@article {6526, title = {A checklist of the dacine fruit flies (Diptera, Tephritidae, Dacinae) of Mozambique}, journal = {African Entomology}, volume = {31}, year = {2023}, month = {Aug-08-2023}, pages = {e15585}, abstract = {

Here we present a checklist of all records of dacine fruit flies (Diptera: Tephritidae: Dacinae) from Mozambique, based on verified specimen records in natural history collections and literature records. In total, 57 Dacinae species are recorded from Mozambique, of which only one is considered endemic. This relatively low species diversity compared to other African countries appears to be related to incomplete sampling. For each species the localities from which it was recorded are given (including geocoordinates), or a general distribution is provided. The checklist is discussed briefly in terms of species richness, endemism and geographic distribution.

}, issn = {2224-8854, 1021-3589}, doi = {10.17159/2254-8854/2023/a15585}, url = {http://dx.doi.org/10.17159/2254-8854/2023/a15585}, author = {De Meyer, Marc and Bota, Luis and Daniel, Beatriz and Mussumbi, Mirene and Vandenbosch, Myriam and Canhanga, Laura and Cambula, Elias and Mansell, Mervyn and Cugala, Domingos and Virgilio, Massimiliano} } @unpublished {6524, title = {Mitochondrial phylogenomics reveal the evolutionary, speciation and biogeographical history of fruit flies (Diptera: Tephritidae) UNDER REVIEW}, year = {2024}, abstract = {

Fruit flies (Diptera: Tephritidae) possess high diversity and globally wide distribution, including a range of important agricultural pests. However, the origin, phylogeny and divergence history remain poorly understood. We undertook the first comprehensive mitogenomic study covering phylogenetic reconstruction, divergence time estimation and historical biogeography analyses by analyzing 147 mitochondrial genomes representing three subfamilies, seven tribes, 11 genera and 82 species. The results recovered all the three subfamilies, seven tribes and 11 genera as monophyletic group. Within Dacini subfamily, our phylogeny strongly supported the sister group relationship of (Zeugodacus + Dacus) + Bactrocera, which further supported to raise Zeugodacus as generic level of Dacini. On the other hand, our molecular phylogenetic analyses did not align well with the currently recognized subgeneric designations within Ceratitis, Dacus and Zeugodacus. Some subgenera were recovered as polyphyletic or paraphyletic, implying the incongruence between morphological characters and mitogenomic data. Neither the taxa within the Ceratitis FARQ complex nor those within the Bactrocera dorsalis complex could be clearly distinguished as distinct species corresponding to the morphospecies by mitochondrial phylogenetic tree. Divergence time estimation and historical biogeography analyses indicated that the earliest common ancestor of the Tephritidae, originated in the Palearctic realm at 138.92-71.44 Ma, with the subsequent divergence into Dacinae + Trypetinae and Tephritinae at 115.19-67.45 Ma equally in the Palearctic realm. Dacini might have originated in Laurasia rather than Gondwana and diverged into Bactrocera and Dacus + Zeugodacus at 48.43-28.70 Ma after India plate docked with Laurasia.

}, doi = {10.22541/au.170669169.95739579/v1}, url = {http://dx.doi.org/10.22541/au.170669169.95739579/v1}, author = {Zhang, Yue and Li, Hu and Feng, Shiqian and Qin, Yujia and Meyer, Marc De and Virgilio, Massimiliano and Singh, Sandeep and Jiang, Fan and Priscilla, Kawi Anastasia and Susanto, Agus and Martinez-Sa{\~n}udo, Isabel and Wu, Jiajiao and BADJI, Kemo and Fekrat, Lida and Davaasambuu, Undarmaa and Li, ZHIHONG} } @article {6522, title = {Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections}, journal = {Biodiversity Data Journal}, volume = {11}, year = {2023}, month = {Oct-27-2023}, pages = {e102317}, abstract = {

Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.

