Taxonomic identity of the invasive fruit fly pest, Bactrocera invadens: concordance in morphometry and DNA barcoding

Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude of species, which are well defined by the complex shape of male genitalia. Here, we explore how well COI barcode data reflect morphological species entities and thus their usability for accelerated species inventorization. We conducted dedicated field surveys in Sri Lanka to collect the species‐rich and highly endemic Sericini chafers (Coleoptera: Scarabaeidae). Congruence among results of a series of protocols for de novo species delimitation and with morphology‐based species identifications was investigated. Different delimitation methods, such as the Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Barcode Index Number (BIN) assignments, resulted in different numbers of molecular operational taxonomic units (MOTUs). All methods showed both over‐splitting and lumping of morphologically identified species. Only 18 of the observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence of delimitation between MOTUs and morphospecies expressed by the match ratio was low, ranging from 0.57 to 0.67. TCS and multirate PTP (mPTP) showed the highest match ratio, while (BIN) assignment resulted in the lowest match ratio and most splitting events. mPTP lumped more species than any other method. Principal coordinate analysis (PCoA) on a match ratio‐based distance matrix revealed incongruent outcomes of multiple DNA delimitation methods, although applied to the same data. Our results confirm that COI barcode data alone are unlikely to correctly delimit all species, in particular, when using only a single delimitation approach. We encourage the integration of various approaches and data, particularly morphology, to validate species boundaries.

Leveraging machine learning tools and algorithms for analysis of fruit fly morphometrics

Analysis of landmark-based morphometric measurements taken on body parts of insects have been a useful taxonomic approach alongside DNA barcoding in insect identification. Statistical analysis of morphometrics have largely been dominated by traditional methods and approaches such as principal component analysis (PCA), canonical variate analysis (CVA) and discriminant analysis (DA). However, advancement in computing power creates a paradigm shift to apply modern tools such as machine learning. Herein, we assess the predictive performance of four machine learning classifiers; K-nearest neighbor (KNN), random forest (RF), support vector machine (the linear, polynomial and radial kernel SVMs) and artificial neural network (ANNs) on fruit fly morphometrics that were previously analysed using PCA and CVA. KNN and RF performed poorly with overall model accuracy lower than "no-information rate" (NIR) (p value > 0.1). The SVM models had a predictive accuracy of > 95%, significantly higher than NIR (p < 0.001), Kappa > 0.78 and area under curve (AUC) of the receiver operating characteristics was > 0.91; while ANN model had a predictive accuracy of 96%, significantly higher than NIR, Kappa of 0.83 and AUC was 0.98. Wing veins 2, 3, 8, 10, 14 and tibia length were of higher importance than other variables based on both SVM and ANN models. We conclude that SVM and ANN models could be used to discriminate fruit fly species based on wing vein and tibia length measurements or any other morphologically similar pest taxa. These algorithms could be used as candidates for developing an integrated and smart application software for insect discrimination and identification. Variable importance analysis results in this study would be useful for future studies for deciding what must be measured.

The Head of Fannia pusio (Fanniidae: Diptera) as A Novel Source of Morphometric Data for Assessing of Variation Along Geographic and Biological Lines

Fannia Robineau-Desvoidy, 1830 is the most diverse genus in the family Fanniidae (Diptera), with 288 species, many of which are include many of sanitary, economic and legal interest. The morphological homogeneity within the genus often makes species determination difficult. The best option for correct identification is to combine molecular and morphological analyses. The variation in the shape of a selection of body characters can be assessed by Geometric Morphometrics using the head as an innovative structure. Sex must be accounted for as a key covariate in this kind of study, since Fannia, as many other Diptera, has a sexually dimorphic head structure, with holoptic males and dicoptic females. Firstly, we analysed a set of Fannia sp. specimens sampled across the Iberian Peninsula (2012-2015), of which Fannia pusio (Wiedemann, 1830) was found to be the most abundant species. Our analyses provide significant morphological information. Fannia pusio exhibits clear intraspecific morphometric variation along an Iberian-wide East-West axis. A similar pattern emerged when comparing a laboratory-bred colony and wild samples.

