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Two fruit fly (Diptera: Tephritidae) species of economic importance: Ceratitis rosa Karsch and Ceratitis quilicii De Meyer, Mwatawala & Virgilio are present in South Africa. The two species were considered as one species prior to 2016, but were subsequently separated. In this study, the distribution and abundance of the two species were quantified in seven provinces in South Africa through trapping with Enriched Ginger Oil as an attractant. Trapping was conducted over three seasons across two years (2020 and 2021): late summer, autumn-winter, and spring-early summer. Host ranges of the two species were investigated by fruit sampling in and outside of trapping sites. Ceratitis quilicii was more widely distributed than C. rosa with the latter being recorded in only three north-eastern provinces. There were geographical limits for both species with no records of them in Northern Cape Province. Catches of C. quilicii were higher in summer with average temperatures varying from 15 to 27°C while for C. rosa , catches remained low and consistent between seasons. Ceratitis quilicii catches decreased at lower rates than those of C. rosa at temperatures below 15°C. The two species were reared from 13 plant species from nine families. Four of these hosts were infested by both C. quilicii and C. rosa in the same province where they occurred. Preferred hosts of the two species belonged to the Myrtaceae family. The characterisation of the distribution, abundance and host ranges of these pests will provide a baseline for pest status determination and implementation of management actions. [ABSTRACT FROM AUTHOR]

The hoverfly genus Eristalinus (Diptera, Syrphidae) contains many widespread pollinators. The majority of the species of Eristalinus occur in the Afrotropics and their molecular systematics still needs to be investigated. This study presents the first complete and annotated mitochondrial genomes for five species of Eristalinus. They were obtained by high-throughput sequencing of total genomic DNA. The total length of the mitogenomes varied between 15 757 and 16 245 base pairs. Gene composition, positions, and orientation were shared across species, and were identical to those observed for other Diptera. Phylogenetic analyses (maximum likelihood and Bayesian inference) based on the 13 protein coding and both rRNA genes suggested that the subgenus Eristalinus was paraphyletic with respect to the subgenus Eristalodes. An analysis of the phylogenetic informativeness of all protein coding and rRNA genes suggested that NADH dehydrogenase subunit 5 (nad5), cytochrome c oxidase subunit 1, nad4, nad2, cytochrome b, and 16S rRNA genes are the most promising mitochondrial molecular markers to result in supported phylogenetic hypotheses of the genus. In addition to the five complete mitogenomes currently available for hoverflies, the five mitogenomes published here will be useful for broader molecular phylogenetic analyses among hoverflies. Keywords: mitogenome, phylogeny, phylogenetic informativeness, flower fly. Les syrphes appartenant au genre Eristalinus (Diptera, Syrphidae) comptent plusieurs pollinisateurs repandus. La majorite des especes d'Eristalinus sont retrouvees dans l'ecozone afrotropicale et leur systematique moleculaire n'a pas ete etudiee. Cette etude presente les premiers genomes mitochondriaux complets et annotes pour cinq especes d'Eristalinus. Ils ont ete obtenus par sequencage a haut debit d'ADN genomique total. La longueur totale des mitogenomes variait entre 15 757 et 16 245 pb. Les catalogues de genes, leurs positions et orientation etaient identiques chez ces especes et identiques a ce qui a ete observe chez d'autres dipteres. Des analyses phylogenetiques (vraisemblance maximale et inference bayesienne) fondees sur 13 genes codant pour des proteines et les deux genes d'ARNr suggerent que le sous-genre Eristalinus est paraphyletique par rapport au sous-genre Eristalodes. Une analyse de la valeur informative phylogenetique de tous les genes codant pour des proteines ou des ARNr suggere que les genes codant pour la sous-unite 5 de la NADH deshydrogenase (nad5), la sous-unite 1 de la cytochrome c oxydase, nad4, nad2, le cytochrome b et les ARNr 16S seraient les marqueurs moleculaires mitochondriaux les plus prometteurs pour obtenir des hypotheses phylogenetiques supportees pour ce genre. Avec les cinq mitogenomes complets deja disponibles pour les syrphes, les cinq mitogenomes rapportes ici seront utiles pour des analyses phylogenetiques moleculaires plus larges au sein des syrphes. [Traduit par la Redaction] Mots-cles : mitogenome, phylogenie, valeur informative en phylogenie, mouche de fleurs., Introduction Four subfamilies are recognized in the family Syrphidae (Insecta: Diptera), also known as hoverflies or flower flies: Microdontinae, Syrphinae, Eristalinae, and Pipizinae (Mengual et al. 2015; Young et al. [...]

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. [ABSTRACT FROM AUTHOR]

Tephritidae is one of the largest families of Diptera, with high diversity and a wide global distribution, and includes numerous important agricultural pests. However, the origin, phylogeny, and evolutionary 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. Within the Dacini subfamily, our phylogeny strongly supported the sister group relationship of (Zeugodacus + Dacus) + Bactrocera, which further supported to the elevation of Zeugodacus to the 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 (formerly FAR complex) nor those within the Bactrocera dorsalis complex could be clearly distinguished by mitochondrial phylogenetic trees as distinct species corresponding to the morphospecies. Divergence time estimation and historical biogeography analyses indicated that the earliest common ancestor of Tephritidae, originated in the Palaearctic realm at 138.92-71.44 Ma (million years ago), with the subsequent divergence into Dacinae + Trypetinae and Tephritinae at 115.19-67.45 Ma equally in the Palaearctic realm. Dacini might have originated in Laurasia rather than Gondwana, and diverged into Bactrocera and Dacus + Zeugodacus at 48.43-28.70 Ma after the India plate docked with Laurasia. [ABSTRACT FROM AUTHOR]