Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach

Comparative Mitogenomic Analyses of Psectrocladius (Diptera: Chironomidae)

Psectrocladius, a genus within the species-rich subfamily Orthocladiinae (Diptera: Chironomidae), remains poorly resolved in molecular phylogenetics due to limited available molecular data. Here, we sequenced and analyzed the complete mitogenomes of five Psectrocladius species, using two Rheocricotopus species as outgroups. Our results reveal that the mitogenomes of Psectrocladius are structurally conserved and retain a presumed ancestral gene order. The nucleotide composition of these newly generated mitogenomes exhibits a pronounced A + T bias, which is characteristic of typical insect mitogenomes. The substitution rates, estimated using Ka/Ks ratios, indicate that all protein-coding genes are under purifying selection. The strongest purifying selection pressure was observed in the CO1 gene, while the weakest was in the ND5 gene. Both the maximum likelihood and Bayesian inference trees consistently show the following topology: ((((P. schlienzi + P. bisetus) + P. barbimanus) + P. oligosetus) + P. aquatronus). This study provides key insights into chironomid mitogenomes and their gene properties, offering valuable reference data for future research.

Species Delimitation and Cryptic Diversity in Rheotanytarsus Thienemann & Bause, 1913 (Diptera: Chironomidae) Based on DNA Barcoding

The genus Rheotanytarsus Thienemann & Bause, 1913 (Diptera: Chironomidae) currently includes more than 120 recognized species worldwide, but precise species-level identification based solely on morphology remains challenging. Pronounced morphological differences among life stages and the time-consuming inefficiency of rearing larvae further complicate life-stage matching in this genus. In this study, we assessed species diversity by integrating morphological examination and DNA barcoding, analyzing 911 DNA barcodes from newly collected samples and a public database. Based on these results, we further constructed a relatively complete life-history framework. Our results show that 911 Rheotanytarsus DNA barcodes belong to 69 putative species. The maximum intraspecific divergence reached 7.35% in R. pentapoda, and the average minimal interspecific distance was 11.44%. Substantial intraspecific divergence in certain species complexes suggests the presence of cryptic species. Therefore, to resolve these potential cryptic species issues, more extensive sampling and morphological examination of specimens from geographically distant regions-supplemented by nuclear and ecological data-are required.

Procladius (Diptera, Chironomidae) of Europe and a global view

A project initiated in 1991 to untangle species-taxonomy of European Procladius (Chironomidae) has been accomplished. Increasing amount of material, loans and especially the development of barcodes and the BIN-system of BOLD, made finalization possible after about 33 years. An iterative process based on detailed studies of male morphology and barcode clusters, BINs, resulted in identification of 27 species present in Europe, most of them also in Asia (China, Japan, Mongolia and Russia) and North America (Canada and the United States). One hundred morphological characters were adopted for species identification of which the 30 most important ones were used to construct a species key and an additional helpdesk. The key contains three characters for each species separation as this is frequently needed for reliable identification. The ratio GspR, the outer length of the gonostylus process versus length of outer margin in gonostylus, proved to be the most important character for species identification. All but two of the 27 species have barcodes and BINs. All but one BIN contained only one species. The exception is a BIN that previously was divided into two BINs each containing one morphologically distinct species. Intraspecific divergence within the species ranged from 0‒3.3% and interspecific divergence from 2.0‒8.8%. Four new species are presented. These are P. exilis Brodin, new species, P. gemma Brodin, new species, P. saeticubitus Brodin, new species and P. tenebricosus Brodin & Hellberg, new species. The other 23 species presented are as follows with new synonyms within brackets: P. appropinquatus (Lundström, 1916) [P. ruris Roback, 1971], P. bellus (Loew, 1866) [Tanypus rufovittatus van der Wulp, 1874, P. latifrons Kieffer, 1922, P. leucocoma Kieffer, 1922, P. profundorum Kieffer, 1923], P. breviatus Remmert, 1953, P. choreus (Meigen, 1804) [Chironomus incomptus Walker, 1856], P. clavus Roback, 1971, P. crassinervis (Zetterstedt, 1838) [Tanypus pectinatus Kieffer, 1909, P. bifasciatus Goetghebuer, 1936, P. cinereus Goetghebuer, 1936, P. abetus Roback, 1971], P. culiciformis (Linnaeus, 1767) [Tanypus sagittalis Kieffer, 1909, Trichotanypus scapularis Kieffer, 1924, P. freemani Sublette, 1964 in part], P. dentus Roback, 1971, P. ferrugineus (Kieffer, 1918) [Trichotanypus parvulus Kieffer, 1918, Trichotanypus fulvus Kieffer, 1924, Trichotanypus profundorum Kieffer, 1924, P. rugulosus Saether 2010], P. fimbriatus Wülker, 1959, P. flavifrons Edwards, 1929, P. floralis Kieffer, 1915, P. frigidus (Holmgren, 1869) [P. gretis Roback, 1971], P. imicola Kieffer, 1922 [P. bathyphilus Kieffer, 1922, P. nietus Roback, 1971], P. islandicus (Goetghebuer, 1931) [P. fuscus Brundin, 1949, P. vesus Roback, 1971], P. longistilus (Kieffer, 1916) [P. suecicus Brundin, 1949], P. lugens Kieffer, 1915 [P. macrotrichus Roback, 1971], P. lugubris (Zetterstedt, 1850) [P. barbatus Brundin, 1949, P. johnsoni Roback, 1980], P. nudipennis Brundin, 1947, P. pruinosus (Kieffer, 1924), P. signatus (Zetterstedt, 1850) [Trichotanypus nigriventris Kieffer, 1924, P. denticulatus Sublette, 1964 in part], P. simplicistilus Freeman, 1948, P. tatrensis Gowin, 1944. In addition, 12 species of Procladius not found in Europe are briefly described and it is indicated where they appear in the species-key. Species of Procladius have been reported from 133 countries or autonomies worldwide. As many as 12 species have been found in extreme cold places of the northern hemisphere, with mean annual temperature ‒10 C or more. Altitude records are at 4 730 m above sea level in the Himalayas. Larvae of most European species are known to be omnivorous, although predation might be more beneficial for growth. Synonyms and dubious names reduce the number of valid (accepted) species of Procladius according to Catalogue of Life and Systema Dipterorum with 34% worldwide. After the inclusion of four new species of the present study and two others from Asia the number or valid species of Procladius worldwide land on 69.

