Molecular characterization and phylogenesis of Steganinae (Diptera, Drosophilidae) inferred by the mitochondrial cytochrome c oxidase subunit 1

Occurrence of Thelazia callipaeda and its vector Phortica variegata in Austria and South Tyrol, Italy, and a global comparison by phylogenetic network analysis

The zoonotic nematode Thelazia callipaeda infects the eyes of domestic and wild animals and uses canids as primary hosts. It was originally described in Asia, but in the last 20 years it has been reported in many European countries, where it is mainly transmitted by the drosophilid fruit fly Phortica variegata. We report the autochthonous occurrence of T. callipaeda and its vector P. variegata in Austria. Nematodes were collected from clinical cases and fruit flies were caught using traps, netting, and from the conjunctival sac of one dog. Fruit flies and nematodes were morphologically identified and a section of the mitochondrial cytochrome c oxidase subunit I gene (COI) was analysed. A DNA haplotype network was calculated to visualize the relation of the obtained COI sequences to published sequences. Additionally, Phortica spp. were screened for the presence of DNA of T. callipaeda by polymerase chain reaction. Thelazia callipaeda and P. variegata were identified in Burgenland, Lower Austria, and Styria. Thelazia callipaeda was also documented in Vienna and P. variegata in Upper Austria and South Tyrol, Italy. All T. callipaeda corresponded to haplotype 1. Twenty-two different haplotypes of P. variegata were identified in the fruit flies. One sequence was distinctly different from those of Phortica variegata and was more closely related to those of Phortica chi and Phortica okadai. Thelazia callipaeda could not be detected in any of the Phortica specimens.

Comparative Mitochondrial Genomes between the Genera Amiota and Phortica (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability

To address the limited number of mitochondrial genomes (mitogenomes) in the subfamily Steganinae (Diptera: Drosophilidae), we assembled 12 complete mitogenomes for six representative species in the genus Amiota and six representative species in the genus Phortica. We performed a series of comparative and phylogenetic analyses for these 12 Steganinae mitogenomes, paying special attention to the commonalities and differences in the D-loop sequences. Primarily determined by the lengths of the D-loop regions, the sizes of the Amiota and Phortica mitogenomes ranged from 16,143-16,803 bp and 15,933-16,290 bp, respectively. Our results indicated that the sizes of genes and intergenic nucleotides (IGNs), codon usage and amino acid usage, compositional skewness levels, evolutionary rates of protein-coding genes (PCGs), and D-loop sequence variability all showed unambiguous genus-specific characteristics and provided novel insights into the evolutionary implications between and within Amiota and Phortica. Most of the consensus motifs were found downstream of the D-loop regions, and some of them showed distinct genus-specific patterns. In addition, the D-loop sequences were phylogenetically informative as the data sets of PCGs and/or rRNAs, especially within the genus Phortica.

Development of Novel Management Tools for Phortica variegata (Diptera: Drosophilidae), Vector of the Oriental Eyeworm, Thelazia callipaeda (Spirurida: Thelaziidae), in Europe

Lachryphagous males of Phortica variegata (Fallén, 1823) are gaining increasing attention in Europe, as they act as vectors of the nematode Thelazia callipaeda Railliet & Henry, 1910, causal agent of thelaziosis, an emergent zoonotic disease. Currently, there are no effective control strategies against the vector, and surveillance and monitoring rely on time-consuming and nonselective sampling methods. Our aim was to improve the knowledge about the population dynamics and the chemical ecology of the species. A total of 5,726 P. variegata flies (96.4% males and 3.6% females, mostly gravid) were collected in field experiments during June-September of 2020 in an oak forest in northern Spain. Our results indicate that 1) by means of sweep netting a significantly higher number of captures were found both around the collector´s body and in the air than at ground level; 2) a positive relationship was detected between the abundance of Phortica flies and temperature, with two significant peaks of abundance at 24 and 33°C; 3) the blend of red wine and cider vinegar was the most attractive bait; 4) yellow traps captured fewer flies compared to black and transparent traps; and 5) a significant reduction toward vinegar and wine was detected in presence of the phenolic monoterpenoid carvacrol. In addition, all the males (n = 690) analyzed by both molecular detection and dissection resulted negative for the presence of T. callipaeda larvae. Overall, these findings provide a better understanding of the vector in terms of monitoring and management strategies.

DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.

A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly

BACKGROUND

The Drosophilidae family is traditionally divided into two subfamilies: Drosophilinae and Steganinae. This division is based on morphological characters, and the two subfamilies have been treated as monophyletic in most of the literature, but some molecular phylogenies have suggested Steganinae to be paraphyletic. To test the paraphyletic-Steganinae hypothesis, here, we used genomic sequences of eight Drosophilidae (three Steganinae and five Drosophilinae) and two Ephydridae (outgroup) species and inferred the phylogeny for the group based on a dataset of 1,028 orthologous genes present in all species (> 1,000,000 bp). This dataset includes three genera that broke the monophyly of the subfamilies in previous works. To investigate possible biases introduced by small sample sizes and automatic gene annotation, we used the same methods to infer species trees from a set of 10 manually annotated genes that are commonly used in phylogenetics.

