that the genetic groups that are identified here be used as a background to guide future studies of African Macrotermes with a positive impact on food science, ecology, taxonomy, phylogeography and phylogenetics.

Abstract

Macrotermes termites play important ecological roles and are consumed by many communities as a delicacy and dietary complement throughout Africa. However, lack of reliable morphological characters has hampered studies of Macrotermes diversity in a wide range of scientific fields including ecology, phylogenetics and food science. In order to place our preliminary assessment of the diversity of Macrotermes in South Africa in context, we analysed a comprehensive dataset of COI sequences for African species including new and publicly available data. Phylogenetic reconstruction and estimates of genetic divergence showed a high level of incongruity between species names and genetic groups, as well as several instances of cryptic diversity. We identified three main clades and 17 genetic groups in the dataset. We propose that this structure be used as a background for future surveys of Macrotermes diversity in Africa, thus mitigating the negative impact of the present taxonomic uncertainties in the genus. The new specimens collected in Limpopo fell into four distinct genetic groups, suggesting that the region harbours remarkable Macrotermes diversity relative to other African regions surveyed in previous studies. This work shows that African Macrotermes have been understudied across the continent, and that the genus contains cryptic diversity undetectable by classic taxonomy. Furthermore, these results may inform future taxonomic revisions in Macrotermes, thus contributing to advances in termitology.

Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets

BACKGROUND

Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes.

RESULTS

Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place.

CONCLUSIONS

Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.

Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data

Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of specimens in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (metaMATE) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. metaMATE requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mitochondrial DNA haplotypes) or nonauthentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. metaMATE (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of nonauthentic ASVs and the collateral effects on the removal of authentic ASVs. The output from metaMATE facilitates decision-making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the metaMATE software (available at https://github.com/tjcreedy/metamate).

Ventral dermatitis in rowi (Apteryx rowi) caused by cutaneous capillariasis

In 2013 there was an outbreak of crusting ventral dermatitis among a group of juvenile rowi (Apteryx rowi), a species of the endangered New Zealand kiwi, that were being raised on an off-shore island sanctuary. Biopsies taken at the time found nematodes migrating within the epidermis of affected skin but the specific identity and origin of the organisms was not established, and sporadic cases of similar skin disease continue to occur on the island. On examination of additional sections from the original skin biopsies, adult nematodes and eggs were identified, the histomorphology of which was consistent with Capillaria sensu lato. PCR was performed on DNA extracted from archived formalin-fixed, paraffin-embedded tissue blocks of skin from eight affected rowi, using primers targeting the 18S region of nuclear ribosomal DNA and the COI gene of mitochondrial DNA of capillarid nematodes. The 18S sequences from all rowi samples were identical and matched sequences from members of the genus Eucoleus. In contrast, two distinct capillarid COI sequences were obtained, in one case both from the same rowi skin biopsy. While there were no close matches, both COI sequences also aligned nearest to sequences identified as Eucoleus spp. It is considered unlikely that two different nematode species are involved in the rowi skin lesions and the possible amplification of a COI pseudogene or “numt” is discussed. A species-level identification of the capillarid nematodes causing skin disease in rowi was not obtained, however based on histological evaluation the infections include reproductively-active adult nematodes. This finding indicates the possibility of perpetuation of the skin disease in the absence of the original source, as well as raising potential for the transfer of infection from the island when the juvenile rowi are translocated to their new habitats.

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Dermatitis associated with nematode migration has been diagnosed in juvenile rowi kiwi.

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Histological and molecular analysis indicates a member of Capillaria sensu lato.

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The possible amplification of a COI pseudogene is discussed.

Phylogeny and species delimitation of the genus Longgenacris and Fruhstorferiola viridifemorata species group (Orthoptera: Acrididae: Melanoplinae) based on molecular evidence

Phylogenetic positions of the genus Longgenacris and one of its members, i.e. L. rufiantennus are controversial. The species boundaries within both of L. rufiantennus+Fruhstorferiola tonkinensis and F. viridifemorata species groups are unclear. In this study, we explored the phylogenetic positions of the genus Longgenacris and the species L. rufiantennus and the relationships among F. viridifemorata group based on the 658-base fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) barcode and the complete sequences of the internal transcribed spacer regions (ITS1 and ITS2) of the nuclear ribosomal DNA. The phylogenies were reconstructed in maximum likelihood framework using IQ-TREE. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. Phylogenetic species concept and NJ tree, K2P distance, the statistical parsimony network as well as the generalized mixed Yule coalescent model (GMYC) were employed to delimitate the species boundaries in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups. The results demonstrated that the genus Longgenacris should be placed in the subfamily Melanoplinae but not Catantopinae, and L. rufiantennus should be a member of the genus Fruhstorferiola but not Longgenacris. Species boundary delimitation confirmed the presence of oversplitting in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups and suggested that each group should be treated as a single species.