Towards the implementation of a DNA barcode library for the identification of Peruvian species of Anastrepha (Diptera: Tephritidae)

The genus Anastrepha is a diverse lineage of fruit-damaging tephritid flies widespread across the Neotropical Region. Accurate taxonomic identification of these flies is therefore of paramount importance in agricultural contexts. DNA barcoding libraries are molecular-based tools based on a short sequence of the mitochondrial COI gene enabling rapid taxonomic identification of biological species. In this study, we evaluate the utility of this method for species identification of Peruvian species of Anastrepha and assemble a preliminary barcode profile for the group. We obtained 73 individual sequences representing the 15 most common species, 13 of which were either assigned to previously recognized or newly established BINs. Intraspecific genetic divergence between sampled species averaged 1.01% (range 0-3.3%), whereas maximum interspecific values averaged 8.67 (range 8.26-17.12%). DNA barcoding was found to be an effective method to discriminate between many Peruvian species of Anastrepha that were tested, except for most species of the fraterculus species group, which were all assigned to the same BIN as they shared similar and, in some cases, identical barcodes. We complemented this newly produced dataset with 86 published sequences to build a DNA barcoding library of 159 sequences representing 56 Peruvian species of Anastrepha (approx. 58% of species reported from that country). We conclude that DNA barcoding is an effective method to distinguish among Peruvian species of Anastrepha outside the fraterculus group, and that complementary methods (e.g., morphometrics, additional genetic markers) would be desirable to assist sensu stricto species identification for phytosanitary surveillance and management practices of this important group of pestiferous flies.

Τhe Complete Mitochondrial Genome of Bactrocera carambolae (Diptera: Tephritidae): Genome Description and Phylogenetic Implications

Bactrocera carambolae is one of the approximately 100 sibling species of the Bactrocera dorsalis complex and considered to be very closely related to B. dorsalis. Due to their high morphological similarity and overlapping distribution, as well as to their economic impact and quarantine status, the development of reliable markers for species delimitation between the two taxa is of great importance. Here we present the complete mitochondrial genome of B. carambolae sourced from its native range in Malaysia and its invaded territory in Suriname. The mitogenome of B. carambolae presents the typical organization of an insect mitochondrion. Comparisons of the analyzed B. carambolae sequences to all available complete mitochondrial sequences of B. dorsalis revealed several species-specific polymorphic sites. Phylogenetic analysis based on Bactrocera mitogenomes supports that B. carambolae is a differentiated taxon though closely related to B. dorsalis. The present complete mitochondrial sequences of B. carambolae could be used, in the frame of Integrative Taxonomy, for species discrimination and resolution of the phylogenetic relationships within this taxonomically challenging complex, which would facilitate the application of species-specific population suppression strategies, such as the sterile insect technique.

Genetic Analysis of Populations of the Peach Fruit Fly, Bactrocera zonata (Diptera: Tephritidae), in Iran

Bactrocera zonata (Saunders) as one of the most devastating species of the genus Bactrocera is a notorious polyphagous fruit fly pest attacking lots of commercially important host plant species in many parts of the world including Iran. Despite economic importance, the population genetics of B. zonata have remained relatively unexplored in the country. In this study, the genetic structure, genetic diversity, and demographic history of this pest in Iran were investigated on the basis of cytochrome oxidase c subunit 1 (COI) sequences. A total of 21 haplotypes were identified from 66 individuals collected from seven locations. Genetic diversity indices (number of haplotypes, haplotype diversity, and nucleotide diversity) revealed high genetic diversity without any isolation by distance among the geographic areas. An overall low level of genetic differentiation between populations revealed by genetic structure analysis reinforces the hypothesis of free movement of flies throughout the geographic areas. Non-significant correlation between genetic distances and geographic distances was an indication of a high level of gene flow among the studied populations of the pest. In addition, the recent population expansion following a recent past bottleneck could be a factor that might be contributed to the overall low level of the genetic structure. Mismatch distribution analysis as well as Tajima's D and Fu's F_S tests strengthens the likelihood of a recent expanded population following a population bottleneck.

