Tephritid Integrative Taxonomy: Where We Are Now, with a Focus on the Resolution of Three Tropical Fruit Fly Species Complexes

Molecular evolution and genetic diversity of defective chorion 1 in Anastrepha fraterculus and Anastrepha obliqua (Diptera, Tephritidae)

The family Tephritidae comprises numerous fruit fly species, some of which are economically significant, such as several in the genus Anastrepha. Most pest species in this genus belong to the fraterculus group, characterized by closely related species that are difficult to differentiate due to recent divergence and gene flow. Identifying genetic markers for their study is paramount for understanding the group's evolution and eventual phytosanitary control. Because there is variation in eggshell morphology among species in the genus, the study of the rapidly evolving defective chorion 1 (dec-1) gene, which is crucial for chorion formation and reproduction, could provide relevant information for Anastrepha differentiation. We compared transcriptome sequences of dec-1 from two of the most important pest species in the genus, Anastrepha fraterculus and Anastrepha obliqua to dec-1 sequences from Anastrepha ludens, which was used for structure prediction. Furthermore, we amplified a conserved exon across populations of these species. These data revealed three alternative transcripts in A. fraterculus and A. obliqua, consistent with patterns found in other Tephritidae; we obtained orthologous sequences for these other tephritids from NCBI to investigate patterns of selection affecting this gene at different hierarchical levels using different methods. These analyses show a general pattern of purifying selection across the whole gene and throughout its history at different hierarchical levels, from populations to more distantly related species. That notwithstanding, we still found evidence of positive and episodic diversifying selection at different levels. Different parts of the gene have shown distinct evolutionary rates, which were associated with the diverse proproteins produced by posttranslational changes of DEC-1, with proproteins that are incorporated in the chorion earlier in egg formation being in general more conserved than others that are incorporated later. This correlation appears more evident in certain lineages, including the branch that separates Anastrepha, as well as other internal branches that differentiate species within the genus. Our data showed that this gene shows remarkable variation across its different exons, which has proven to be informative at different evolutionary levels. These changes hold promise not only for studying differentiation in Anastrepha but also for the eventual management of selected pest species.

Population Dynamics of Bactrocera dorsalis (Diptera: Tephritidae) in Four Counties of Yunnan, China, by Electronic Monitoring System

Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) is a global economic pest that poses a serious threat to the fruit industry. In the southwest of China, Yunnan Province sustains a severe infestation of B. dorsalis. An automated monitoring system designed for B. dorsalis was employed in this study to elucidate the annual population dynamics of B. dorsalis in four counties: Yuanjiang, Huaping, Guangnan, and Ludian in Yunnan. The system utilizes sex parapheromone and image recognition technology. The data uploaded by the device are used to analyze the annual population dynamics of B. dorsalis in different regions. The results showed that the populations of adult B. dorsalis in all four counties peaked twice annually, with Yuanjiang experiencing the earliest peak periods, followed by Huaping, Guangnan, and Ludian. Adult B. dorsalis occurred in Yuanjiang throughout the year, and Yuanjiang had the highest number of B. dorsalis monitored. In Huaping, adult B. dorsalis occurred in March-December and was highly active, with a high population density in 2019. Bactrocera dorsalis did not occur in December in Guangnan but only in May-October in Ludian. Bactrocera dorsalis abundance was correlated with temperature in all four areas. The outcomes of this experiment provide a practical foundation for developing control strategies targeting B. dorsalis in various orchards across each county.

Phylogenetics, Molecular Species Delimitation and Geometric Morphometrics of All Reddish-Brown Species in the Genus Neotriplax Lewis, 1887 (Coleoptera: Erotylidae: Tritomini)