Mitochondrial DNA intra-individual variation in a bumblebee species: A challenge for evolutionary studies and molecular identification

Mitochondrial DNA (mtDNA) regions have been widely used as molecular markers in evolutionary studies and species identification. However, the presence of heteroplasmy and NUMTs may represent obstacles. Heteroplasmy is a state where an organism has different mitochondrial haplotypes. NUMTs are nuclear pseudogenes originating from mtDNA sequences transferred to nuclear DNA. Evidences of heteroplasmy were already verified in the bumblebee Bombus morio in an earlier study. The present work investigated in more detail the presence of intra-individual haplotypes variation in this species. Heteroplasmy was detected in individuals from all the ten sampled locations, with an average of six heteroplasmic haplotypes per individual. In addition, some of these heteroplasmic haplotypes were shared among individuals from different locations, suggesting the existence of stable heteroplasmy in B. morio. These results demonstrated that heteroplasmy is likely to affect inferences based on mtDNA analysis, especially in phylogenetic, phylogeographic and population genetics studies. In addition, NUMTs were also detected. These sequences showed divergence of 2.7% to 12% in relation to the mitochondrial haplotypes. These levels of divergence could mislead conclusions in evolutionary studies and affect species identification through DNA barcoding.

Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification

Molecular information is crucial for species identification when facing challenging morphology-based specimen identifications. The use of DNA barcodes partially solves this problem, but in some cases when PCR is not an option (i.e., primers are not available, problems in reaction standardization), amplification-free approaches could be an optimal alternative. Recent advances in DNA sequencing, like the MinION device from Oxford Nanopore Technologies (ONT), allow to obtain genomic data with low laboratory and technical requirements, and at a relatively low cost. In this study, we explore ONT sequencing for molecular species identification from a total DNA sample obtained from a neotropical rodent and we also test the technology for complete mitochondrial genome reconstruction via genome skimming. We were able to obtain "de novo" the complete mitogenome of a specimen from the genus Melanomys (Cricetidae: Sigmodontinae) with average depth coverage of 78X using ONT-only data and by combining multiple assembly routines. Our pipeline for an automated species identification was able to identify the sample using unassembled sequence data (raw) in a reasonable computing time, which was substantially reduced when a priori information related to the organism identity was known. Our findings suggest ONT sequencing as a suitable candidate to solve species identification problems in metazoan nonmodel organisms and generate complete mtDNA datasets.

A method to generate multilocus barcodes of pinned insect specimens using MiSeq

For molecular insect identification, amplicon sequencing methods are recommended because they offer a cost-effective approach for targeting small sets of informative genes from multiple samples. In this context, high-throughput multilocus amplicon sequencing has been achieved using the MiSeq Illumina sequencing platform. However, this approach generates short gene fragments of <500 bp, which then have to be overlapped using bioinformatics to achieve longer sequence lengths. This increases the risk of generating chimeric sequences or leads to the formation of incomplete loci. Here, we propose a modified nested amplicon sequencing method for targeting multiple loci from pinned insect specimens using the MiSeq Illumina platform. The modification exists in using a three-step nested PCR approach targeting near full-length loci in the initial PCR and subsequently amplifying short fragments of between 300 and 350 bp for high-throughput sequencing using Illumina chemistry. Using this method, we generated 407 sequences of three loci from 86% of all the specimens sequenced. Out of 103 pinned bee specimens of replicated species, 71% passed the 95% sequence similarity threshold between species replicates. This method worked best for pinned specimens aged between 0 and 5 years, with a limit of 10 years for pinned and 14 years for ethanol-preserved specimens. Hence, our method overcomes some of the challenges of amplicon sequencing using short read next generation sequencing and improves the possibility of creating high-quality multilocus barcodes from insect collections.