Shedding light on dark taxa: exploring a cryptic diversity of parasitoid wasps affected by artificial light at night

Artificial light at night (ALAN) contributes to the globally observed insect decline. ALAN attracts nocturnal insects from their native ecosystems and disturbs their functions in the food web. Road lights in this context are ubiquitous and relevant ALAN sources that are often not considered in conservation approaches. In a previous study we showed that shielded LED road lights are suited to be part of conservation measures by effectively reducing the attraction of nocturnal insects. Here we show that this positive effect holds true for parasitoid wasps in an experimental BACI design (Before-After-Control-Impact). Combining morphological with molecular and phylogenetic analyses, we identified 106 individuals (62 morphotypes) of a minimum of 45 genera out of 13 Hymenoptera families. We were able to identify 21 species, 11 of which are newly reported in Southern Germany (Baden-Württemberg). Further combining knowledge on life history and host appearance from our data and the literature, we discuss potential impacts of ALAN ranging from an influence on nocturnal pollination via parasitoid pressure on moth species and biological control of invasive pest species to tritrophic interactions between primary and secondary parasitoids. We conclusively think that shielded LED road lights will reduce the ecological impact of ALAN on parasitoid wasps in a large and undescribed number of taxa with different host associations, likely affecting associated ecosystem functions such as biological control.

COI Insights into Diversity and Species Delimitation of Immature Stages of Non-Biting Midges (Diptera: Chironomidae)

The diversity of non-biting midges (Chironomidae, Diptera) remains an unresolved topic, with estimates of species numbers ranging from 6000 to 15,000 according to various authors. To assess Chironomidae diversity in Lithuania, we evaluate the effectiveness of COI gene-based species delimitation methods for providing rapid diversity estimates. Nevertheless, differences between tree-based and distance-based approaches can result in varying group classifications, which may cause species numbers to be overestimated or underestimated. For our study, we analyzed a dataset of 109 specimens sampled from six Lithuanian streams. By applying multiple methods, such as Assemble Species by Automatic Partitioning (ASAP), Automatic Barcode Gap Discovery (ABGD), the generalized mixed Yule-coalescent (GMYC) model, and the Bayesian implementation of the Poisson Tree Processes (bPTP) model, we found that species estimates ranged from 28 to 58. Among these methods, ASAP proved to be the most effective for our dataset, identifying 58 putative species. These results reinforce our assumption that the current understanding of Chironomidae species diversity is incomplete.