To date, five species of reddish-brown Neotriplax have been described, but their highly similar body color and other phenotypic traits make accurate taxonomy challenging. To clarify species-level taxonomy and validate potential new species, the cytochrome oxidase subunit I (COI) was used for phylogenetic analysis and the geometric morphometrics of elytron, pronotum, and hind wing were employed to distinguish all reddish-brown Neotriplax species. Phylogenetic results using maximum likelihood and Bayesian analyses of COI sequences aligned well with the current taxonomy of the Neotriplax species group. Significant K2P divergences, with no overlap between intra- and interspecific genetic distances, were obtained in Neotriplax species. The automatic barcode gap discovery (ABGD), assemble species by automatic partitioning (ASAP), and generalized mixed Yule coalescent (GMYC) approaches concurred, dividing the similar species into eight molecular operational taxonomic units (MOTUs). Geometric morphometric analysis using pronotum, elytron, hind wing shape and wing vein patterns also validated the classification of all eight species. By integrating these analytical approaches with morphological evidence, we successfully delineated the reddish-brown species of Neotriplax into eight species with three new species: N. qinghaiensis sp. nov., N. maoershanensis sp. nov., and N. guangxiensis sp. nov. Furthermore, we documented the first record of N. lewisii in China. This study underscores the utility of an integrative taxonomy approach in species delimitation within Neotriplax and serves as a reference for the taxonomic revision of other morphologically challenging beetles through integrative taxonomy.

A comparative analysis of the chromosomes of three FARQ species complex members, Ceratitis rosa, C. quilicii, and C. fasciventris F2 (Diptera: Tephritidae)

The Ceratitis FARQ species complex consists of four highly destructive agricultural pests of Africa, namely C. fasciventris, C. anonae, C. rosa, and C. quilicii. The members of the complex are considered very closely related and the species limits among them are rather obscure. Their economic significance and the need for developing biological methods for their control makes species identification within the complex an important issue, which has become clear that can only be addressed by multidisciplinary approaches. Chromosomes, both mitotic and polytene, can provide a useful tool for species characterization and phylogenetic inference among closely related dipteran species. In the current study, we present the mitotic karyotype and the polytene chromosomes of C. rosa and C. quilicii together with in situ hybridization data. We performed a comparative cytogenetic analysis among the above two species and C. fasciventris, the only other cytogenetically studied member of the FARQ complex, by comparing the mitotic complement and the banding pattern of the polytene chromosomes of each species to the others, as well as by studying the polytene chromosomes of hybrids between them. Our analysis revealed no detectable chromosomal rearrangements discriminating the three FARQ members studied, confirming their close phylogenetic relationships.

Genetical, Morphological, Behavioral, and Ecological Traits Support the Existence of Three Brazilian Species of the Anastrepha fraterculus Complex of Cryptic Species

Within the Neotropical genus Anastrepha, the nominal species Anastrepha fraterculus is widely distributed from Mexico through northern Argentina. Currently it is believed to comprises a complex of at least eight cryptic species—known as the Anastrepha fraterculus complex (AF complex)—three of which occur in Brazil: A. sp.1 aff. fraterculus, A. sp.2 aff. fraterculus, and A. sp.3 aff. fraterculus. In this study, we present the results of a broad integrated analysis of multiple biological attributes in samples of the three species collected in sympatric areas. Analyses of the mitotic chromosomes confirm that all of them differ in sex chromosomes, and that the relative frequency of the distinct karyotypes is associated with variation in altitude. In these sympatric areas, a single female hybrid karyotype was detected within a significant sample of individuals. Population samples were analyzed for the ribosomal transcribed spacer ITS1, confirming that the three species have specific sequence types. Observations of reproductive behavior under laboratory conditions revealed that A. sp.1 and A. sp.2 mate early in the morning, while A. sp.3 mates in the middle of the day. A bimodal distribution of mating time was observed in the laboratory for hybrids, obtained between A. sp.1 and A. sp.3. In a mating choice experiment, most of the mating pairs were homospecific. In addition, through a list of the most frequent hosts associated with geographical occurrence, a bioclimatic model of their potential distribution was generated. The set of data allowed for the construction of explanatory hypothesis about the observed geographical pattern and the differential use of host fruits. Morphometric analyses of wings clearly demonstrated differences among the three species, for both males and females. Based on a wing image of the A. fraterculus (Wiedemann, 1830) type specimen, the morphometric analysis indicated that the type specimen would correspond to a male of A. sp.2 aff. fraterculus. The information provided by this report is not only useful for taxonomic purposes, but also reveals aspects to be considered in any reconstruction of an evolutionary scenario of the Anastrepha fraterculus complex.