Delineating the Asphondylia prosopidis Complex (Diptera: Cecidomyiidae): Possible Biological Control Agents of Honey Mesquite

The Asphondylia prosopidis Cockrell complex with its fungal associate produces four distinct bud galls on honey mesquite (Prosopis glandulosa). They are considered as potential biological control agents to reduce seed production of invasive mesquites. Previous studies suggest that the complex may consist of more than one gall midge species or biotype. Therefore, before conducting host specificity tests, it is essential to understand the relationships among the gall midges in the complex. Each gall type was collected from sympatric regions in Arizona, New Mexico, and Texas for four years. Here we show that midges producing each gall type were clearly separated based on phylogenetic analysis using DNA sequences in the cytochrome oxidase subunit I region. Furthermore, we confirmed that morphological differences between pupae from each gall type were discernible, although variable, using a scanning electron microscope. Based on these differences, we suggest that the A. prosopidis complex consists of four different gall midge species, three of which are cryptic species. Among them, Asphondylia species producing a barrel gall type and A. prosopidis producing the original gall type are potential biological control agents of P. glandulosa because they are multivoltine species with four to five generations per year that complete their annual life cycle exclusively on flower buds of mesquite.

Categorization of species as native or nonnative using DNA sequence signatures without a complete reference library

New genetic diagnostic approaches have greatly aided efforts to document global biodiversity and improve biosecurity. This is especially true for organismal groups in which species diversity has been underestimated historically due to difficulties associated with sampling, the lack of clear morphological characteristics, and/or limited availability of taxonomic expertise. Among these methods, DNA sequence barcoding (also known as "DNA barcoding") and by extension, meta-barcoding for biological communities, has emerged as one of the most frequently utilized methods for DNA-based species identifications. Unfortunately, the use of DNA barcoding is limited by the availability of complete reference libraries (i.e., a collection of DNA sequences from morphologically identified species), and by the fact that the vast majority of species do not have sequences present in reference databases. Such conditions are critical especially in tropical locations that are simultaneously biodiversity rich and suffer from a lack of exploration and DNA characterization by trained taxonomic specialists. To facilitate efforts to document biodiversity in regions lacking complete reference libraries, we developed a novel statistical approach that categorizes unidentified species as being either likely native or likely nonnative based solely on measures of nucleotide diversity. We demonstrate the utility of this approach by categorizing a large sample of specimens of terrestrial insects and spiders (collected as part of the Moorea BioCode project) using a generalized linear mixed model (GLMM). Using a training data set of known endemic (n = 45) and known introduced species (n = 102), we then estimated the likely native/nonnative status for 4,663 specimens representing an estimated 1,288 species (412 identified species), including both those specimens that were either unidentified or whose endemic/introduced status was uncertain. Using this approach, we were able to increase the number of categorized specimens by a factor of 4.4 (from 794 to 3,497), and the number of categorized species by a factor of 4.8 from (147 to 707) at a rate much greater than chance (77.6% accuracy). The study identifies phylogenetic signatures of both native and nonnative species and suggests several practical applications for this approach including monitoring biodiversity and facilitating biosecurity.

Singleton molecular species delimitation based on COI-5P barcode sequences revealed high cryptic/undescribed diversity for Chinese katydids (Orthoptera: Tettigoniidae)

Background

DNA barcoding has been developed as a useful tool for species discrimination. Several sequence-based species delimitation methods, such as Barcode Index Number (BIN), REfined Single Linkage (RESL), Automatic Barcode Gap Discovery (ABGD), a Java program uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Generalized Mixed Yule Coalescent (GMYC), and Bayesian implementation of the Poisson Tree Processes model (bPTP), were used. Our aim was to estimate Chinese katydid biodiversity using standard DNA barcode cytochrome c oxidase subunit I (COI-5P) sequences.

Results

Detection of a barcoding gap by similarity-based analyses and clustering-base analyses indicated that 131 identified morphological species (morphospecies) were assigned to 196 BINs and were divided into four categories: (i) MATCH (83/131 = 64.89%), morphospecies were a perfect match between morphospecies and BINs (including 61 concordant BINs and 22 singleton BINs); (ii) MERGE (14/131 = 10.69%), morphospecies shared its unique BIN with other species; (iii) SPLIT (33/131 = 25.19%, when 22 singleton species were excluded, it rose to 33/109 = 30.28%), morphospecies were placed in more than one BIN; (iv) MIXTURE (4/131 = 5.34%), morphospecies showed a more complex partition involving both a merge and a split. Neighbor-joining (NJ) analyses showed that nearly all BINs and most morphospecies formed monophyletic cluster with little variation. The molecular operational taxonomic units (MOTUs) were defined considering only the more inclusive clades found by at least four of seven species delimitation methods. Our results robustly supported 61 of 109 (55.96%) morphospecies represented by more than one specimen, 159 of 213 (74.65%) concordant BINs, and 3 of 8 (37.5%) discordant BINs.