Chironomids (Diptera) from Central European stream networks: new findings and taxonomic issues

Background

Chironomidae, with over 7,300 described species, are amongst the most diverse and abundant insect families in freshwater ecosystems worldwide. Chironomids are known for their widespread distribution from various water types. The level of documentation of chironomid fauna varies considerably amongst European countries, with more comprehensive knowledge for Western Europe compared to other regions. Despite the recent extensive sampling effort and the increasing number of available data, the chironomid fauna of Central European countries still remains poorly known.

New information

This study contributes to the knowledge of chironomid fauna in three river catchments in Croatia, Hungary and Czechia. A combination of morphological and molecular techniques was employed, with a focus on larvae, although pupae and exuviae were also examined. We found 207 taxa, amongst which 170 were identified to species level. In Croatia, 14 species were recorded for the first time and two species were newly recorded in Czechia. DNA barcoding of 31 specimens resulted in 23 BINs, including eight new ones to BOLD. We provided detailed notes on taxa with taxonomic problems and/or morphological peculiarities. Our results highlight that extensive studies conducted in relatively small areas and a limited range of habitats (only streams in hilly regions) can remarkably contribute to the local and global knowledge on Chironomidae fauna, especially when the taxonomically difficult and often problematic larvae are investigated.

Chironomidae (Diptera) of the Šventoji and Žeimena sub-basins in Lithuania

Background

Chironomidae, commonly known as non-biting midges, are key indicators of the health and biodiversity of freshwater ecosystems. They are also one of the most abundant and diverse groups of aquatic invertebrates. Although Chironomidae are ecologically important, abundant and diverse, there has been limited focused research on this group in Lithuania. Our study addresses this gap by analysing the diversity of Chironomidae in six Lithuanian streams.

New information

In this study, we present a comprehensive list of Chironomidae collected from six streams with similar hydrological characteristics: three dammed and three undammed. Lithuania is home to 158 species of known species of Chironomidae, comprised of 22 species in the subfamily Tanypodinae, 87 in the Chironominae, 42 in the Orthocladiinae, four in the Diamesinae and three in the Prodiamesinae. Throughout our research, we collected 11,296 chironomid specimens using a D-shaped aquatic net. Amongst these specimens, we identified 89 species representing 65 genera and five subfamilies, including 37 species and 12 genera, were recorded for the first time in Lithuania. The subfamily Chironominae, with 28 genera and 6,816 specimens, has exhibited the highest abundance of non-biting midges both in terms of genera and individuals. Amongst the streams investigated, the Luknelė was the richest in diversity, harbouring 37 genera and 2,657 individuals, accounting for about 55% of the Chironomidae genera found during the research. Our findings significantly enhance the understanding of the Lithuanian Chironomidae fauna, marking the first comprehensive study of such a kind, as previous knowledge of this fauna has been derived only from related studies.

The first record of Chironomusnuditarsis Keyl, 1961 from Sevan Lake (Armenia) confirmed by morphology, karyotype and COI gene sequence

Chironomusnuditarsis Keyl, 1961 is recorded from Sevan Lake for the first time. This species is widespread in Europe, the Caucasus, and Siberia. For species identification, we used a comprehensive approach that included morphological, cytogenetic and molecular genetic analyses. Morphological analysis showed a high similarity with the description. Nine chromosome banding sequences ndtA1, ndtA2, ndtB2, ndtC1, ndtD1, ndtE1, ndtF1, ndtG1, and ndtG2 were found. The banding sequences ndtA1, ndtA2, ndtG1, and ndtG2 are species-specific for C.nuditarsis and allow us to accurately distinguish it from the sibling species Ch.curabilis Belyanina, Sigareva et Loginova, 1990. Molecular-genetic analysis of the COI gene sequences has shown low genetic distances of 0.38-0.95% in the sibling species Ch.nuditarsis and Ch.curabilis complex and the insufficiency of using a single COI as a molecular marker for their separation.