Phylogenomic approach reveals strong signatures of introgression in the rapid diversification of neotropical true fruit flies (Anastrepha: Tephritidae)

New sequencing techniques have allowed us to explore the variation on thousands of genes and elucidate evolutionary relationships of lineages even in complex scenarios, such as when there is rapid diversification. That seems to be the case of species in the genus Anastrepha, which shows great species diversity that has been divided into 21 species groups, several of which show wide geographical distribution. The fraterculus group has several economically important species and it is also an outstanding model for speciation studies, since it includes several lineages that have diverged recently possibly in the presence of interspecific gene flow. Our main goal is to test whether we can infer phylogenetic relationships of recently diverged taxa with gene flow, such as what is expected for the fraterculus group and determine whether certain genes remain informative even in this complex scenario. An analysis of thousands of orthologous genes derived from transcriptome datasets of 10 different lineages across the genus, including some of the economically most important pests, revealed signals of incomplete lineage sorting, vestiges of ancestral introgression between more distant lineages and ongoing gene flow between closely related lineages. Though these patterns affect the phylogenetic signal, the phylogenomic inferences consistently show that the morphologically identified species here investigated are in different evolutionary lineages, with the sole exception involving Brazilian lineages of A. fraterculus, which has been suggested to be a complex assembly of cryptic species. A tree space analysis suggested that genes with greater phylogenetic resolution have evolved under similar selection pressures and are more resilient to intraspecific gene flow, which would make it more likely that these genomic regions may be useful for identifying fraterculus group lineages. Our findings help establish relationships among the most important Anastrepha species groups, as well as bring further data to indicate that the diversification of fraterculus group lineages, and even other lineages in the genus Anastrepha, has been strongly influenced by interspecific gene flow.

Geographic distribution of sex chromosome polymorphism in Anastrepha fraterculus sp. 1 from Argentina

BACKGROUND

Anastrepha fraterculus is recognized as a quarantine pest in several American countries. This fruit fly species is native to the American continent and distributed throughout tropical and subtropical regions. It has been reported as a complex of cryptic species, and at least eight morphotypes have been described. Only one entity of this complex, formerly named Anastrepha fraterculus sp. 1, is present in Argentina. Previous cytogenetic studies on this morphotype described the presence of sex chromosome variation identified by chromosomal size and staining patterns. In this work, we expanded the cytological study of this morphotype by analyzing laboratory strains and wild populations to provide information about the frequency and geographic distribution of these sex chromosome variants. We analyzed the mitotic metaphases of individuals from four laboratory strains and five wild populations from the main fruit-producing areas of Argentina, including the northwest (Tucumán and La Rioja), northeast (Entre Ríos and Misiones), and center (Buenos Aires) of the country.

RESULTS

In wild samples, we observed a high frequency of X1X1 (0.94) and X1Y5 (0.93) karyomorphs, whereas X1X2 and X1Y6 were exclusively found at a low frequency in Buenos Aires (0.07 and 0.13, respectively), Entre Ríos (0.16 and 0.14, respectively) and Tucumán (0.03 and 0.04, respectively). X2X2 and X2Y5 karyomorphs were not found in wild populations but were detected at a low frequency in laboratory strains. In fact, karyomorph frequencies differed between wild populations and laboratory strains. No significant differences among A. fraterculus wild populations were evidenced in either karyotypic or chromosomal frequencies. However, a significant correlation was observed between Y5 chromosomal frequency and latitude.

CONCLUSIONS

We discuss the importance of cytogenetics to understand the possible route of invasion and dispersion of this pest in Argentina and the evolutionary forces acting under laboratory conditions, possibly driving changes in the chromosomal frequencies. Our findings provide deep and integral genetic knowledge of this species, which has become of relevance to the characterization and selection of valuable A. fraterculus sp. 1 strains for mass rearing production and SIT implementation.