Conclusions

Molecular species delimitation analyses generated a larger number of MOTUs compared with morphospecies. If these MOTU splits are proven to be true, Chinese katydids probably contain a seemingly large proportion of cryptic/undescribed taxa. Future amplification of additional molecular markers, particularly from the nuclear DNA, may be especially useful for specimens that were identified here as problematic taxa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1404-5) contains supplementary material, which is available to authorized users.

Possibility of numt co-amplification from gigantic genome of Orthoptera: testing efficiency of standard PCR protocol in producing orthologous COI sequences

Mitochondrial DNA has been the preferential genome biodiversity studies. However, several factors contribute to its inadequacy. Numts constitute one of the main complications that prevent obtaining orthologous mitochondrial sequences. Orthoptera have been a model group in numt studies because of their huge genome size. In this study we aimed to; (i) test efficiency of standard PCR protocol in producing orthologous sequences of cytochrome C oxidase, (ii) study presence/absence of numts in several unstudied Orthoptera species, (iii) test if there is a threshold between the length of mtDNA targeted for amplification and possibility of encountering numts, and (iv) estimate reliability of the sequences in databases in light of these findings. For these aims we studied 38 species of Orthoptera representing different sublineages and genome sizes. DNA extracted from each sample was used to amplify five different fragments of COI region by standard PCR protocol. Sequenced PCR amplicons were checked for numt possibility by several different numt criteria. No sequences without numt signs were obtained for the first fragment. The number of samples with numt signs for the other four fragments differed between the suborders Ensifera and Caelifera. The percentage of samples with numt signs was higher in Caelifera than Ensifera for all fragments. The numt percentage considerably decreased for the longest two fragments. Numts are more prevalent in families with larger genome size. We arrived at the following conclusions: (i) numts are common in all members of Orthoptera, but, their prevalence differs among intra-lineages, especially more prevalent in Caelifera, (ii) there seems a correlation between numt rate and genome size, (iii) there is no threshold to avoid numt co-amplification, but, a 1,000 bp length may be a threshold for Ensifera, (iv) Folmer region of COI doesn't seem an appropriate marker for animal barcoding. Additionally, a phylogenetic tree produced from the numt sequences of fragment four detected in genus Anterastes suggested a paleonumt gained in generic ancestor a 3.5-4 times slower divergence rate for numt sequences.

DNA barcoding Brooklyn (New York): A first assessment of biodiversity in Marine Park by citizen scientists

DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA barcoding has many practical applications including furthering the study of taxonomy and monitoring biodiversity. In addition to these uses, DNA barcoding is a powerful tool to empower, engage, and educate students in the scientific method while conducting productive and creative research. The study presented here provides the first assessment of Marine Park (Brooklyn, New York, USA) biodiversity using DNA barcoding. New York City citizen scientists (high school students and their teachers) were trained to identify species using DNA barcoding during a two-week long institute. By performing NCBI GenBank BLAST searches, students taxonomically identified 187 samples (1 fungus, 70 animals and 116 plants) and also published 12 novel DNA barcodes on GenBank. Students also identified 7 ant species and demonstrated the potential of DNA barcoding for identification of this especially diverse group when coupled with traditional taxonomy using morphology. Here we outline how DNA barcoding allows citizen scientists to make preliminary taxonomic identifications and contribute to modern biodiversity research.

Molecular Characterization of the 2016 New World Screwworm (Diptera: Calliphoridae) Outbreak in the Florida Keys

New World screwworm (NWS), Cochliomyia hominivorax (Coquerel 1858) (Diptera: Calliphoridae), is a myiasis-causing fly that can be a serious threat to the health of livestock, wildlife, and humans. Its progressive eradication from the southern United States, Mexico, and Central America from the 1950s to 2000s is an excellent example of successful pest management using sterile insect technique (SIT). In late 2016, autochthonous NWS were detected in the Florida Keys, representing this species' first invasion in the United States in >30 yr. Rapid use of quarantine and SIT was successful in eliminating the infestation by early 2017; however, the geographic source of this infestation remains unknown. Here, we use amplicon sequencing to generate mitochondrial and nuclear sequence data representing all confirmed cases of NWS from this infestation, and compare these sequences to preexisting data sets sampling the native distribution of NWS. We ask two questions regarding the FL Keys outbreak. First, is this infestation the result of a single invasion from one source, or multiple invasions from different sources? And second, what is the geographic origin of this invasion? We found virtually no sequence variation between specimens collected from the FL Keys outbreak, which is consistent with a single source of introduction. However, we also found very little geographic resolution in any of the data sets, which precludes identification of the source of this outbreak. Our lack of success in answering our second question speaks to the need for finer-scale genetic or genomic assessments of NWS population structure, which would facilitate source determination of potential future outbreaks.