Image-based recognition of parasitoid wasps using advanced neural networks

Hymenoptera has some of the highest diversity and number of individuals among insects. Many of these species potentially play key roles as food sources, pest controllers and pollinators. However, little is known about the diversity and biology and ~80% of the species have not yet been described. Classical taxonomy based on morphology is a rather slow process but DNA barcoding has already brought considerable progress in identification. Innovative methods such as image-based identification and automation can further speed up the process. We present a proof of concept for image data recognition of a parasitic wasp family, the Diapriidae (Hymenoptera), obtained as part of the GBOL III project. These tiny (1.2-4.5mm) wasps were photographed and identified using DNA barcoding to provide a solid ground truth for training a neural network. Taxonomic identification was used down to the genus level. Subsequently, three different neural network architectures were trained, evaluated and optimised. As a result, 11 different genera of diaprids and one mixed group of 'other Hymenoptera' can be classified with an average accuracy of 96%. Additionally, the sex of the specimen can be classified automatically with an accuracy of >97%.

The InBIO Barcoding Initiative Database: DNA barcodes of Orthoptera from Portugal

Background

The InBIO Barcoding Initiative (IBI) Orthoptera dataset contains records of 420 specimens covering all the eleven Orthoptera families occurring in Portugal. Specimens were collected in continental Portugal from 2005 to 2021 and were morphologically identified to species level by taxonomists. A total of 119 species were identified corresponding to about 77% of all the orthopteran species known from continental Portugal.

New information

DNA barcodes of 54 taxa were made public for the first time at the Barcode of Life Data System (BOLD). Furthermore, the submitted sequences were found to cluster in 129 BINs (Barcode Index Numbers), 35 of which were new additions to the Barcode of Life Data System (BOLD). All specimens have their DNA barcodes publicly accessible through BOLD online database. Stenobothruslineatus is recorded for the first time for continental Portugal. This dataset greatly increases the knowledge on the DNA barcodes and distribution of Orthoptera from Portugal. All DNA extractions and most specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.

How non-target chironomid communities respond to mosquito control: Integrating DNA metabarcoding and joint species distribution modelling

The conservation and management of riparian ecosystems rely on understanding the ecological consequences of anthropogenic stressors that impact natural communities. In this context, studies investigating the effects of anthropogenic stressors require reliable methods capable of mapping the relationships between taxa occurrence or abundance and environmental predictors within a spatio-temporal framework. Here, we present an integrative approach using DNA metabarcoding and Hierarchical Modelling of Species Communities (HMSC) to unravel the intricate dynamics and resilience of chironomid communities exposed to Bacillus thuringiensis var. israelensis (Bti). Chironomid emergence was sampled from a total of 12 floodplain pond mesocosms, half of which received Bti treatment, during a 16-week period spanning spring and summer of 2020. Subsequently, we determined the community compositions of chironomids and examined their genus-specific responses to the Bti treatment, considering their phylogenetic affiliations and ecological traits of the larvae. Additionally, we investigated the impact of the Bti treatment on the body size distribution of emerging chironomids. Our study revealed consistent responses to Bti among different chironomid genera, indicating that neither phylogenetic affiliations nor larval feeding strategies significantly contributed to the observed patterns. Both taxonomic and genetic diversity were positively correlated with the number of emerged individuals. Furthermore, our findings demonstrated Bti-related effects on chironomid body size distribution, which could have relevant implications for size-selective terrestrial predators. Hence, our study highlights the value of employing a combination of DNA metabarcoding and HMSC to unravel the complex dynamics of Bti-related non-target effects on chironomid communities. The insights gained from this integrated framework contribute to our understanding of the ecological consequences of anthropogenic stressors and provide a foundation for informed decision-making regarding the conservation and management of riparian ecosystems.

Abundant, diverse, unknown: Extreme species richness and turnover despite drastic undersampling in two closely placed tropical Malaise traps

Arthropods account for a large proportion of animal biomass and diversity in terrestrial systems, making them crucial organisms in our environments. However, still too little is known about the highly abundant and megadiverse groups that often make up the bulk of collected samples, especially in the tropics. With molecular identification techniques ever more evolving, analysis of arthropod communities has accelerated. In our study, which was conducted within the Global Malaise trap Program (GMP) framework, we operated two closely placed Malaise traps in Padang, Sumatra, for three months. We analyzed the samples by DNA barcoding and sequenced a total of more than 70,000 insect specimens. For sequence clustering, we applied three different delimitation techniques, namely RESL, ASAP, and SpeciesIdentifier, which gave similar results. Despite our (very) limited sampling in time and space, our efforts recovered more than 10,000 BINs, of which the majority are associated with "dark taxa". Further analysis indicates a drastic undersampling of both sampling sites, meaning that the true arthropod diversity at our sampling sites is even higher. Regardless of the close proximity of both Malaise traps (< 360 m), we discovered significantly distinct communities.