Unexpected Diversity of Wolbachia Associated with Bactrocera dorsalis (Diptera: Tephritidae) in Africa

Bactrocera dorsalis (Hendel) is an important pest of fruit-bearing plants in many countries worldwide. In Africa, this pest has spread rapidly and has become widely established since the first invasion report in 2003. Wolbachia is a vertically transmitted endosymbiont that can significantly influence aspects of the biology and, in particular, the reproduction of its host. In this study, we screened B. dorsalis specimens collected from several locations in Africa between 2005 and 2017 for Wolbachia using a PCR-based assay to target the Wolbachia surface protein wsp. Of the 357 individuals tested, 10 were positive for Wolbachia using the wsp assay. We identified four strains of Wolbachia infecting two B. dorsalis mitochondrial haplotypes. We found no strict association between the infecting strain and host haplotype, with one strain being present in two different host haplotypes. All the detected strains belonged to Super Group B Wolbachia and did not match any strains reported previously in B. dorsalis in Asia. These findings indicate that diverse Wolbachia infections are present in invasive populations of B. dorsalis.

Infestation Levels and Molecular Identification Based on Mitochondrial COI Barcode Region of Five Invasive Gelechiidae Pest Species in Kenya

Invasive Gelechiidae pest species, namely Tuta absoluta, Phthorimaea operculella, Aproaerema simplixella, Sitotroga cerealella, and Pectinophora gossypiella are among the major constraints hampering agricultural economy in Kenya. Infestation levels were determined on respective host crops sampled from different localities and P. operculella recorded the highest infestation of 68.00 ± 4.92% on stored potato. Aproaerema simplixella and T. absoluta accounted for 61.33 ± 5.35% and 51.56 ± 5.22% maximal infestation on groundnuts and tomato leaves, respectively. Stored maize was significantly infested by S. cerealella (54.33 ± 5.31%) while no infestation was observed on the freshly harvested grains. Infestation on open bolls by P. gossypiella was relatively low (6.11 ± 3.46%) compared to Anatrachyntis simplex (45.67 ± 7.84%) that emerged as the key pest of cotton. The species were discriminated based on sequence similarities, evolutionary divergences, and phylogenetic analyses. A 658-bp fragment of mitochondrial cytochrome c oxidase subunit I (COI) gene was obtained from 302 specimens. Generally, genetic variations were low within and between Gelechiid populations, with an average of 0.02% and all intraspecific divergences were less than 2% except for S. cerealella. The Gelechiids data set generated eight Barcode Index Numbers (BINs), five of which were concordant and three belonging to S. cerealella were singleton. All species were separated into distinct clusters on a maximum likelihood tree. Data on infestation levels will be useful in defining the pest status of these Gelechiids in Kenya. DNA barcoding is also presented as a valuable tool to complement traditional taxonomy for rapid and accurate identification of these species of agronomic interest.

Size and shape analysis of Trioza erytreae Del Guercio (Hemiptera: Triozidae), vector of citrus huanglongbing disease

BACKGROUND

The African citrus triozid (ACT) Trioza erytreae Del Guercio (Hemiptera: Triozidae) is one of the most devastating pests of citrus with a well-known role as a vector of the phloem-limited bacteria (Candidatus Liberibacter africanus) associated with huanglongbing (citrus greening disease), currently considered the world's most serious disease of citrus. Although the pest can successfully develop and reproduce on non-citrus host plants, there is no documented information on the geometric morphometry of ACT. We determine the effect of host plants on ACT morphometry under controlled laboratory conditions using traditional and geometric analysis.

RESULTS

ACT reared on C. limon and Citroncirus spp. was significantly larger than when reared on the other host plant species. ACT reared on C. anisata and C. tangelo was consistently smaller than that reared on M. koenigii and C. sinensis. Based on warped outline drawings, ACT reared on Citroncirus spp. and Murraya koenigii had narrower wings than when reared on C. anisata, C. limon, and C. sinensis with slightly broader wing patterns.

