Horticulture is one of the most important agricultural subsectors in Africa, providing income, creating employment opportunities, and enhancing food and nutritional security. However, tephritid fruit flies are responsible for both direct and indirect losses, with alien invasive species often having the most severe ecological and economic impact. In the past 20 years, systematic analysis of tephritids has provided comparative information on taxonomy, synonymy, and character-state differentiation. New molecular techniques are now available for identifying species, reconstructing phylogenies, and studying population genetic structures. Research on biology, host range and shifts, thermotolerance, and demography has provided useful information for developing predictive and ecological niche models to guide management methods. In recent years, the responses of various species to attractants have been documented. Several suppression methods, including the release of coevolved parasitoid species targeting invasives, have been promoted within the context of integrated pest management, leading to improvement in the quality and quantity of fruits and vegetables produced. However, there is still the need for wide-scale availability of these technologies to smallholder growers across Africa.

Taxonomy, ecology, and management of native and exotic fruit fly species in Africa.

Higher phylogeny of frugivorous flies (Diptera, Tephritidae, Dacini): Localised partition conflicts and a novel generic classification

This paper reviews all available information regarding the occurrence and biology of the melon fly, Zeugodacus cucurbitae (Coquillett), in the Afrotropical Region, including data on invasion history, distribution patterns, population genetics, host range, and interspecific competition. Although limited intraspecific variability has been observed within the region regarding the above mentioned aspects, there seems to be no indication that Zeugodacus cucurbitae represents a species complex. A checklist of all of the species included in Zeugodacus as recently proposed by Virgilio et al. (2015) is provided.

/pdf/a-review-of-the-current-knowledge-on-zeugodacus-cucurbitae-4e47hkvzzw.pdf

A review of the current knowledge on Zeugodacus cucurbitae (Coquillett) (Diptera, Tephritidae) in Africa, with a list of species included in Zeugodacus

We propose a general working strategy to deal with incomplete reference libraries in the DNA barcoding identification of species. Considering that (1) queries with a large genetic distance with their best DNA barcode match are more likely to be misidentified and (2) imposing a distance threshold profitably reduces identification errors, we modelled relationships between identification performances and distance thresholds in four DNA barcode libraries of Diptera (n = 4270), Lepidoptera (n = 7577), Hymenoptera (n = 2067) and Tephritidae (n = 602 DNA barcodes). In all cases, more restrictive distance thresholds produced a gradual increase in the proportion of true negatives, a gradual decrease of false positives and more abrupt variations in the proportions of true positives and false negatives. More restrictive distance thresholds improved precision, yet negatively affected accuracy due to the higher proportions of queries discarded (viz. having a distance query-best match above the threshold). Using a simple linear regression we calculated an ad hoc distance threshold for the tephritid library producing an estimated relative identification error <0.05. According to the expectations, when we used this threshold for the identification of 188 independently collected tephritids, less than 5% of queries with a distance query-best match below the threshold were misidentified. Ad hoc thresholds can be calculated for each particular reference library of DNA barcodes and should be used as cut-off mark defining whether we can proceed identifying the query with a known estimated error probability (e.g. 5%) or whether we should discard the query and consider alternative/complementary identification methods.

/pdf/identifying-insects-with-incomplete-dna-barcode-libraries-h5va7qrsg6.pdf

Identifying insects with incomplete DNA barcode libraries, African fruit flies (Diptera: Tephritidae) as a test case.

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures.

/pdf/evaluating-phylogenetic-congruence-in-the-post-genomic-era-2yge4pfkzq.pdf

Evaluating Phylogenetic Congruence in the Post-Genomic Era

African Dacus (Diptera: Tephritidae: molecular data and host plant associations do not corroborate morphology based classifications.

This paper summarizes current knowledge of the occurrence of Dacini fruit flies in the Comoro archipelago of the Indian Ocean. Ten species are confirmed as occurring there: Bactrocera invadens Drew, Tsuruta & White, 2005, Dacus bivittatus (Bigot, 1858), D. ciliatus Loew, 1862, D. etiennellus Munro, 1984, D. punctatifrons Karsch, 1887, D. vertebratus Bezzi, 1908 (all Dacina), Ceratitis capitata (Wiedemann, 1824), C. malgassa Munro, 1939, Neoceratitis cyanescens (Bezzi, 1923), and Trirhithrum nigerrimum (Bezzi, 1913) (all Ceratitidina). Records of Bactrocera Cucurbitae (Coquillett, 1899) remain unconfirmed. The fauna of the Comoros is briefly compared to that of other islands in the western Indian Ocean.

https://bioone.org/journals/african-invertebrates/volume-53/issue-1/afin.053.0104/Records-of-Frugivorous-Fruit-Flies-Diptera--Tephritidae--Dacini/10.5733/afin.053.0104.pdf

Records of Frugivorous Fruit Flies (Diptera: Tephritidae: Dacini) from the Comoro Archipelago

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African Dacus (Diptera: Tephritidae: molecular data and host plant associations do not corroborate morphology based classifications.

Records of Frugivorous Fruit Flies (Diptera: Tephritidae: Dacini) from the Comoro Archipelago