}, issn = {1314-2828, 1314-2836}, doi = {10.3897/bdj.11.e102317}, url = {http://dx.doi.org/10.3897/bdj.11.e102317}, author = {Ferrari, Giada and Esselens, Lore and Hart, Michelle and Janssens, Steven and Kidner, Catherine and Mascarello, Maurizio and Pe{\~n}alba, Joshua and Pezzini, Fl{\'a}via and von Rintelen, Thomas and Sonet, Gontran and Vangestel, Carl and Virgilio, Massimiliano and Hollingsworth, Peter} } @article {6516, title = {Eating eggplants as a cucurbit feeder: Dietary shifts affect the gut microbiome of the melon fly Zeugodacus cucurbitae (Diptera, Tephritidae)}, volume = {11}, year = {2022}, month = {Aug-01-2022}, issn = {2045-8827, 2045-8827}, doi = {10.1002/mbo3.1307}, url = {http://dx.doi.org/10.1002/mbo3.1307}, author = {Hendrycks, Wouter and Delatte, H{\'e}l{\`e}ne and Moquet, Laura and Bourtzis, Kostas and Mullens, Nele and De Meyer, Marc and Backeljau, Thierry and Virgilio, Massimiliano} } @article {6509, title = {Large-scale and small-scale population genetic structure of the medically important gastropod species Bulinus truncatus (Gastropoda, Heterobranchia)}, volume = {15}, year = {2022}, month = {Sep-19-2022}, abstract = {

Abstract Background Gastropod snails remain strongly understudied, despite their important role in transmitting parasitic diseases. Knowledge of their distribution and population dynamics increases our understanding of the processes driving disease transmission. We report the first study to use high-throughput sequencing (HTS) to elucidate the population genetic structure of the hermaphroditic snail Bulinus truncatus (Gastropoda, Heterobranchia) on a regional (17\–150\ km) and inter-regional (1000\–5400\ km) scale. This snail species acts as an intermediate host of Schistosoma haematobium and Schistosoma bovis, which cause human and animal schistosomiasis respectively. Methods Bulinus truncatus snails were collected in Senegal, Cameroon, Egypt and France and identified through DNA barcoding. A single-end genotyping-by-sequencing (GBS) library, comprising 87 snail specimens from the respective countries, was built and sequenced on an Illumina HiSeq 2000 platform. Reads were mapped against S. bovis and S. haematobium reference genomes to identify schistosome infections, and single nucleotide polymorphisms (SNPs) were scored using the Stacks pipeline. These SNPs were used to estimate genetic diversity, assess population structure and construct phylogenetic trees of B. truncatus. Results A total of 10,750 SNPs were scored and used in downstream analyses. The phylogenetic analysis identified five clades, each consisting of snails from a single country but with two distinct clades within Senegal. Genetic diversity was low in all populations, reflecting high selfing rates, but varied between locations due to habitat variability. Significant genetic differentiation and isolation by distance patterns were observed at both spatial scales, indicating that gene flow is not strong enough to counteract the effects of population bottlenecks, high selfing rates and genetic drift. Remarkably, the population genetic differentiation on a regional scale (i.e. within Senegal) was as large as that between populations on an inter-regional scale. The blind GBS technique was able to pick up parasite DNA in snail tissue, demonstrating the potential of HTS techniques to further elucidate the role of snail species in parasite transmission. Conclusions HTS techniques offer a valuable toolbox to further investigate the population genetic patterns of intermediate schistosome host snails and the role of snail species in parasite transmission. Graphical Abstract