CONCLUSION

This study clearly demonstrates that host plant species affect morphometric variation in ACT, which might have a direct impact on fitness parameters of the pest as well as its potential for dispersion. Wing shape and size appear to be useful in separating populations of ACT into different groups. © 2018 Society of Chemical Industry.

First Record of an Invasive Fruit Fly Belonging to Bactrocera dorsalis Complex (Diptera: Tephritidae) in Europe

Emerging pests are increasingly threatening fruit orchard health across the Mediterranean area. Tephritidae, representing serious threats for Europe, are numerous, and the fruit flies Bactrocera zonata and those belonging to Bactrocera dorsalis complex are among the most alarming species. These species are highly polyphagous and B. zonata has already spread to some Mediterranean countries. Due to these ongoing threats, in the Campania Region (southern Italy), a survey with traps and infested fruits analysis was performed with the aim of detecting the presence of species of Bactrocera dorsalis complex. In two mixed fruit-trees fields, some adults belonging to a species of Bactrocera were captured in traps baited with the highly attractive male lure (methyl eugenol). They were distinguished from similar-looking Bactrocera spp. by morphological and molecular comparative analyses. Considering the existing morphological keys, specimens were tentatively identified as B. dorsalis but molecular characterization with COI split them into two clades. Some specimens were grouped with B. dorsalis similar to B. kandiensis and B. kandiensis and others in a clade including B. dorsalis and B. invadens (syn. B. dorsalis). ITS1 sequences instead confirmed morphological identification. The integrative approach allowed identifying all the specimens collected as belonging to the B. dorsalis complex. This finding represents the first field interception in Europe of a member of one of the most dangerous groups of fruit flies.

DNA Barcode Reference Library for the African Citrus Triozid, Trioza erytreae (Hemiptera: Triozidae): Vector of African Citrus Greening

Citrus (Citrus spp.) production continues to decline in East Africa, particularly in Kenya and Tanzania, the two major producers in the region. This decline is attributed to pests and diseases including infestation by the African citrus triozid, Trioza erytreae (Del Guercio) (Hemiptera: Triozidae). Besides direct feeding damage by adults and immature stages, T. erytreae is the main vector of 'Candidatus Liberibacter africanus', the causative agent of Greening disease in Africa, closely related to Huanglongbing. This study aimed to generate a novel barcode reference library for T. erytreae in order to use DNA barcoding as a rapid tool for accurate identification of the pest to aid phytosanitary measures. Triozid samples were collected from citrus orchards in Kenya, Tanzania, and South Africa and from alternative host plants. Sequences generated from populations in the study showed very low variability within acceptable ranges of species. All samples analyzed were linked to T. erytreae of GenBank accession number KU517195. Phylogeny of samples in this study and other Trioza reference species was inferred using the Maximum Likelihood method. The phylogenetic tree was paraphyletic with two distinct branches. The first branch had two clusters: 1) cluster of all populations analyzed with GenBank accession of T. erytreae and 2) cluster of all the other GenBank accession of Trioza species analyzed except T. incrustata Percy, 2016 (KT588307.1), T. eugeniae Froggatt (KY294637.1), and T. grallata Percy, 2016 (KT588308.1) that occupied the second branch as outgroups forming sister clade relationships. These results were further substantiated with genetic distance values and principal component analyses.

Genetic diversity and population structure in Bactrocera correcta (Diptera: Tephritidae) inferred from mtDNA cox1 and microsatellite markers

Bactrocera correcta is one of the most destructive pests of horticultural crops in tropical and subtropical regions. Despite the economic risk, the population genetics of this pest have remained relatively unexplored. This study explores population genetic structure and contemporary gene flow in B. correcta in Chinese Yunnan Province and attempts to place observed patterns within the broader geographical context of the species’ total range. Based on combined data from mtDNA cox1 sequences and 12 microsatellite loci obtained from 793 individuals located in 7 countries, overall genetic structuring was low. The expansion history of this species, including likely human-mediated dispersal, may have played a role in shaping the observed weak structure. The study suggested a close relationship between Yunnan Province and adjacent countries, with evidence for Western and/or Southern Yunnan as the invasive origin of B. correcta within Yunnan Province. The information gleaned from this analysis of gene flow and population structure has broad implications for quarantine, trade and management of this pest, especially in China where it is expanding northward. Future studies should concentrate effort on sampling South Asian populations, which would enable better inferences of the ancestral location of B. correcta and its invasion history into and throughout Asia.

