The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes.

Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes.

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

The Afrotropical representatives of the hover fly genus Rondani, 1857 (Diptera) are divided into two subgenera, namely s.s. and Séguy, 1951 and, in this present work, the subgenus Mesembrius s.

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

The representatives of the Afrotropical hover fly genus Macquart (Diptera) are revised. In total, ten species are recognized. (Bezzi) is herewith placed as junior synonym of Macquart, (Bezzi) is herewith placed as junior synonym of (Macquart) and (Bezzi) is herewith placed as junior synonym of (Gerstaecker).

Taxonomic revision of the Afrotropical Phytomia Guérin-Méneville (Diptera: Syrphidae).

The Afrotropical representatives of the hoverfly genus Phytomia Guérin-Méneville (Diptera) are revised. In total, 19 species are recognized of which three are new to science: Phytomia austeni sp. nov.

Ethiopian muscids (Diptera, Muscidae) egg-carriers of Stylogaster Macquart (Diptera, Conopidae).

We here report for the first time on the presence of three species of the conopid genus Stylogaster Macquart (Diptera, Conopidae) in Ethiopia, viz. S. nitens Brunetti, S.

First mitochondrial genomes of five hoverfly species of the genus s (Diptera: Syrphidae).

The hoverfly genus (Diptera, Syrphidae) contains many widespread pollinators. The majority of the species of 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 .

Mycobacterium ulcerans Population Genomics To Inform on the Spread of Buruli Ulcer across Central Africa.

Buruli ulcer is a neglected tropical disease of skin and subcutaneous tissue caused by infection with the pathogen Many critical issues for disease control, such as understanding the mode of transmission and identifying source reservoirs of , are still largely unknown. Here, we used genomics to reconstruct in detail the evolutionary trajectory and dynamics of populations at a central African scale and at smaller geographical village scales. Whole-genome sequencing (WGS) data were analyzed from 179 strains isolated from all Buruli ulcer foci in the Democratic Republic of the Congo, The Republic of Congo, and Angola that have ever yielded positive cultures.

DNA barcoding fishes from the Congo and the Lower Guinean provinces: Assembling a reference library for poorly inventoried fauna.

The Congolese and Lower Guinean ichthyological provinces are understudied hotspots of the global fish diversity. Here, we barcoded 741 specimens from the Lower and Middle Congo River and from three major drainage basins of the Lower Guinean ichthyological province, Kouilou-Niari, Nyanga and Ogowe. We identified 194 morphospecies belonging to 82 genera and 25 families.

Multiple Introductions and Recent Spread of the Emerging Human Pathogen Mycobacterium ulcerans across Africa.

Buruli ulcer (BU) is an insidious neglected tropical disease. Cases are reported around the world but the rural regions of West and Central Africa are most affected. How BU is transmitted and spreads has remained a mystery, even though the causative agent, Mycobacterium ulcerans, has been known for more than 70 years.

Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle (Mollusca: Gastropoda).

We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cyt gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago.

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae).

Background: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies.

Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika.

We obtained 398 cytochrome c oxidase subunit I barcodes of 96 morphospecies of Lake Tanganyika (LT) cichlids from the littoral zone. The potential of DNA barcoding in these fishes was tested using both species identification and species delineation methods. The best match (BM) and best close match (BCM) methods were used to evaluate the overall identification success.

An integrative approach to unravel the Ceratitis FAR (Diptera, Tephritidae) cryptic species complex: a review.

This paper reviews all information gathered from different disciplines and studies to resolve the species status within the Ceratitis FAR (Ceratitis fasciventris, Ceratitis anonae, Ceratitis rosa) complex, a group of polyphagous fruit fly pest species (Diptera, Tephritidae) from Africa. It includes information on larval and adult morphology, wing morphometrics, cuticular hydrocarbons, pheromones, microsatellites, developmental physiology and geographic distribution. The general consensus is that the FAR complex comprises Ceratitis anonae, two species within Ceratitis rosa (so-called R1 and R2) and two putatitve species under Ceratitis fasciventris.

A second New World hoverfly, Toxomerus floralis (Fabricius) (Diptera: Syrphidae), recorded from the Old World, with description of larval pollen-feeding ecology.