}, issn = {1756-3305}, doi = {10.1186/s13071-022-05445-x}, url = {http://dx.doi.org/10.1186/s13071-022-05445-x}, author = {Maes, Tim and De Corte, Zo{\"e} and Vangestel, Carl and Virgilio, Massimiliano and Smitz, Nathalie and Djuikwo-Teukeng, F{\'e}licit{\'e} F. and Papadaki, Maria Ioanna and Huyse, Tine} } @article {6497, title = {Systematics of Afrotropical Eristalinae (Diptera: Syrphidae) using mitochondrial phylogenomics}, journal = {Systematic Entomology}, volume = {47}, year = {2022}, month = {Jan-11-2022}, pages = {315 {\textendash} 328}, issn = {0307-6970, 1365-3113}, doi = {10.1111/syen.12532}, url = {http://dx.doi.org/10.1111/syen.12532}, author = {Mullens, Nele and Sonet, Gontran and Virgilio, Massimiliano and Goergen, Georg and Janssens, Steven B. and De Meyer, Marc and Jordaens, Kurt} } @article {6486, title = {Comparative Microbiomics of Tephritid Frugivorous Pests (Diptera: Tephritidae) From the Field: A Tale of High Variability Across and Within Species}, journal = {Frontiers in Microbiology}, volume = {11}, year = {2020}, month = {Nov-08-2020}, doi = {10.3389/fmicb.2020.01890}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.01890/full}, author = {De Cock, Maarten and Virgilio, Massimiliano and Vandamme, Peter and Bourtzis, Kostas and De Meyer, Marc and Willems, Anne} } @article {6485, title = {Mitogenomic characterization and systematic placement of the Congo blind barb Caecobarbus geertsii (Cypriniformes: Cyprinidae)}, journal = {International Journal of Biological Macromolecules}, volume = {161}, year = {2020}, month = {Jan-10-2020}, pages = {292 - 298}, issn = {01418130}, doi = {10.1016/j.ijbiomac.2020.05.248}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0141813020334140}, author = {Mullens, Nele and Sonet, Gontran and Decru, Eva and Virgilio, Massimiliano and Snoeks, Jos and Vreven, Emmanuel} } @article {4700, title = {Impact of Sample Preservation and Manipulation on Insect Gut Microbiome Profiling. A Test Case With Fruit Flies (Diptera, Tephritidae)}, journal = {Frontiers in Microbiology}, volume = {10}, year = {2019}, month = {Jan-12-2020}, doi = {10.3389/fmicb.2019.02833}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2019.02833/}, author = {De Cock, Maarten and Virgilio, Massimiliano and Vandamme, Peter and Augustinos, Antonios and Bourtzis, Kostas and Willems, Anne and De Meyer, Marc} } @article {4697, title = {First mitochondrial genomes of five hoverfly species of the genus Eristalinus (Diptera: Syrphidae)}, journal = {Genome}, volume = {62}, year = {2019}, month = {Aug-07-2019}, pages = {677 - 687}, issn = {0831-2796}, doi = {10.1139/gen-2019-0009}, url = {http://www.nrcresearchpress.com/doi/10.1139/gen-2019-0009}, author = {Sonet, Gontran and De Smet, Yannick and Tang, Min and Virgilio, Massimiliano and Young, Andrew D. and Skevington, Jeffrey H. and Mengual, Ximo and Backeljau, Thierry and Liu, Shanlin and Zhou, Xin and De Meyer, Marc and Jordaens, Kurt} } @article {4689, title = {First genomic study on Lake Tanganyika sprat Stolothrissa tanganicae: a lack of population structure calls for integrated management of this important fisheries target species}, journal = {BMC Evolutionary Biology}, volume = {19}, year = {2019}, month = {Jan-12-2019}, pages = {6}, doi = {10.1186/s12862-018-1325-8}, url = {https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-018-1325-8}, author = {De Keyzer, Els L. R. and De Corte, Zo{\"e} and Van Steenberge, Maarten and Raeymaekers, Joost A. M. and Calboli, Federico C. F. and Kmentov{\'a}, Nikol and N{\textquoteright}Sibula Mulimbwa, Th{\'e}ophile and Virgilio, Massimiliano and Vangestel, Carl and Mulungula, Pascal Masilya and Volckaert, Filip A. M. and Vanhove, Maarten P. M.