The status of Bactrocera invadens Drew, Tsuruta & White (Diptera: tephritidae) inferred from complete mitochondrial genome analysis

In this study, the complete 15,911 bp mitochondrial genome (mitogenome) of Bactrocera invadens was sequenced. To estimate the status of B. invadens, all available mitogenomes of Bactrocera were downloaded from GenBank for phylogenetic analysis. Phylogenetic analyses showed that B. invadens, B. philippinensis, B. papayae, and three B. dorsalis sequences formed a well-supported clade with very short terminal branch lengths, indicting the relatively close evolutionary relationships of these taxa. The results further supported that B. invadens, the same as B. philippinensis and B. papayae, belongs to the same species as B. dorsalis.

DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests

Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases. Aside from developing the reference library needed to guide specimen identifications, past barcode studies have revealed that a significant fraction of arthropod pests are a complex of allied taxa. Because of their importance as pests and disease vectors impacting global agriculture and forestry, DNA barcode results on these arthropods have significant implications for quarantine detection, regulation, and management. The current review discusses these implications in light of the presence of cryptic species in plant pests exposed by DNA barcoding.

Effects of Methyl Eugenol Feeding on Mating Compatibility of Asian Population of Bactrocera dorsalis (Diptera: Tephritidae) with African Population and with B. carambolae

Males of some species included in the Bactrocera dorsalis complex are strongly attracted to methyl eugenol (ME) (1,2-dimethoxy-4-(2-propenyl) benzene), a natural compound occurring in a variety of plant species. ME feeding of males of the B. dorsalis complex is known to enhance their mating competitiveness. Within B. dorsalis, recent studies show that Asian and African populations of B. dorsalis are sexually compatible, while populations of B. dorsalis and Bactrocera carambolae are relatively incompatible. The objectives of this study were to examine whether ME feeding by males affects mating compatibility between Asian and African populations of B. dorsalis and ME feeding reduces male mating incompatibility between B. dorsalis (Asian population) and B. carambolae. The data confirmed that Asian and African populations of B. dorsalis are sexually compatible for mating and showed that ME feeding only increased the number of matings. Though ME feeding also increased the number of matings of B. dorsalis (Asian population) and B. carambolae males but the sexual incompatibility between both species was not reduced by treatment with ME. These results conform to the efforts resolving the biological species limits among B. dorsalis complex and have implications for fruit fly control programs in fields and horticultural trade.

Identification of aphid (Hemiptera: Aphididae) species of economic importance in Kenya using DNA barcodes and PCR-RFLP-based approach

Aphids are among pests of economic importance throughout the world. Together with transmitting plant viruses, aphids are capable of inflicting severe crop production losses. They also excrete honeydew that favours the growth of sooty mold which reduces the quality of vegetables and fruits and hence their market values. Rapid and accurate identification of aphids to the species level is a critical component in effective pest management and plant quarantine systems. Even though morphological taxonomy has made a tremendous impact on species-level identifications, polymorphism, morphological plasticity and immature stages are among the many challenges to accurate identification. In addition, their small size, presence of cryptic species and damaged specimens dictate the need for a strategy that will ensure timely and accurate identification. In this study, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)-based on mitochondrial cytochrome c oxidase subunit I gene and DNA barcoding were applied to identify different aphid species collected from different agro-ecological zones of Kenya. Three restriction enzymes RsaI, AluI and Hinf1 produced patterns that allowed unambiguous identification of the species except Aphis craccivora and Aphis fabae. Analyses of the barcode region indicated intraspecific and interspecific sequence divergences of 0.08 and 6.63%, respectively. DNA barcoding identified all species, including the morphologically indistinguishable A. craccivora and A. fabae and separated two subspecies of A. fabae. Based on these results, both PCR-RFLPs and DNA barcoding could provide quick and accurate tools for identification of aphid species within Aphididae subsequently aiding in effective pest management programmes and enhance plant quarantine systems.