Instances of erroneous DNA barcoding of metazoan invertebrates: Are universal cox1 gene primers too "universal"?

The cytochrome c oxidase subunit I (cox1) gene is the main mitochondrial molecular marker playing a pivotal role in phylogenetic research and is a crucial barcode sequence. Folmer’s “universal” primers designed to amplify this gene in metazoan invertebrates allowed quick and easy barcode and phylogenetic analysis. On the other hand, the increase in the number of studies on barcoding leads to more frequent publishing of incorrect sequences, due to amplification of non-target taxa, and insufficient analysis of the obtained sequences. Consequently, some sequences deposited in genetic databases are incorrectly described as obtained from invertebrates, while being in fact bacterial sequences. In our study, in which we used Folmer’s primers to amplify COI sequences of the crustacean fairy shrimp Branchipus schaefferi (Fischer 1834), we also obtained COI sequences of microbial contaminants from Aeromonas sp. However, when we searched the GenBank database for sequences closely matching these contaminations we found entries described as representatives of Gastrotricha and Mollusca. When these entries were compared with other sequences bearing the same names in the database, the genetic distance between the incorrect and correct sequences amplified from the same species was c.a. 65%. Although the responsibility for the correct molecular identification of species rests on researchers, the errors found in already published sequences data have not been re-evaluated so far. On the basis of the standard sampling technique we have estimated with 95% probability that the chances of finding incorrectly described metazoan sequences in the GenBank depend on the systematic group, and variety from less than 1% (Mollusca and Arthropoda) up to 6.9% (Gastrotricha). Consequently, the increasing popularity of DNA barcoding and metabarcoding analysis may lead to overestimation of species diversity. Finally, the study also discusses the sources of the problems with amplification of non-target sequences.

The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species Complex

Molecular species identification using suboptimal PCR primers can over-estimate species diversity due to coamplification of nuclear mitochondrial (NUMT) DNA/pseudogenes. For the agriculturally important whitefly Bemisia tabaci cryptic pest species complex, species identification depends primarily on characterization of the mitochondrial DNA cytochrome oxidase I (mtDNA COI) gene. The lack of robust PCR primers for the mtDNA COI gene can undermine correct species identification which in turn compromises management strategies. This problem is identified in the B. tabaci Africa/Middle East/Asia Minor clade which comprises the globally invasive Mediterranean (MED) and Middle East Asia Minor I (MEAM1) species, Middle East Asia Minor 2 (MEAM2), and the Indian Ocean (IO) species. Initially identified from the Indian Ocean island of Réunion, MEAM2 has since been reported from Japan, Peru, Turkey and Iraq. We identified MEAM2 individuals from a Peruvian population via Sanger sequencing of the mtDNA COI gene. In attempting to characterize the MEAM2 mitogenome, we instead characterized mitogenomes of MEAM1. We also report on the mitogenomes of MED, AUS, and IO thereby increasing genomic resources for members of this complex. Gene synteny (i.e., same gene composition and orientation) was observed with published B. tabaci cryptic species mitogenomes. Pseudogene fragments matching MEAM2 partial mtDNA COI gene exhibited low frequency single nucleotide polymorphisms that matched low copy number DNA fragments (<3%) of MEAM1 genomes, whereas presence of internal stop codons, loss of expected stop codons and poor primer annealing sites, all suggested MEAM2 as a pseudogene artifact and so not a real species.

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 of crickets, katydids and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany and Switzerland

We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life and Swiss Barcode of Life. Our data set includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. Ninety-three of these 122 species (76.2%, including all Ensifera) can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the species concerned are phylogenetically young and hybridization has been previously observed. We also highlight the problem of nuclear mitochondrial pseudogenes (numts), a known problem in the barcoding of orthopteran species, and the possibility of Wolbachia infections. Finally, we discuss the possible taxonomic implications of our barcoding results and point out future research directions.