The Dacini fruit fly fauna of Sulawesi fits Lydekker's line but also supports Wallacea as a biogeographic region (Diptera, Tephritidae)

Although there is scientific consensus on most of the major biogeographic regions in the world, the demarcation of the area connecting Southeast Asia with Australia and Oceania remains debated. Two candidate boundaries potentially explain faunistic diversity patterns in the regions: Lydekker's and Wallace's lines. The islands in between both 'lines' are jointly termed Wallacea, with Sulawesi as the largest landmass. We surveyed Dacini fruit flies (Tephritidae: Dacinae) in Sulawesi between 2016 and 2019 using traps baited with male lures, resulting in 4,517 collected flies. We identified all specimens to species level, which adds 15 new species records to the island, bringing the total number of Dacini species in Sulawesi to 83. The biogeographic affinity of species in the updated checklist reveals a strong connection with former 'Sunda' (41% of species); validating Lydekker's line, but also a high level of endemism (47% of species), confirming the uniqueness of Wallacea as a biogeographic region. We further describe a new species, Bactrocera (Bactrocera) niogreta Doorenweerd, sp. nov. and discuss the taxonomy of several interesting species.

Relative Tolerance of Three Morphotypes of the Anastrepha fraterculus Complex (Diptera: Tephritidae) to Cold Phytosanitary Treatment

The Anastrepha fraterculus (Wiedemann) complex is currently comprised of at least eight morphotypes, including several that are likely to be described as new species. It is critical to evaluate whether the morphotypes differ in tolerance to phytosanitary treatments. Temperatures from 0 to 3°C are used as a phytosanitary treatment for some commodities exported from the region and at risk of infestation by the A. fraterculus complex. Description of A. fraterculus morphotypes as new species could result in the annulation of phytosanitary treatment schedules for the new species. This study compared the relative cold tolerance of five populations from three morphotypes of the A. fraterculus complex: Andean, Peruvian, and Brazilian-1. Both a laboratory and wild strain of the Brazilian-1 morphotype were studied. Differences in mortality of third instars of the five A. fraterculus populations reared on nectarines were observed only with short treatment durations at temperatures ranging from 1.38 ± 0.04°C to 1.51 ± 0.08°C (mean ± SEM). Estimated times to achieve the LT99.99682 (probit 9) showed that Brazilian-1 wild, Brazilian-1 laboratory, and Cusco population were the most cold tolerant, followed by Andean and Peruvian, the least cold tolerant morphotype (i.e., Brazilian-1 wild = Brazilian-1 laboratory = Cusco population > Andean > Peruvian). These findings suggest that the current cold treatment schedules of 15 d at ≤ 1.11°C and 17 d at ≤ 1.67°C can be applied as cold treatments to any potential new species that may arise from the A. fraterculus complex.

Male-biased Adult Production of the Striped Fruit Fly, Zeugodacus scutellata, by Feeding dsRNA Specific to Transformer-2

Sterile insect release technique (SIT) is effective for eradicating quarantine insects including various tephritid fruit flies. When SIT is used for fruit flies, it is challenging to remove females from sterile males due to oviposition-associated piercing damage. This study developed a sex transition technique by feeding double-stranded RNA (dsRNA) specific to a sex-determining gene, Transformer-2 (Zs-Tra2) of the striped fruit fly, Zeugodacus scutellata. Zs-Tra2 is homologous to other fruit fly orthologs. It is highly expressed in female adults. RNA interference (RNAi) of Zs-Tra2 by injecting or feeding its specific dsRNA to larvae significantly increased male ratio. Recombinant Escherichia coli cells expressing dsRNA specific to Zs-Tra2 were prepared and used to feed larvae to suppress Zs-Tra2 gene expression levels. When these recombinant bacteria were fed to larvae during the entire feeding stage, the test population was significantly male-biased. Some females treated with such recombinant E. coli exhibited mosaic morphological characters such as the presence of male-specific abdominal setae in females. This study proposes a novel technique by feeding dsRNA specific to Transformer-2 to reduce female production during mass-rearing of tephritid males for SIT.

