DNA Barcoding to Improve the Taxonomy of the Afrotropical Hoverflies (Insecta: Diptera: Syrphidae)

Local-Scale DNA Barcoding of Afrotropical Hoverflies (Diptera: Syrphidae): A Case Study of the Eastern Free State of South Africa

The Afrotropical hoverflies remain an understudied group of hoverflies. One of the reasons for the lack of studies on this group resides in the difficulties to delimit the species using the available identification keys. DNA barcoding has been found useful in such cases of taxonomical uncertainty. Here, we present a molecular study of hoverfly species from the eastern Free State of South Africa using the mitochondrial cytochrome-c oxidase subunit I gene (COI). The identification of 78 specimens was achieved through three analytical approaches: genetic distances analysis, species delimitation models and phylogenetic reconstructions. In this study, 15 nominal species from nine genera were recorded. Of these species, five had not been previously reported to occur in South Africa, namely, Betasyrphus inflaticornis Bezzi, 1915, Mesembrius strigilatus Bezzi, 1912, Eristalinus tabanoides Jaennicke, 1876, Eristalinus vicarians Bezzi, 1915 and Eristalinus fuscicornis Karsch, 1887. Intra- and interspecific variations were found and were congruent between neighbour-joining and maximum likelihood analyses, except for the genus Allograpta Osten Sacken, 1875, where identification seemed problematic, with a relatively high (1.56%) intraspecific LogDet distance observed in Allograpta nasuta Macquart, 1842. Within the 78 specimens analysed, the assembled species by automatic partitioning (ASAP) estimated the presence of 14-17 species, while the Poisson tree processes based on the MPTP and SPTP models estimated 15 and 16 species. The three models showed similar results (10 species) for the Eristalinae subfamily, while for the Syrphinae subfamily, 5 and 6 species were suggested through MPTP and SPTP, respectively. Our results highlight the necessity of using different species delimitation models in DNA barcoding for species diagnoses.

Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data

The Afrotropical representatives of the hover fly genus Mesembrius Rondani, 1857 (Diptera) are divided into two subgenera, namely Mesembrius s.s. and Vadonimyia Séguy, 1951 and, in this present work, the subgenus Mesembrius s.s. is revised. A total of 23 Mesembrius s.s. species are recognised for the Afrotropics. Known species are re-described and six species new to science are described: Mesembriusarcuatussp. nov., M.copelandisp. nov., M.longipilosussp. nov., M.sulcussp. nov., M.tibialissp. nov. and M.vockerothisp. nov. Mesembriusafricanus (Verrall, 1898) is considered a junior synonym of M.senegalensis (Macquart, 1842), M.ctenifer Hull, 1941 a junior synonym of M.caffer (Loew, 1858), M.lagopus (Loew, 1869) a junior synonym of M.capensis (Macquart, 1842) and M.platytarsis Curran, 1929 a junior synonym of M.simplicipes Curran, 1929. The females of Mesembriuschapini Curran, 1939, M.rex Curran, 1927 and M.regulus (Hull, 1937) are described for the first time. Lectotypes are designated for Mesembriuscaffer, M.capensis, M.cyanipennis (Bezzi, 1915), M.minor (Bezzi, 1915), M.senegalensis, M.strigilatus (Bezzi, 1912) and M.tarsatus (Bigot, 1883). Separate identification keys for males and females are presented. We obtained 236 DNA barcodes for 18 species. The relationships amongst the different Mesembrius species are briefly discussed, based on morphological and DNA barcode data.

Taxonomic revision of the Afrotropical hover fly genus Senaspis Macquart (Diptera, Syrphidae)

The representatives of the Afrotropical hover fly genus Senaspis Macquart (Diptera) are revised. In total, ten species are recognized. Senaspisapophysata (Bezzi) is herewith placed as junior synonym of S.flaviceps Macquart, S.livida (Bezzi) is herewith placed as junior synonym of S.dentipes (Macquart) and S.griseifacies (Bezzi) is herewith placed as junior synonym of S.haemorrhoa (Gerstaecker). All species are redescribed and an identification key is provided. DNA barcoding analysis (7 species, 64 barcodes) showed that the technique can be used to unambiguously identify the species. The relationships among the different Senaspis species are discussed based on morphological and DNA data.

A world review of reported myiases caused by flower flies (Diptera: Syrphidae), including the first case of human myiasis from Palpada scutellaris (Fabricius, 1805)

Rat-tailed larvae of the syrphid species Palpada scutellaris (Fabricius, 1805) are documented causing an enteric human myiasis in Costa Rica. This is the first time that the genus Palpada is recorded as a human myiasis agent. We report a 68-year-old woman with intestinal pain and bloody diarrhea with several live Palpada larvae present in the stool. Using molecular techniques (DNA barcodes) and both electronic and optical microscopy to study the external morphology, the preimaginal stages of the fly were unambiguously identified. An identification key to all syrphid genera actually known as agents of human and animal myiases is provided for larvae, puparia, and adults. Moreover, a critical world review of more than 100 references of Syrphidae as myiasis agents is also given, with emphasis on the species with rat-tailed larvae.