Reassessment of Species Diversity of the Subfamily Denticollinae (Coleoptera: Elateridae) through DNA Barcoding

The subfamily Denticollinae is a taxonomically diverse group in the family Elateridae. Denticollinae includes many morphologically similar species and crop pests, as well as many undescribed species at each local fauna. To construct a rapid and reliable identification system for this subfamily, the effectiveness of molecular species identification was assessed based on 421 cytochrome c oxidase subunit I (COI) sequences of 84 morphologically identified species. Among the 84 morphospecies, molecular species identification of 60 species (71.4%) was consistent with their morphological identifications. Six cryptic and/or pseudocryptic species with large genetic divergence (>5%) were confirmed by their sympatric or allopatric distributions. However, 18 species, including a subspecies, had ambiguous genetic distances and shared overlapping intra- and interspecific genetic distances (range: 2.12%–3.67%) suggesting incomplete lineage sorting, introgression of mitochondrial genome, or affection by endosymbionts, such as Wolbachia infection, between species and simple genetic variation within species. In this study, we propose a conservative threshold of 3.6% for convenient molecular operational taxonomic unit (MOTU) identification in the subfamily Denticollinae based on the results of pairwise genetic distances analyses using neighbor-joining, mothur, Automatic Barcode Gap Discovery analysis, and tree-based species delimitation by Poisson Tree Processes analysis. Using the 3.6% threshold, we identified 87 MOTUs and found 8 MOTUs in the interval between 2.5% to 3.5%. Evaluation of MOTUs identified in this range requires integrative species delimitation, including review of morphological and ecological differences as well as sensitive genetic markers. From this study, we confirmed that COI sequence is useful for reassessing species diversity for polymorphic and polytypic species occurring in sympatric and allopatric distributions, and for a single species having an extensively large habitat.

18S rRNA and COI haplotype diversity of Trichodorus obtusus from turfgrass in South Carolina

The stubby-root nematode, Trichodorus obtusus, was recently identified on zoysiagrass in South Carolina, USA. In Florida, T. obtusus causes more damage than other stubby-root nematodes encountered in turfgrass. The objective of this study was to use morphological analysis, mitochondrial DNA (COI: cytochrome oxidase 1) and nuclear (18S rRNA) sequence data to study the genetic structure and haplotype diversity of populations recovered from turfgrasses in South Carolina. Numerous morphological differences were observed among populations. Three 18S haplotypes were shared among South Carolina and Florida populations, and six mitochondrial haplotypes were identified in South Carolina samples. Of the six COI haplotypes, four haplotypes were restricted to one population from St Augustinegrass. The lowest haplotype diversity was found in samples from zoysiagrass. Sequences of the COI mtDNA gene of T. obtusus were published in GenBank and represent the first mtDNA sequences for the genus Trichodorus.

Rhynchophorus palmarum in Disguise: Undescribed Polymorphism in the "Black" Palm Weevil

During studies to adapt pheromone trapping of Rhynchophorus palmarum to the special coconut growing conditions at the Colombian Pacific coast, 152 atypically-colored specimens were captured in a total collection of 53,802 of the normally completely black weevil. Five specimens had the typical coloration of Rhynchophorus ferrugineus, an invasive species recently introduced to Aruba and Curação. A regional expansion of this invasion to the South American continent was feared and all atypical specimens were submitted to taxonomic analysis. Both conventional and molecular methods were employed. Conventional taxonomics confirmed the samples as belonging to R. palmarum but registered undescribed and species-atypical morphological variability in the subgular suture (wide vs. narrow), the ratio between intraocular distance and width of antennal scrobes (>0.35 vs. < 0.29) and the indentation of the mandibles (up to three mandibular teeth vs. bilobed). Molecular analysis placed all samples inspected, black and reddish alike, firmly within the R. palmarum group and the hypothesis of having inter-specific hybrids was rejected using co-dominant single sequence repeat markers with allelic specificity for both species.

DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

Metabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80-90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.

High genetic diversity and geographic subdivision of three lance nematode species (Hoplolaimus spp.) in the United States

Lance nematodes (Hoplolaimus spp.) feed on the roots of a wide range of plants, some of which are agronomic crops. Morphometric values of amphimictic lance nematode species overlap considerably, and useful morphological characters for their discrimination require high magnification and significant diagnostic time. Given their morphological similarity, these Hoplolaimus species provide an interesting model to investigate hidden diversity in crop agroecosystems. In this scenario, H. galeatus may have been over-reported and the related species that are morphologically similar could be more widespread in the United States that has been recognized thus far. The main objectives of this study were to delimit Hoplolaimus galeatus and morphologically similar species using morphology, phylogeny, and a barcoding approach, and to estimate the genetic diversity and population structure of the species found. Molecular analyses were performed using sequences of the cytochrome c oxidase subunit 1 (Cox1) and the internal transcribed spacer (ITS1) on 23 populations. Four morphospecies were identified: H. galeatus, H. magnistylus, H. concaudajuvencus, and H. stephanus, along with a currently undescribed species. Pronounced genetic structure correlated with geographic origin was found for all species, except for H. galeatus. Hoplolaimus galeatus also exhibited low genetic diversity and the shortest genetic distances among populations. In contrast, H. stephanus, the species with the fewest reports from agricultural soils, was the most common and diverse species found. Results of this project may lead to better delimitation of lance nematode species in the United States by contributing to the understanding the diversity within this group.