Development of internal COI primers to improve and extend barcoding of fruit flies (Diptera: Tephritidae: Dacini)

Accurate species-level identifications underpin many aspects of basic and applied biology; however, identifications can be hampered by a lack of discriminating morphological characters, taxonomic expertise or time. Molecular approaches, such as DNA "barcoding" of the cytochrome c oxidase (COI) gene, are argued to overcome these issues. However, nuclear encoding of mitochondrial genes (numts) and poor amplification success of suboptimally preserved specimens can lead to erroneous identifications. One insect group for which these molecular and morphological problems are significant are the dacine fruit flies (Diptera: Tephritidae: Dacini). We addressed these issues associated with COI barcoding in the dacines by first assessing several "universal" COI primers against public mitochondrial genome and numt sequences for dacine taxa. We then modified a set of four primers that more closely matched true dacine COI sequence and amplified two overlapping portions of the COI barcode region. Our new primers were tested alongside universal primers on a selection of dacine species, including both fresh preserved and decades-old dry specimens. Additionally, Bactrocera tryoni mitochondrial and nuclear genomes were compared to identify putative numts. Four numt clades were identified, three of which were amplified using existing universal primers. In contrast, our new primers preferentially amplified the "true" mitochondrial COI barcode in all dacine species tested. The new primers also successfully amplified partial barcodes from dry specimens for which full length barcodes were unobtainable. Thus we recommend these new primers be incorporated into the suites of primers used by diagnosticians and quarantine labs for the accurate identification of dacine species.

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.

What Can Integrated Analysis of Morphological and Genetic Data Still Reveal about the Anastrepha fraterculus (Diptera: Tephritidae) Cryptic Species Complex?

The South American fruit fly Anastrepha fraterculus (Wiedemann) is a complex of cryptic species, the so-called “Anastrepha fraterculus complex”, for which eight morphotypes are currently recognized. A previous analysis of ITS1 in samples of the Anastrepha fraterculus complex, while revealing high distinctiveness among samples from different localities of South America, Central America, and Mexico, no direct association was made between sequence type and morphotype. In the present report, a correlated analysis of morphometry and ITS1 data involved individuals belonging to the same population samples. Although showing a low level of intra-populational nucleotide variability, the ITS1 analysis indicated numerous inter-population sequence type variants. Morphotypes identified by morphometric analysis based on female wing shape were highly concordant with ITS1 genetic data. The correlation of genetic divergence and morphological differences among the tested samples gives strong evidence of a robust dataset, thereby indicating the existence of various taxonomic species within the A. fraterculus complex. However, the data revealed genetic and morphological variations in some regions, suggesting that further analysis is still required for some geographic regions.

Agricultural insect hybridization and implications for pest management

Biological invasions, the expansion of agricultural frontiers, and climate change favor encounters of divergent lineages of animals and plants, increasing the likelihood of hybridization. However, hybridization of insect species and its consequences for agroecosystems have not received sufficient attention. Gene exchange between distinct and distant genetic pools can improve the survival and reproduction of insect pests, and threaten beneficial insects in disturbed agricultural environments. Hybridization may be the underlying explanation for the recurrent pest outbreaks and control failures in putative hybrid zones, as suspected for bollworm, corn borer, whiteflies, and stink bugs. Reliable predictions of the types of changes that can be expected in pest insect genomes and fitness, and of their impacts on the fate of species and populations remain elusive. Typical steps in pest management, such as insect identification, pest monitoring, and control are likely affected by gene flow and adaptive introgression mediated by hybridization, and we do not have ways to respond to or mitigate the problem. To address the adverse effects of farming intensification and global trade, we must ensure that current integrated pest management programs incorporate up-to-date monitoring and diagnostic tools. The rapid identification of hybrids, quantification of levels of introgression, and in-depth knowledge of what genes have been transferred may help to explain and predict insect population outbreaks and control failures in the future. © 2019 Society of Chemical Industry.