The complete mitochondrial genome of Melanostoma orientale (Diptera: Syrphidae)

The mitochondrial genome of Melanostoma orientale has been decoded by Illumina sequencing. The mitogenomic size is 16,229 bp with 40.96% A, 40.29% T, 10.60% C, and 8.15% G. It is encoded with 13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNAs. The phylogenetic tree showed that 10 species of Syrphidae, belonging to six genera, were clustered into two clades. This is the first mitochondrial genome for the genus Melanostoma.

Eristalinus arvorum (Fabricius, 1787) (Diptera: Syrphidae) in Human Skull: A New Fly Species of Forensic Importance

A body of an unknown adult female was found within a shallow burial ground in Malaysia whereas the skull was exposed and visible on the ground. During autopsy examination, nine insect larvae were recovered from the interior of the human skull and subsequently preserved in 70% ethanol. The larvae were greyish in appearance, each with a posterior elongated breathing tube. A week after the autopsy, more larvae were collected at the burial site, and some of them were reared into adults. Adult specimens and larvae from the skull and from the burial site were sequenced to obtain DNA barcodes. Results showed all adult flies reared from the burial site, as well as the larvae collected from the skull were identified as Eristalinus arvorum (Fabricius, 1787) (Diptera: Syrphidae). Here, we report the colonization of E. arvorum larvae on a human corpse for the first time.

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring

This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.

Close relatives of Mediterranean endemo-relict hoverflies (Diptera, Syrphidae) in South Africa: Morphological and molecular evidence in the Merodon melanocerus subgroup

An ongoing study of the genus Merodon Meigen, 1803 in the Republic of South Africa (RSA) has revealed the existence of new species related to M. melanocerus Bezzi, 1915. The M. melanocerus subgroup belongs to the Afrotropical lineage of the M. desuturinus group. Revision of all available material from museums and detailed analyses of newly -collected specimens from our own expeditions to RSA resulted in delimitation of five species: M. capensis Hurkmans sp. n., M. commutabilis Radenković et Vujić sp. n., M. drakonis Vujić et Radenković sp. n., M. flavocerus Hurkmans sp. n. and M. melanocerus. In addition to classical morphological characters, sequences of the mitochondrial COI gene are provided for four related taxa. Results of molecular phylogenetic analyses supports monophyly of the M. desuturinus group and confirmed delimitation between species. Links between Palaearctic and Afrotropical faunas of this group, as well as possible evolutionary paths, are discussed. Based on phylogenetic analyses, four lineages (putative subgenera) have been recognized within the genus Merodon; besides the three previously established ones, albifrons+desuturinus, aureus (sensu lato) and avidus-nigritarsis, one new lineage named natans is distinguished.

Taxonomy and Identification of the Genus Scolopendra in China Using Integrated Methods of External Morphology and Molecular Phylogenetics

The centipede Scolopendra has important medicinal value and high toxicity, making it to be an interesting subject for evolutionary studies. However, species identification in China is difficult because of limited resource exploration and lack of recent taxonomic revision. To improve the identification and taxonomy of the genus Scolopendra in China, an in-depth investigation was conducted, and an integrated method that combined morphological characteristics with molecular data was applied. The identification key was revised to show the main difference among species. Our results indicated that morphologically-delimited species were consistent with the molecular analysis inferred from the COI sequences with genetic distances and phylogenetic trees. Additional morphometrics of four characteristics provided criteria for shape variation. These results suggested that the members of the genus Scolopendra in China could be delineated as 14 separate species. A new species from Lufeng county, Yunnan province, was proposed according to its characteristics, which was named as S. lufengia sp. nov. Our results comprehensively ascertained the taxonomic status of Scolopendra species in China, explored their phylogenetic relationships, showed a high success in the identification of medicinal centipedes.

Molecular species delimitation in the genus Eumerus (Diptera: Syrphidae)

Eumerus is one of the most diverse genera of hoverfly worldwide. Species delimitation within genus is considered to be difficult due to: (a) lack of an efficient key; (b) non-defined taxonomical status of a large number of species; and (c) blurred nomenclature. Here, we present the first molecular study to delimit species of the genus by using a fragment of the mitochondrial cytochrome-c oxidase subunit I gene (COI) gene. We assessed 75 specimens assigned to 28 taxa originating from two biogeographic zones: 22 from the western Palaearctic and six from the Afrotropical region. Two datasets were generated based on different sequence lengths to explore the significance of availability of more polymorphic sites for species delimitation; dataset A with a total length of 647 bp and dataset B with 746 bp. Various tree inference approaches and Poisson tree processes models were applied to evaluate the putative 'taxonomical' vs. 'molecular' taxa clusters. All analyses resulted in high taxonomic resolution and clear species delimitation for both the dataset lengths. Furthermore, we revealed a high number of mitochondrial haplotypes and high intraspecific variability. We report two major monophyletic clades, and seven 'molecular' groups of taxa formed, which are congruent with morphology-based taxonomy. Our results support the use of the mitochondrial COI gene in species diagnosis of Eumerus.