Numts: an impediment to DNA barcoding of Polyclinids, Tunicata

The mitochondrial cytochrome c oxidase subunit I (COI) gene, a widely accepted molecular marker for species identification and classification, has been questioned because of the presence of Numts. In this study we found the presence of Numts in the COI chromatogram of two tunicates, Polyclinum indicum and Polyclinum madrasensis belonging to the genus Polyclinum. Numts were also present in our sequence (Accession Number: KJ944391) and in other sequences belonging to genus Polyclinum in the GenBank record. The GeneBank database of genus Polyclinum contains COI-like sequences and COI pseudogenes, but no record of COI gene from Polyclinids. The prevalence of Numts in Polyclinids belonging to Tunicata, is an impediment to DNA barcoding studies of Polyclinum species.

Rampant nuclear insertion of mtDNA across diverse lineages within Orthoptera (Insecta)

Nuclear mitochondrial pseudogenes (numts) are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies.

Reliable molecular identification of nine tropical whitefly species

The identification of whitefly species in adult stage is problematic. Morphological differentiation of pupae is one of the better methods for determining identity of species, but it may vary depending on the host plant on which they develop which can lead to misidentifications and erroneous naming of new species. Polymerase chain reaction (PCR) fragment amplified from the mitochondrial cytochrome oxidase I (COI) gene is often used for mitochondrial haplotype identification that can be associated with specific species. Our objective was to compare morphometric traits against DNA barcode sequences to develop and implement a diagnostic molecular kit based on a RFLP-PCR method using the COI gene for the rapid identification of whiteflies. This study will allow for the rapid diagnosis of the diverse community of whiteflies attacking plants of economic interest in Colombia. It also provides access to the COI sequence that can be used to develop predator conservation techniques by establishing which predators have a trophic linkage with the focal whitefly pest species.

Systematics of spiny predatory katydids (Tettigoniidae: Listroscelidinae) from the Brazilian Atlantic Forest based on morphology and molecular data

Listroscelidinae (Orthoptera: Tettigoniidae) are insectivorous Pantropical katydids whose taxonomy presents a long history of controversy, with several genera incertae sedis. This work focused on species occurring in the Brazilian Atlantic Forest, one of the world's most threatened biomes. We examined material deposited in scientific collections and visited 15 conservation units from Rio de Janeiro to southern Bahia between November 2011 and January 2012, catching 104 specimens from 10 conservation units. Based on morphological and molecular data we redefined Listroscelidini, adding a new tribe, new genus and eight new species to the subfamily. Using morphological analysis, we redescribed and added new geographic records for six species, synonymized two species and built a provisional identification key for the Atlantic Forest Listroscelidinae. Molecular results suggest two new species and a new genus to be described, possibly by the fission of the genus Hamayulus. We also proposed a 500 bp region in the final portion of the COI to be used as a molecular barcode. Our data suggest that the Atlantic Forest Listroscelidinae are seriously endangered, because they occur in highly preserved forest remnants, show high rates of endemism and have a narrow geographic distribution. Based on our results, we suggest future collection efforts must take into account the molecular barcode data to accelerate species recognition.

Heteroplasmy and ancient translocation of mitochondrial DNA to the nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) complex

The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts) as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2) and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.

DNA barcoding and species boundary delimitation of selected species of Chinese Acridoidea (Orthoptera: Caelifera)

We tested the performance of DNA barcoding in Acridoidea and attempted to solve species boundary delimitation problems in selected groups using COI barcodes. Three analysis methods were applied to reconstruct the phylogeny. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. "Best match (BM)", "best close match (BCM)", "all species barcodes (ASB)" and "back-propagation neural networks (BP-based method)" were utilized to test the success rate of species identification. Phylogenetic species concept and network analysis were employed to delimitate the species boundary in eight selected species groups. The results demonstrated that the COI barcode region performed better in phylogenetic reconstruction at genus and species levels than at higher-levels, but showed a little improvement in resolving the higher-level relationships when the third base data or both first and third base data were excluded. Most overlaps and incorrect identifications may be due to imperfect taxonomy, indicating the critical role of taxonomic revision in DNA barcoding study. Species boundary delimitation confirmed the presence of oversplitting in six species groups and suggested that each group should be treated as a single species.

