An integrative taxonomic treatment of the Mycetophilidae (Diptera: Bibionomorpha) from Singapore reveals 115 new species on 730km²

Abstract

"Open ended" or "dark taxa" are species-rich clades that are so abundant and diverse that conventional taxonomic methods tend to struggle with the onslaught of specimens and species. New approaches based on presorting specimens to putative species with affordable barcodes may make tackling these taxa manageable. However, this will still require limiting the geographic scope of revisions, given that most countries and biogeographic regions will have too many specimens and species for comprehensive coverage. We demonstrate the power of this approach by carrying out a revision of the fungus gnats (Diptera: Mycetophilidae) of Singapore. The material revised here was obtained from 496 Malaise trap samples caught by 71 Malaise traps placed at 107 collecting sites in different habitats: mangroves, swamp forests, freshwater swamps, primary rainforests, and different types of secondary forests (old, maturing, young, urban). Based on molecular and morphological data for more than 1,456 specimens, we delimit 120 species with molecular and morphological data. Of these, only 4 or 5 are species previously described. The remaining 115 are new to science and described here. However, we only name only 99 species, since two species lacks molecular data and 14 others are currently only known from females where we cannot prepare a fully satisfying morphological diagnosis. The match ratio between morphology and standard MOTUs (3% clusters) was overall high (95%) with even higher match ratios (99%) observed for 5% Objective Clustering and MOTUs obtained with ABGD (P=0.060). Overall, the ratio of undescribed to described is an astonishing 23:1., Only revising the Singapore fauna increases the number of described species of Oriental Mycetophilidae by over 25%. This highlights the size of the taxonomic impediment for fungus gnats. Most of the Singapore Mycetophilidae diversity belongs to three of 22 genera-Neoempheria Osten-Sacken (31 species), Epicypta Winnertz (29 species) and Manota Williston (14 species), but we also describe a new genus, Integricypta, gen. n. based on three species. It belongs to Mycetophilinae Mycetophilini and is the putative sistergroup of Aspidionia Colless. The species sequenced, illustrated, and named are: Leptomorphus rafflesi, sp. n.; Monoclona simhapura, sp. n.; Azana demeijeri, sp. n.; Azana leekongchiani, sp. n. (Sciophilinae); Tetragoneura crawfurdi, sp. n.; Tetragoneura chola, sp. n.; Tetragoneura dayuan, sp. n.; Tetragoneura farquhari, sp. n.; Ectrepesthoneura johor, sp. n. (Tetragoneurinae); Mohelia zubirsaidi, sp. n.; Allactoneura tumasik, sp. n.; Allactoneura limbosengi, sp. n.; Manota banzu, sp. n.; Manota tantocksengi, sp. n.; Manota bukittimah, sp. n.; Manota chiamassie, sp. n.; Manota danmaxi, sp. n.; Manota mahuan, sp. n.; Manota temenggong, sp. n.; Clastobasis sritribuana, sp. n.; Clastobasis bugis, sp. n.; Clastobasis oranglaut, sp. n. (Leiinae); Parempheriella mait, sp. n.; Parempheriella longyamen, sp. n.; Parempheriella peranakan, sp. n.; Neoempheria sachmatich, sp. n.; Neoempheria merlio, sp. n.; Neoempheria sabana, sp. n.; Neoempheria sangabo, sp. n.; Neoempheria shicheng, sp. n.; Neoempheria ujong, sp. n.; Neoempheria subaraji, sp. n.; Neoempheria kokoiyeeae, sp. n.; Neoempheria mandai, sp. n.; Neoempheria malacca, sp. n.; Neoempheria sinkapho, sp. n.; Neoempheria singapura, sp. n.; Neoempheria xinjiapo, sp. n.; Neoempheria puluochung, sp. n.; Neoempheria merdeka, sp. n.; Neoempheria neesoon, sp. n.; Neoempheria pulau, sp. n.; Neoempheria cinkappur, sp. n.; Neoempheria