Taxonomy and phenotypic relationships of the Anastrepha fraterculus complex in the Mesoamerican and Pacific Neotropical dominions (Diptera, Tephritidae)

Previous morphometric studies based on linear measurements of female structures of the aculeus, mesonotum, and wing revealed the existence of seven morphotypes within the Anastrepha fraterculus cryptic species complex along the Neotropical Region. The current research followed linear and geometric morphometric approaches in 40 population samples of the nominal species Anastrepha fraterculus (Wiedemann) spread throughout the Meso-American and Pacific Neotropical dominions (including Mexico, Central America, Venezuela, Colombia, Ecuador, and Peru). The goals were to explore the phenotypic relationships of the morphotypes in these biogeographical areas; evaluate the reliability of procedures used for delimitation of morphotypes; and describe their current distribution. Findings determined that morphotypes previously recognized via the linear morphometrics were also supported by geometric morphometrics of the wing shape. In addition, we found an eighth morphotype inhabiting the highlands of Ecuador and Peru. Morphotypes are related into three natural phenotypic groups nominated as Mesoamerican-Caribbean lineage, Andean lineage, and Brazilian lineage. The hypothesis that lineages are not directly related to each other is discussed, supported by their large morphological divergence and endemicity in these three well-defined biogeographic areas. In addition, this hypothesis of the non-monophyly of the Anastrepha fraterculus complex is also supported by evidence from other authors based on molecular studies and the strong reproductive isolation between morphs from different lineages.

Historical perspective on the synonymization of the four major pest species belonging to the Bactrocera dorsalis species complex (Diptera, Tephritidae)

An FAO/IAEA-sponsored coordinated research project on integrative taxonomy, involving close to 50 researchers from at least 20 countries, culminated in a significant breakthrough in the recognition that four major pest species, Bactroceradorsalis, Bactroceraphilippinensis, Bactrocerapapayae and Bactrocerainvadens, belong to the same biological species, Bactroceradorsalis. The successful conclusion of this initiative is expected to significantly facilitate global agricultural trade, primarily through the lifting of quarantine restrictions that have long affected many countries, especially those in regions such as Asia and Africa that have large potential for fresh fruit and vegetable commodity exports. This work stems from two taxonomic studies: a revision in 1994 that significantly increased the number of described species in the Bactroceradorsalis species complex; and the description in 2005 of Bactrocerainvadens, then newly incursive in Africa. While taxonomically valid species, many biologists considered that these were different names for one biological species. Many disagreements confounded attempts to develop a solution for resolving this taxonomic issue, before the FAO/IAEA project commenced. Crucial to understanding the success of that initiative is an accounting of the historical events and perspectives leading up to the international, multidisciplinary collaborative efforts that successfully achieved the final synonymization. This review highlights the 21 year journey taken to achieve this outcome.

Geographical distribution and frequencies of organophosphate-resistant Ace alleles and morphometric variations in olive fruit fly populations

BACKGROUND

In the Mediterranean basin, organophosphate (OP) insecticides have been used intensively to control olive fly populations. Acetylcholinesterase (Ace) is the molecular target of OP insecticides, and three resistance-associated mutations that confer different levels of OP insensitivity have been identified. In this study, genotypes of olive fly Ace were determined in field-collected populations from broad geographical areas in Turkey. In addition, the levels of asymmetry of wing and leg characters were compared in these populations.

RESULTS

Our study revealed the existence of a genetically smooth stratification pattern in OP resistance allele distribution in the olive fly populations of Turkey. In contrast to earlier findings, the frequency of Δ3Q was found to be lower in the Aegean region, where the populations have been subjected to high selection pressure. Results based on the morphological differences among the samples revealed a similar pattern for both sides and did not demonstrate a clear separation.