Molecular phylogeny and species delimitation of the genus Dicerapanorpa (Mecoptera: Panorpidae)

Given that species is the fundamental unit in systematic biology, rigorous species delimitation is crucial for taxonomic studies, yet routine species delimitation remains an ongoing challenge in the taxonomic practice of insects. The two-horned scorpionfly Dicerapanorpa is a small genus in Panorpidae (Mecoptera) endemic to the Qinling-Bashan and Hengduan mountains, a biodiversity hotspot. However, species of Dicerapanorpa are difficult to delineate owing to marked intraspecific variation and interspecific similarity. Here, we investigate the diversity and species boundaries of Dicerapanorpa using an integrative approach based on DNA barcoding, morphological, geometric morphometric and molecular phylogenetic analyses. This integrative analyses confirmed the 13 described species of Dicerapanorpa and revealed three new species: Dicerapanorpa lativalva sp. nov., Dicerapanorpa hualongshana sp. nov. and Dicerapanorpa minshana sp. nov. Most molecular operational taxonomic units are in congruence with morphological clusters. Possible reasons for several discordances in Dicerapanorpa are tentatively discussed.

Social and nutritional factors shape larval aggregation, foraging, and body mass in a polyphagous fly

The majority of insect species have a clearly defined larval stage during development. Larval nutrition is crucial for individuals’ growth and development, and larval foraging success often depends on both resource availability and competition for those resources. To date, however, little is known about how these factors interact to shape larval development and behaviour. Here we manipulated the density of larvae of the polyphagous fruit fly pest Bactrocera tryoni (‘Queensland fruit fly’), and the diet concentration of patches in a foraging arena to address this gap. Using advanced statistical methods of machine learning and linear regression models, we showed that high larval density results in overall high larval aggregation across all diets except in extreme diet dilutions. Larval aggregation was positively associated with larval body mass across all diet concentrations except in extreme diet dilutions where this relationship was reversed. Over time, larvae in low-density arenas also tended to aggregate while those in high-density arenas tended to disperse, an effect that was observed for all diet concentrations. Furthermore, larvae in high-density arenas displayed significant avoidance of low concentration diets – a behaviour that was not observed amongst larvae in low-density arenas. Thus, aggregation can help, rather than hinder, larval growth in high-density environments, and larvae may be better able to explore available nutrition when at high-density than when at low-density.

Lima A, Nakamura AM, Fernandes F, Sobrinho I, de Brito RA. Evidence for Introgression Among Three Species of the Anastrepha fraterculus Group, a Radiating Species Complex of Fruit Flies

Introgression should no longer be considered as rare a phenomenon as once thought, since several studies have recently documented gene flow between closely related and radiating species. Here, we investigated evolutionary relationships among three closely related species of fruit flies of the Anastrepha fraterculus group (Anastrepha fraterculus, A. obliqua and A. sororcula). We sequenced a set of 20 genes and implemented a combined populational and phylogenetic inference with a model selection approach by an ABC framework in order to elucidate the demographic history of these species. The phylogenetic histories inferred from most genes showed a great deal of discordance and substantial shared polymorphic variation. The analysis of several population and speciation models reveal that this shared variation is better explained by introgression rather than convergence by parallel mutation or incomplete lineage sorting. Our results consistently showed these species evolving under an isolation with migration model experiencing a continuous and asymmetrical pattern of gene flow involving all species pairs, even though still showed a more closely related relationship between A. fraterculus and A. sororcula when compared with A. obliqua. This suggests that these species have been exchanging genes since they split from their common ancestor ∼2.6 MYA ago. We also found strong evidence for recent population expansion that appears to be consequence of anthropic activities affecting host crops of fruit flies. These findings point that the introgression here found may have been driven by genetic drift and not necessary by selection, which has implications for tracking and managing fruit flies.