} } @article {4684, title = {Using next-generation sequencing to improve DNA barcoding: lessons from a small-scale study of wild bee species (Hymenoptera, Halictidae)}, journal = {Apidologie}, volume = {49}, year = {2018}, month = {Jul-08-2020}, pages = {671 {\textendash} 685}, issn = {0044-8435}, doi = {10.1007/s13592-018-0594-y}, url = {http://link.springer.com/10.1007/s13592-018-0594-y}, author = {Sonet, Gontran and Pauly, A and Nagy, Zolt{\'a}n T. and Virgilio, Massimiliano and Jordaens, Kurt and Van Houdt, Jeroen and Worms, Sebastian and De Meyer, Marc and Backeljau, Thierry} } @article {4668, title = {Tephritid Integrative Taxonomy: Where We Are Now, with a Focus on the Resolution of Three Tropical Fruit Fly Species Complexes}, journal = {Annual Review of Entomology}, volume = {62}, year = {2017}, month = {Jul-01-2019}, pages = {147 - 164}, issn = {0066-4170}, doi = {10.1146/annurev-ento-031616-035518}, url = {http://www.annualreviews.org/doi/10.1146/annurev-ento-031616-035518}, author = {Schutze, Mark K. and Virgilio, Massimiliano and Norrbom, Allen and Clarke, Anthony R.} } @article {4660, title = {Description of new Ceratitis species (Diptera: Tephritidae) from Africa, or how morphological and DNA data are complementary in discovering unknown species and matching sexes}, journal = {European Journal of Taxonomy}, year = {2016}, month = {Feb-09-2018}, doi = {10.5852/ejt.2016.233}, url = {http://www.europeanjournaloftaxonomy.eu/index.php/ejt/article/view/357}, author = {De Meyer, Marc and Mwatawala, Maulid and Copeland, Robert S. and Virgilio, Massimiliano} } @article {4632, title = {Taxonomy, Ecology, and Management of Native and Exotic Fruit Fly Species in Africa}, journal = {Annual Review of Entomology}, volume = {61}, year = {2015}, month = {Oct-09-2015}, issn = {0066-4170}, doi = {10.1146/annurev-ento-010715-023603}, url = {http://www.annualreviews.org/doi/10.1146/annurev-ento-010715-023603}, author = {Ekesi, Sunday and De Meyer, Marc and Mohamed, Samira A. and Virgilio, Massimiliano and Borgemeister, Christian} } @article {4630, title = {Preference of Zeugodacus cucurbitae (Coquillett) for three commercial fruit vegetable hosts in natural and semi natural conditions}, journal = {Fruits}, volume = {70}, year = {2015}, month = {Jan-11-2015}, pages = {333 - 339}, issn = {0248-1294}, doi = {10.1051/fruits/2015034}, url = {http://www.fruits-journal.org/10.1051/fruits/2015034}, author = {Mwatawala, Maulid and Kudra, Abdul and Mkiga, Abdullah and Godfrey, Editha and Jeremiah, Sigalla and Virgilio, Massimiliano and De Meyer, Marc} } @article {4629, title = {Population structure and cryptic genetic variation in the mango fruit fly, Ceratitis cosyra (Diptera, Tephritidae)}, journal = {ZooKeys}, volume = {540}, year = {2015}, month = {Feb-11-2017}, pages = {525 - 538}, issn = {1313-2989}, doi = {10.3897/zookeys.540.9618}, url = {http://zookeys.pensoft.net/articles.php?id=6221}, author = {Virgilio, Massimiliano and Delatte, H{\'e}l{\`e}ne and Nzogela, Yasinta Beda and Simiand, Christophe and Quilici, Serge and De Meyer, Marc and Mwatawala, Maulid} } @article {4627, title = {A review of the current knowledge on Zeugodacus cucurbitae (Coquillett) (Diptera, Tephritidae) in Africa, with a list of species included in Zeugodacus}, journal = {ZooKeys}, volume = {540}, year = {2015}, month = {Feb-11-2017}, pages = {539 - 557}, issn = {1313-2989}, doi = {10.3897/zookeys.540.9672}, url = {http://zookeys.pensoft.net/articles.php?id=6225}, author = {De Meyer, Marc and Delatte, H{\'e}l{\`e}ne and Mwatawala, Maulid and Quilici, Serge and Vayssieres, Jean-Fran{\c c}ois and Virgilio, Massimiliano} } @article {4625, title = {Wing morphometrics as a possible tool for the diagnosis of the Ceratitis fasciventris, C. anonae, C. rosa complex (Diptera, Tephritidae)}, journal = {ZooKeys}, volume = {540}, year = {2015}, month = {Feb-11-2017}, pages = {489 - 506}, issn = {1313-2989}, doi = {10.3897/zookeys.540.9724}, url = {http://zookeys.pensoft.net/articles.php?id=6226}, author = {Van Cann, Joannes and Virgilio, Massimiliano and Jordaens, Kurt and De Meyer, Marc} } @article {4623, title = {DNA barcoding to improve the taxonomy of the Afrotropical hoverflies (Insecta: Diptera: Syrphidae)}, journal = {PLOS ONE}, volume = {10}, year = {2015}, month = {Apr-10-2016}, pages = {e0140264}, doi = {10.1371/journal.pone.0140264}, url = {http://dx.plos.org/10.1371/journal.pone.0140264}, author = {Jordaens, Kurt and