CONCLUSION

The frequencies and geographic range of resistance alleles indicate that they were selected in the Aegean coast of Turkey and then spread westward towards Europe. One possible explanation for the absence of morphological asymmetry in olive fly samples might be the presence of modifier allele(s) that compensate for the increase in asymmetry.

DNA barcoding: complementing morphological identification of mosquito species in Singapore

BACKGROUND

Taxonomy that utilizes morphological characteristics has been the gold standard method to identify mosquito species. However, morphological identification is challenging when the expertise is limited and external characters are damaged because of improper specimen handling. Therefore, we explored the applicability of mitochondrial cytochrome C oxidase subunit 1 (COI) gene-based DNA barcoding as an alternative tool to identify mosquito species. In the present study, we compared the morphological identification of mosquito specimens with their differentiation based on COI barcode, in order to establish a more reliable identification system for mosquito species found in Singapore.

METHODS

We analysed 128 adult mosquito specimens, belonging to 45 species of 13 genera. Phylogenetic trees were constructed for Aedes, Anopheles, Culex and other genera of mosquitoes and the distinctive clustering of different species was compared with their taxonomic identity.

RESULTS

The COI-based DNA barcoding achieved a 100% success rate in identifying the mosquito species. We also report COI barcode sequences of 16 mosquito species which were not available previously in sequence databases.

CONCLUSIONS

Our study utilised for the first time DNA barcoding to identify mosquito species in Singapore. COI-based DNA barcoding is a useful tool to complement taxonomy-based identification of mosquito species.

The Bactrocera dorsalis species complex: comparative cytogenetic analysis in support of Sterile Insect Technique applications

Background

The Bactrocera dorsalis species complex currently harbors approximately 90 different members. The species complex has undergone many revisions in the past decades, and there is still an ongoing debate about the species limits. The availability of a variety of tools and approaches, such as molecular-genomic and cytogenetic analyses, are expected to shed light on the rather complicated issues of species complexes and incipient speciation. The clarification of genetic relationships among the different members of this complex is a prerequisite for the rational application of sterile insect technique (SIT) approaches for population control.

Results

Colonies established in the Insect Pest Control Laboratory (IPCL) (Seibersdorf, Vienna), representing five of the main economic important members of the Bactrocera dorsalis complex were cytologically characterized. The taxa under study were B. dorsalis s.s., B. philippinensis, B. papayae, B. invadens and B. carambolae. Mitotic and polytene chromosome analyses did not reveal any chromosomal characteristics that could be used to distinguish between the investigated members of the B. dorsalis complex. Therefore, their polytene chromosomes can be regarded as homosequential with the reference maps of B. dorsalis s.s.. In situ hybridization of six genes further supported the proposed homosequentiallity of the chromosomes of these specific members of the complex.

Conclusions

The present analysis supports that the polytene chromosomes of the five taxa under study are homosequential. Therefore, the use of the available polytene chromosome maps for B. dorsalis s.s. as reference maps for all these five biological entities is proposed. Present data provide important insight in the genetic relationships among the different members of the B. dorsalis complex, and, along with other studies in the field, can facilitate SIT applications targeting this complex. Moreover, the availability of 'universal' reference polytene chromosome maps for members of the complex, along with the documented application of in situ hybridization, can facilitate ongoing and future genome projects in this complex.

Using DNA chips for identification of tephritid pest species

BACKGROUND

The ability correctly to identify species in a rapid and reliable manner is critical in many situations. For insects in particular, the primary tools for such identification rely on adult-stage morphological characters. For a number of reasons, however, there is a clear need for alternatives. This paper reports on the development of a new method employing DNA biochip technology for the identification of pest species within the family Tephritidae.

RESULTS

The DNA biochip developed and tested here quickly and efficiently identifies and discriminates between several tephritid species, except for some that are members of a complex of closely related taxa and that may in fact not represent distinct biological species. The use of these chips offers a number of potential advantages over current methods. Results can be obtained in less than 5 h using material from any stage of the life cycle and with greater sensitivity than other methods currently available.

CONCLUSIONS

This technology provides a novel tool for the rapid and reliable identification of several major pest species that may be intercepted in imported fruits or other commodities. The existing chips can also easily be expanded to incorporate additional markers and species as needed.