RESULTS

Most of the 1,028 gene trees depicted Steganinae as paraphyletic with distinct topologies, but the most common topology depicted it as monophyletic (43.7% of the gene trees). Despite the high levels of gene tree heterogeneity observed, species tree inference in ASTRAL, in PhyloNet, and with the concatenation approach strongly supported the monophyly of both subfamilies for the 1,028-gene dataset. However, when using the concatenation approach to infer a species tree from the smaller set of 10 genes, we recovered Steganinae as a paraphyletic group. The pattern of gene tree heterogeneity was asymmetrical and thus could not be explained solely by incomplete lineage sorting (ILS).

CONCLUSIONS

Steganinae was clearly a monophyletic group in the dataset that we analyzed. In addition to ILS, gene tree discordance was possibly the result of introgression, suggesting complex branching processes during the early evolution of Drosophilidae with short speciation intervals and gene flow. Our study highlights the importance of genomic data in elucidating contentious phylogenetic relationships and suggests that phylogenetic inference for drosophilids based on small molecular datasets should be performed cautiously. Finally, we suggest an approach for the correction and cleaning of BUSCO-derived genomic datasets that will be useful to other researchers planning to use this tool for phylogenomic studies.

Detection of Thelazia callipaeda in Phortica variegata and spread of canine thelaziosis to new areas in Spain

Background

The fruit fly Phortica variegata (Drosophilidae: Steganinae) feeds on the ocular secretions of animals and humans, and has been described as an intermediate host of the eye worm Thelazia callipaeda (Spirurida: Thelaziidae) in Italy. Despite the increased detection of T. callipaeda in many European countries, information about its vector role in natural conditions is still limited. In the Iberian Peninsula, thelaziosis caused by T. callipaeda has been reported in dogs, cats, red foxes, wild rabbits and humans.

Methods

In the last seven years, we have detected increased numbers of cases of canine thelaziosis at three locations in mainland Spain: Site 1, La Vera region (Cáceres Province, central-western Spain; 51 cases); Site 2, El Escorial municipality (Madrid Community, central Spain; 23 cases); and Site 3, Miraflores de la Sierra municipality (Madrid Community, central Spain; 41 cases). Site 1 is considered endemic for T. callipaeda while the other two sites have been recently recognised as risk zones for T. callipaeda infection.

Results

From June 2016 to September 2017, 2162 flies were collected and morphologically identified as Phortica spp. (Site 1, n = 395; Site 2, n = 1544; and Site 3, n = 223). Upon dissection, third-stage T. callipaeda larvae were found in two out of 155 flies examined from Site 1, and both these larvae tested molecularly positive for the eye worm. Of the 395 flies collected from Site 1, 371 were molecularly processed for arthropod species identification and T. callipaeda detection. All 371 flies were identified as P. variegata and 28 (7.5%; 95% CI: 4.8–10%) tested positive for T. callipaeda DNA haplotype 1.

Conclusions

Our findings indicate that T. callipaeda circulates among dogs and P. variegata in Spain, where zoonotic cases have been also reported. The co-existence of canine thelaziosis and Phortica spp. in geographical areas previously considered free of the eye worm indicates a risk of infection for both animals and humans living in this region.

Competence of Phortica variegata from the United States as an Intermediate Host of the Thelazia callipaeda Eyeworm

Over the past 20 years, Thelazia callipaeda (the oriental eyeworm) has become endemic in Europe, infecting domestic and wild carnivores and humans. The vector of this nematode, the fruit fly Phortica variegata, has recently been discovered in the United States, and its vector competence is demonstrated for T. callipaeda in this article, therefore representing a potential new threat for infection of carnivores and humans in the United States.

Drosophilidae feeding on animals and the inherent mystery of their parasitism

Insect evolution, from a free to a parasitic lifestyle, took eons under the pressure of a plethora of ecological and environmental drivers in different habitats, resulting in varying degrees of interactions with their hosts. Most Drosophilidae are known to be adapted to feeding on substrates rich in bacteria, yeasts and other microfungi. Some of them, mainly those in the Steganinae subfamily, display a singular behaviour, feeding on animal tissues or secretions. This behaviour may represent an evolving tendency towards parasitism. Indeed, while the predatory attitude is typical for the larval stages of a great proportion of flies within this subfamily, adult males of the genera Amiota, Apsiphortica and Phortica display a clearly zoophilic attitude, feeding on the lachrymal secretions of living mammals (also referred as to lachryphagy). Ultimately, some of these lachryphagous species act as vectors and intermediate hosts for the spirurid nematode Thelazia callipaeda, which parasitizes the eyes of domestic and wild carnivores and also humans. Here we review the scientific information available and provide an opinion on the roots of their evolution towards the parasitic behaviour. The distribution of T. callipaeda and its host affiliation is also discussed and future trends in the study of the ecology of Steganinae are outlined.