Climate and soil type together explain the distribution of microendemic species in a biodiversity hotspot

The grasshopper genus Caledonula, endemic to New Caledonia, was studied to understand the evolution of species distributions in relation to climate and soil types. Based on a comprehensive sampling of 80 locations throughout the island, the genus was represented by five species, four of which are new to science, of which three are described here. All the species have limited distributions in New Caledonia. Bioclimatic niche modelling shows that all the species were found in association with a wet climate and reduced seasonality, explaining their restriction to the southern half of the island. The results suggest that the genus was ancestrally constrained by seasonality. A molecular phylogeny was reconstructed using two mitochondrial and two nuclear markers. The partially resolved tree showed monophyly of the species found on metalliferous soils, and molecular dating indicated a rather recent origin for the genus. Adaptation to metalliferous soils is suggested by both morphological changes and radiation on these soils. The genus Caledonula is therefore a good model to understand the origin of microendemism in the context of recent and mixed influences of climate and soil type.

Potential of DNA barcoding for detecting quarantine fungi

The detection of live quarantine pathogenic fungi plays an important role in guaranteeing regional biological safety. DNA barcoding, an emerging species identification technology, holds promise for the reliable, quick, and accurate detection of quarantine fungi. International standards for phytosanitary guidelines are urgently needed. The varieties of quarantine fungi listed for seven countries/regions, the currently applied detection methods, and the status of DNA barcoding for detecting quarantine fungi are summarized in this study. Two approaches have been proposed to apply DNA barcoding to fungal quarantine procedures: (i) to verify the reliability of known internal transcribed spacer (ITS)/cytochrome c oxidase subunit I (COI) data for use as barcodes, and (ii) to determine other barcodes for species that cannot be identified by ITS/COI. As a unique, standardizable, and universal species identification tool, DNA barcoding offers great potential for integrating detection methods used in various countries/regions and establishing international detection standards based on accepted DNA barcodes. Through international collaboration, interstate disputes can be eased and many problems related to routine quarantine detection methods can be solved for global trade.

Molecular identification of cryptic bumblebee species from degraded samples using PCR-RFLP approach

The worldwide decline and local extinctions of bumblebees have raised a need for fast and accurate tools for species identification. Morphological characters are often not sufficient, and molecular methods have been increasingly used for reliable identification of bumblebee species. Molecular methods often require high-quality DNA which makes them less suitable for analysis of low-quality or older samples. We modified the PCR-RFLP protocol for an efficient and cost-effective identification of four bumblebee species in the subgenus Bombus s. str. (B. lucorum, B. terrestris, B. magnus and B. cryptarum). We used a short partial mitochondrial COI fragment (446 bp) and three diagnostic restriction enzymes (Hinf I, Hinc II and Hae III) to identify species from degraded DNA material. This approach allowed us to efficiently determine the correct species from all degraded DNA samples, while only a subset of samples 64.6% (31 of 48) resulted in successful amplification of a longer COI fragment (1064 bp) using the previously described method. This protocol can be applied for conservation and management of bumblebees within this subgenus and is especially useful for fast species identification from degraded samples.

Conflicting patterns of DNA barcoding and taxonomy in the cicada genus Tettigettalna from Southern Europe (Hemiptera: Cicadidae)

DNA barcodes have great potential to assist in species identification, especially when high taxonomical expertise is required. We investigated the utility of the 5' mitochondrial cytochrome c oxidase I (COI) region to discriminate between 13 European cicada species. These included all nine species currently recognized under the genus Tettigettalna, from which seven are endemic to the southern Iberian Peninsula. These cicadas have species-specific male calling songs but are morphologically very similar. Mean COI divergence between congeners ranged from 0.4% to 10.6%, but this gene was proven insufficient to determine species limits within genus Tettigettalna because a barcoding gap was absent for several of its species, that is, the highest intraspecific distance exceeded the lowest interspecific distance. The genetic data conflicted with current taxonomic classification for T. argentata and T. mariae. Neighbour-joining and Bayesian analyses revealed that T. argentata is geographically structured (clades North and South) and might constitute a species complex together with T. aneabi and T. mariae. The latter diverges very little from the southern clade of T. argentata and shares with it its most common haplotype. T. mariae is often in sympatry with T. argentata but it remains unclear whether introgression or incomplete lineage sorting may be responsible for the sharing of haplotypes. T. helianthemi and T. defauti also show high intraspecific variation that might signal hidden cryptic diversity. These taxonomic conflicts must be re-evaluated with further studies using additional genes and extensive morphological and acoustic analyses.