Field Trapping Bactrocera latifrons (Diptera: Tephritidae) with Select Eugenol Analogs That Have Been Found to Attract Other 'Non-Responsive' Fruit Fly Species

Bactrocera latifrons (Hendel) (Diptera: Tephritidae) is a pest fruit fly species native to Oriental Asia which has invaded and established in Hawaii and Tanzania and has been recovered in detection trapping in California. It is largely non-responsive to the male lures cuelure and methyl eugenol. Alpha-ionol + cade oil is a moderately effective male B. latifrons attractant, but is not as attractive as cuelure or methyl eugenol are to other fruit fly species. An improved attractant is therefore desired. With the recent success in finding other non-responsive fruit fly species attracted to isoeugenol, methyl-isoeugenol, or dihydroeugenol in Australia and other countries, we wanted to assess whether B. latifrons might also respond to these “eugenol analogs.” Working with wild B. latifrons populations in Hawaii, we assessed the relative catch of B. latifrons in traps baited with the eugenol analogs with catch in traps baited with alpha-ionol, alpha-ionol + cade oil, or alpha-ionol + eugenol. Catch was significantly higher in traps baited with alpha-ionol + cade oil relative to traps with any of the other baits. There was, though, some male B. latifrons catch in traps baited with dihydroeugenol or isoeugenol but none in traps baited with methyl-isoeugenol.

HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.

HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.

A global checklist of the 932 fruit fly species in the tribe Dacini (Diptera, Tephritidae)

The correct application of the scientific names of species is neither easy nor trivial. Mistakes can lead to the wrong interpretation of research results or, when pest species are involved, inappropriate regulations and limits on trade, and possibly quarantine failures that permit the invasion of new pest species. Names are particularly challenging to manage when groups of organisms encompass a large number of species, when different workers employ different philosophical views, or when species are in a state of taxonomic flux. The fruit fly tribe Dacini is a species-rich taxon within Tephritidae and contains around a fifth of all known species in the family. About 10% of the 932 currently recognized species are pests of commercial fruits and vegetables, precipitating quarantines and trade embargos. Authoritative species lists consist largely of scattered regional treatments and outdated online resources. The checklist presented here is the first global overview of valid species names for the Dacini in almost two decades, and includes new lure records. By publishing this list both in paper and digitally, we aim to provide a resource for those studying fruit flies as well as researchers studying components of their impact on agriculture. The list is largely a consolidation of previous works, but following the results from recent phylogenetic work, we transfer one subgenus and eight species to different genera: members of the Bactrocera subgenus Javadacus Hardy, considered to belong to the Zeugodacus group of subgenera, are transferred to genus Zeugodacus; Bactrocera pseudocucurbitae White, 1999, stat. rev., is transferred back to Bactrocera from Zeugodacus; Zeugodacus arisanicus Shiraki, 1933, stat. rev., is transferred back to Zeugodacus from Bactrocera; and Z. brevipunctatus (David & Hancock, 2017), comb. n.; Z. javanensis (Perkins, 1938), comb. n.; Z. montanus (Hardy, 1983), comb. n.; Z. papuaensis (Malloch, 1939), comb. n.; Z. scutellarius (Bezzi, 1916), comb. n.; Z. semisurstyli (Drew & Romig, 2013), comb. n.; and Z. trilineatus (Hardy, 1955), comb. n. are transferred from Bactrocera to Zeugodacus.

Functional characterization of BdB1, a well-conserved carboxylesterase among tephritid fruit flies associated with malathion resistance in Bactrocera dorsalis (Hendel)

There are many evidences that insect carboxylesterase possess important physiological roles in xenobiotic metabolism and are implicated in the detoxification of organophosphate (OP) insecticides. Despite the ongoing resistance development in the oriental fruit fly, Bactrocera dorsalis (Hendel), the molecular basis of carboxylesterase and its ability to confer OP resistance remain largely obscure. This study was initiated to provide a better understanding of carboxylesterase-mediated resistance mechanism in a tephritid pest fly. Here, we narrow this research gap by demonstrating a well-conserved esterase B1 gene, BdB1, mediates malathion resistance development via gene upregulation with the use of a laboratory selected malathion-resistant strain (MR) of B. dorsalis. No sequence mutation of BdB1 was detected between MR and the susceptible strain (MS) of B. dorsalis. BdB1 is predominantly expressed in the midgut, a key insect tissue for detoxification. As compared with transcripts in MS, BdB1 was significantly more abundant in multiple tissues in the MR. RNA interference (RNAi)-mediated knockdown of BdB1 significantly increased malathion susceptibility. Furthermore, heterologous expression along with cytotoxicity assay revealed BdB1 could probably have the function of malathion detoxification.