Towards area-wide control of Bactrocera invadens: prospects of the sterile insect technique and molecular entomology

It is 10 years since the first detection of the invader fruit fly, Bactrocera invadens, in sub-Saharan Africa. The pest continues to hamper fruit production and create barriers to trade. Strategies currently employed to control B. invadens are insufficient, and more effective area-wide strategies are needed. The sterile insect technique and molecular entomology approaches have high potential and could help to bring about effective area-wide control of the pest if adopted and used as components of area-wide integrated pest management.

Niche overlap of congeneric invaders supports a single-species hypothesis and provides insight into future invasion risk: implications for global management of the Bactrocera dorsalis complex

Background

The invasive fruit fly, Bactrocera invadens, has expanded its range rapidly over the past 10 years. Here we aimed to determine if the recent range expansion of Bactrocera invadens into southern Africa can be better understood through niche exploration tools, ecological niche models (ENMs), and through incorporating information about Bactrocera dorsalis s.s., a putative conspecific species from Asia. We test for niche overlap of environmental variables between Bactrocera invadens and Bactrocera dorsalis s.s. as well as two other putative conspecific species, Bactrocera philippinensis and B. papayae. We examine overlap and similarity in the geographical expression of each species’ realised niche through reciprocal distribution models between Africa and Asia. We explore different geographical backgrounds, environmental variables and model complexity with multiple and single Bactrocera species hypotheses in an attempt to predict the recent range expansion of B. invadens into northern parts of South Africa.

Principal Findings

Bactrocera invadens has a high degree of niche overlap with B. dorsalis s.s. (and B. philippinensis and B. papayae). Ecological niche models built for Bactrocera dorsalis s.s. have high transferability to describe the range of B. invadens, and B. invadens is able to project to the core range of B. dorsalis s.s. The ENMs of both Bactrocera dorsalis and B. dorsalis combined with B. philipenesis and B. papayae have significantly higher predictive ability to capture the distribution points in South Africa than for B. invadens alone.

Conclusions/Significance

Consistent with other studies proposing these Bactrocera species as conspecific, niche similarity and overlap between these species is high. Considering these other Bactrocera dorsalis complex species simultaneously better describes the range expansion and invasion potential of B. invadens in South Africa. We suggest that these species should be considered the same–at least functionally–and global quarantine and management strategies applied equally to these Bactrocera species.

Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation

Background

Rapid and reliable identification of quarantine pests is essential for plant inspection services to prevent introduction of invasive species. For insects, this may be a serious problem when dealing with morphologically similar cryptic species complexes and early developmental stages that lack distinctive characters useful for taxonomic identification. DNA based barcoding could solve many of these problems. The standard barcode fragment, an approx. 650 base pairs long sequence of the 5′end of the mitochondrial cytochrome oxidase I (COI), enables differentiation of a very wide range of arthropods. However, problems remain in some taxa, such as Tephritidae, where recent genetic differentiation among some of the described species hinders accurate molecular discrimination.

Results

In order to explore the full species discrimination potential of COI, we sequenced the barcoding region of the COI gene of a range of economically important Tephritid species and complemented these data with all GenBank and BOLD entries for the systematic group available as of January 2012. We explored the limits of species delimitation of this barcode fragment among 193 putative Tephritid species and established operational taxonomic units (OTUs), between which discrimination is reliably possible. Furthermore, to enable future development of rapid diagnostic assays based on this sequence information, we characterized all single nucleotide polymorphisms (SNPs) and established “near-minimal” sets of SNPs that differentiate among all included OTUs with at least three and four SNPs, respectively.

Conclusions

We found that although several species cannot be differentiated based on the genetic diversity observed in COI and hence form composite OTUs, 85% of all OTUs correspond to described species. Because our SNP panels are developed based on all currently available sequence information and rely on a minimal pairwise difference of three SNPs, they are highly reliable and hence represent an important resource for developing taxon-specific diagnostic assays. For selected cases, possible explanations that may cause composite OTUs are discussed.