Recently (2013-2014), several hoverfly specimens from two localities in Benin and Cameroon (West and Central Africa) were caught from a species that we could not identify using existing identification keys for Afrotropical Syrphidae. Specific identification as Toxomerus floralis (Fabricius) was accomplished using morphology and various Neotropical identification keys. Corroboration of this identification was made by sequencing of the standard COI barcode region and a subsequent BLAST-IDS in BOLD that revealed a 100% sequence similarity with Toxomerus floralis from Suriname (South America).

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

The identification of Afrotropical hoverflies is very difficult because of limited recent taxonomic revisions and the lack of comprehensive identification keys. In order to assist in their identification, and to improve the taxonomy of this group, we constructed a reference dataset of 513 COI barcodes of 90 of the more common nominal species from Ghana, Togo, Benin and Nigeria (W Africa) and added ten publically available COI barcodes from nine nominal Afrotropical species to this (total: 523 COI barcodes; 98 nominal species; 26 genera). The identification accuracy of this dataset was evaluated with three methods (K2P distance-based, Neighbor-Joining (NJ) / Maximum Likelihood (ML) analysis, and using SpeciesIdentifier).

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

The phylogenetic relationships within and among subtribes of the fruit fly tribe Dacini (Ceratitidina, Dacina, Gastrozonina) were investigated by sequencing four mitochondrial and one nuclear gene fragment. Bayesian, maximum likelihood and maximum parsimony analyses were implemented on two datasets. The first, aiming at obtaining the strongest phylogenetic signal (yet, having lower taxon coverage), consisted of 98 vouchers and 2338 concatenated base pairs (bp).

Predominance of a single phylogenetic species in colonization events among a sextet of decollate land snail, Rumina decollata (Mollusca: Pulmonata: Subulinidae), species.

The hermaphroditic, facultatively selfing, land snail Rumina decollata is a common, widespread species that is indigenous to the Mediterranean region and that has been introduced to many other regions of the world. However, recent DNA sequence analyses have indicated that R. decollata is a complex of several phylogenetic species, two of which correspond to previously distinguished allozyme strains with different body colors (light vs.

Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification.

Identification by DNA barcoding is more likely to be erroneous when it is based on a large distance between the query (the barcode sequence of the specimen to identify) and its best match in a reference barcode library. The number of such false positive identifications can be decreased by setting a distance threshold above which identification has to be rejected. To this end, we proposed recently to use an ad hoc distance threshold producing identifications with an estimated relative error probability that can be fixed by the user (e.

Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France.

Fly larvae living on dead corpses can be used to estimate post-mortem intervals. The identification of these flies is decisive in forensic casework and can be facilitated by using DNA barcodes provided that a representative and comprehensive reference library of DNA barcodes is available. We constructed a local (Belgium and France) reference library of 85 sequences of the COI DNA barcode fragment (mitochondrial cytochrome c oxidase subunit I gene), from 16 fly species of forensic interest (Calliphoridae, Muscidae, Fanniidae).

DNA barcoding and the differentiation between North American and West European Phormia regina (Diptera, Calliphoridae, Chrysomyinae).

Phormia regina (the black fly) is a common Holarctic blow fly species which serves as a primary indicator taxon to estimate minimal post mortem intervals. It is also a major research model in physiological and neurological studies on insect feeding. Previous studies have shown a sequence divergence of up to 4.

DNA barcodes and phylogenetic affinities of the terrestrial slugs Arion gilvus and A. ponsi (Gastropoda, Pulmonata, Arionidae).

The Iberian Peninsula is a region with a high endemicity of species of the terrestrial slug subgenus Mesarion. Many of these species have been described mainly on subtle differences in their proximal genitalia. It therefore remains to be investigated 1) whether these locally diverged taxa also represent different species under a phylogenetic species concept as has been shown for other Mesarion species outside the Iberian Peninsula, and 2) how these taxa are phylogenetically related.

Insertion sequence element single nucleotide polymorphism typing provides insights into the population structure and evolution of Mycobacterium ulcerans across Africa.

Buruli ulcer is an indolent, slowly progressing necrotizing disease of the skin caused by infection with Mycobacterium ulcerans. In the present study, we applied a redesigned technique to a vast panel of M. ulcerans disease isolates and clinical samples originating from multiple African disease foci in order to (i) gain fundamental insights into the population structure and evolutionary history of the pathogen and (ii) disentangle the phylogeographic relationships within the genetically conserved cluster of African M.