Drosophilidae feeding on animals and the inherent mystery of their parasitism

Insect evolution, from a free to a parasitic lifestyle, took eons under the pressure of a plethora of ecological and environmental drivers in different habitats, resulting in varying degrees of interactions with their hosts. Most Drosophilidae are known to be adapted to feeding on substrates rich in bacteria, yeasts and other microfungi. Some of them, mainly those in the Steganinae subfamily, display a singular behaviour, feeding on animal tissues or secretions. This behaviour may represent an evolving tendency towards parasitism. Indeed, while the predatory attitude is typical for the larval stages of a great proportion of flies within this subfamily, adult males of the genera Amiota, Apsiphortica and Phortica display a clearly zoophilic attitude, feeding on the lachrymal secretions of living mammals (also referred as to lachryphagy). Ultimately, some of these lachryphagous species act as vectors and intermediate hosts for the spirurid nematode Thelazia callipaeda, which parasitizes the eyes of domestic and wild carnivores and also humans. Here we review the scientific information available and provide an opinion on the roots of their evolution towards the parasitic behaviour. The distribution of T. callipaeda and its host affiliation is also discussed and future trends in the study of the ecology of Steganinae are outlined.

Phylogeny of the African and Asian Phortica (Drosophilidae) deduced from nuclear and mitochondrial DNA sequences

Phylogenetic relationships of 26 Phortica species were investigated based on DNA sequence data of two mitochondrial (ND2, COI) and one nuclear (28S rRNA) genes. Five monophyletic groups were recovered in the genus Phortica, of which three were established as new subgenera, Alloparadisa, Ashima, and Shangrila. The subgenus Allophortica was suggested as the most basal lineage in Phortica, followed by the lineage of P. helva + P. sobodo + P. varipes. The remaining Phortica species, most of Oriental distribution, formed a monophyletic group, and were subdivided into three lineages (i.e., the subgenera Ashima, Phortica, and Shangrila). The subgenera Shangrila and Phortica were suggested as sister taxa, and four clades were recovered in the subgenus Ashima. The result of reconstruction of ancestral distribution and estimation of divergence times indicates that, the ancestor of the genus Phortica restricted to Africa, its initial diversification was dated back to ca. 23 Mya (coinciding with the Oligocene/Miocene boundary); sympatric speciation and an Africa-to-Asia dispersal was proposed to account for the current distribution of Allophortica and the rest Phortica; most of the rest diversification of Phortica occurred in southern China, and the divergence between the African clade and its Oriental counterpart was suggested as a result of vicariance following a dispersal of their ancestral species from southern China to Africa.

Molecular phylogenetic analysis of the Stegana ornatipes species group (Diptera: Drosophilidae) in China, with description of a new species

A new species of the Stegana (Steganina) ornatipes species group (Diptera: Drosophilidae) is described from Hainan, China, S. (S.) xipengi sp. nov. Based on the mitochondrial ND2 and COI gene sequences, the relationships among eight species from mainland China of the ornatipes group, and their relationships to the undulata, nigrolimbata and shirozui species groups of the same subgenus, are investigated, using two species of the subgenus Stegana, S. emeiensis and S. quadrata, as outgroups. The result shows that S. (S.) mengla is debarred from the ornatipes group.

Molecular identification of Cinara cupressi and Cinara tujafilina (Hemiptera, Aphididae)

A condition called "cypress mortality" affects forest of Austrocedrus chilensis (D. Don) Pic. Ser et Bizarri in Argentina. Their classic groups of symptoms has been described as a slow process of defoliation that culminating in death of the tree; nevertheless, dying and recently dead trees with abundant foliage are frequently observed in which foliage changes to red. Cinara (Cupressobium) cupressi (Buckton) is considered the agent responsible for reddening this indigenous conifer in Chile. Therefore, the relationship between the presence of C. cupressi and the new aerial symptoms in A. chilensis from Argentina required evaluation. However, Cinara (Cupressobium) tujafilina (del Guercio) also has been reported from this host, and the differentiation of both species of Cinara is time consuming and requires a great expertise because they share many morphologic and microscopic characters. A rapid molecular method of identification of C. cupressi and C. tujafilina is desirable to detect and differentiate them. We report the development and evaluation of a polymerase chain reaction-restriction fragment length polymorphism method based on the mitochrondial cytochrome oxidase I gene to identify C. cupressi and C. tujafilina in colonies of aphids. The first detection of C. cupressi from A. chilensis in Argentina, is reported based on the new method.