Goergen, Georg and Virgilio, Massimiliano and Backeljau, Thierry and Vokaer, Audrey and De Meyer, Marc}, editor = {Casiraghi, Maurizio} } @article {4603, title = {Higher phylogeny of frugivorous flies (Diptera, Tephritidae, Dacini): Localised partition conflicts and a novel generic classification}, journal = {Molecular Phylogenetics and Evolution}, year = {2015}, month = {Jan-02-2015}, issn = {10557903}, doi = {10.1016/j.ympev.2015.01.007}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1055790315000111http://api.elsevier.com/content/article/PII:S1055790315000111?httpAccept=text/xmlhttp://api.elsevier.com/content/article/PII:S1055790315000111?httpAccept=text/plain}, author = {Virgilio, Massimiliano and Jordaens, Kurt and Verwimp, Christophe and White, Ian M. and De Meyer, Marc} } @article {4599, title = {A set of multi-entry identification keys to African frugivorous flies (Diptera, Tephritidae)}, journal = {ZooKeys}, volume = {428}, year = {2014}, month = {Dec-07-2015}, pages = {97 - 108}, issn = {1313-2989}, doi = {10.3897/zookeys.428.7366}, url = {http://www.pensoft.net/journals/zookeys/article/7366/abstract/a-set-of-multi-entry-identification-keys-to-african-frugivorous-flies-diptera-tephritidae-}, author = {Virgilio, Massimiliano and White, Ian and De Meyer, Marc} } @article {4483, title = {Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification}, journal = {ZooKeys}, volume = {365}, year = {2013}, month = {Jun-12-2015}, pages = {329 - 336}, issn = {1313-2989}, doi = {10.3897/zookeys.365.6034}, url = {http://www.pensoft.net/journals/zookeys/article/6034/abstract/adhoc-an-r-package-to-calculate-ad-hoc-distance-thresholds-for-dna-barcoding-identification}, author = {Sonet, Gontran and Jordaens, Kurt and Nagy, Zoltan T and Breman, Floris and De Meyer, Marc and Backeljau, Thierry and Virgilio, Massimiliano} } @article {4458, title = {Macrogeographic population structuring in the cosmopolitan agricultural pest Bactrocera cucurbitae (Diptera: Tephritidae)}, journal = {Molecular Ecology}, volume = {19}, year = {2010}, month = {Jan-07-2010}, pages = {2713 - 2724}, doi = {10.1111/mec.2010.19.issue-1310.1111/j.1365-294X.2010.04662.x}, author = {Virgilio, Massimiliano and DELATTE, H. and Backeljau, Thierry and De Meyer, Marc} } @article {4423, title = {Isolation and characterisation of sixteen microsatellite markers cross-amplifying in a complex of three African agricultural pests (Ceratitis rosa, C. anonae and C. fasciventris, Diptera: Tephritidae)}, journal = {Conservation Genetics Resources}, volume = {5}, year = {2013}, month = {Jan-03-2013}, pages = {31 - 34}, issn = {1877-7252}, doi = {10.1007/s12686-012-9722-6}, author = {Delatte, H and Virgilio, Massimiliano and Simiand, C and Quilici, S and De Meyer, Marc} } @article {4407, title = {Discrepancies between subgeneric classification and molecular phylogeny of Ceratitis (Diptera: Tephritidae), can the evolution of host use provide some clues?}, journal = {Molecular Phylogenetics and Evolution}, volume = {60}, year = {2011}, month = {8/2011}, pages = {259 - 264}, issn = {10557903}, doi = {10.1016/j.ympev.2011.04.004}, author = {Erbout, Nathalie and Virgilio, Massimiliano and Lens, Luc and Barr, Norman and De Meyer, Marc} } @article {4386, title = {Comparative performances of DNA barcoding across insect orders}, journal = {BMC Bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {206}, issn = {1471-2105}, doi = {10.1186/1471-2105-11-206}, author = {Virgilio, Massimiliano and Backeljau, Thierry and Nevado, Bruno and De Meyer, Marc} } @article {4384, title = {Identifying Insects with Incomplete DNA Barcode Libraries, African Fruit Flies (Diptera: Tephritidae) as a Test Case}, journal = {PLoS ONE}, volume = {7}, year = {2012}, month = {2/2012}, pages = {e31581}, doi = {10.1371/journal.pone.0031581.t001}, author = {Virgilio, Massimiliano and Jordaens, Kurt and Breman, Floris C and Backeljau, Thierry and De Meyer, Marc} }