temasek, sp. n.; Neoempheria polunini, sp. n.; Neoempheria fajar, sp. n.; Neoempheria riatanae, sp. n. (Mycomyinae); Allodia glorialimae, sp. n.; Brachycampta murphyi, sp. n.; Brachycampta limtzepengi, sp. n.; Brachycampta teopohlengi, sp. n.; Exechia tanswiehiani, sp. n.; Exechia alinewongae, sp. n.; Mycetophila chngseoktinae, sp. n.; Mycetophila georgettechenae, sp. n.; Mycetophila aishae, sp. n.; Platyprosthiogyne phanwaithongae, sp. n.; Platyprosthiogyne gohsookhimae, sp. n.; Platyprosthiogyne rahimahae, sp. n.; Platyprosthiogyne lynetteseahae, sp. n.; Platyprosthiogyne neilaae, sp. n.; Platyprosthiogyne snehalethaae, sp. n.; Platurocypta adeleneweeae, sp. n.; Platurocypta tanhoweliangi, sp. n.; Epicypta constancesingamae, sp. n.; Epicypta jennylauae, sp. n.; Epicypta limchiumeiae, sp. n.; Epicypta janetyeeae, sp. n.; Epicypta kohkhenglianae, sp. n.; Epicypta daintoni, sp. n.; Epicypta holltumi, sp.n.; Epicypta alii, sp. n.; Epicypta ridleyi, sp. n.; Epicypta chezaharaae, sp. n.; Epicypta tanjiakkimi, sp. n.; Epicypta gehminae, sp. n.; Epicypta jackieyingae, sp. n.; Epicypta khatijunae, sp. n.; Epicypta purchoni, sp. n.; Epicypta foomaoshengi , sp. n.; Epicypta ganengsengi, sp. n.; Epicypta nanyangu, sp. n.; Epicypta nus, sp. n.; Epicypta peterngi, sp. n.; Epicypta maggielimae, sp. n.; Epicypta yupeigaoae, sp. n.; Epicypta annwee, sp. n.; Epicypta wallacei, sp. n.; Epicypta lamtoongjini, sp. n.; Epicypta catherinelimae, sp. n.; Epicypta grootaerti, sp. n.; Epicypta joaquimae, sp. n.; Aspidionia cheesweeleeae, sp. n.; Aspidionia janetjesudasonae, sp. n.; Aspidionia fatimahae, sp. n.; Integricypta fergusondavie, sp. n.; Integricypta teosoonkimae, sp. n.; Integricypta shirinae, sp. n.; Integricypta hoyuenhoeae, sp. n. (Mycetophilinae). The previously described species are: Metanepsia malaysiana Kallweit, Eumanota racola Soeli, Parempheriella defectiva (Edwards), and Neoempheria dizonalis (Edwards) (all known from Sumatra and/or the Malaysian peninsula). Two females belong to a species of Chalastonepsia that may be one of the described species of the genus. The gnoristine genus Vecella Wu & Yang is here proposed as a new synonym to Parempheriella, with P. guadunana (Wu & Yang), n. comb., corresponding to an additional Palearctic species of the genus. Barcodes for a second set of 1,567 specimens suggest the presence of an additional 24 MOTUs. We thus estimate that approximately 85% of all the species that routinely enter Malaise traps are here identified or described. The revision concludes with a discussion of the biogeography and generic composition of the mycetophilid fauna at the southern end of the Malay Peninsula.

“Dark taxonomy”: a new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment

“…Some Oriental species, especially those from Sri Lanka, cannot be resolved because the descriptions are insufficiently detailed and the types were lost or are unavailable. We here assumed that the species from Singapore are allospecific based on geography, which is consistent with high endemism for Mycetophilidae species in South America (Amorim and Santos 2018), although our revision (Amorim et al 2023) also includes a species whose distribution ranges from Japan through Singapore and Sumatra to Thailand. Future study will have to reveal if any of the Sri Lankan species are conspecific with the material studied in Singapore.…”

“…Note, however, that this identification in BOLD is problematic given that the record is of a single female from Malaysia, while C. hokkaidensis Kallweit was described from Japan. The remaining 113 new species with molecular and morphological data are described and illustrated in the companion taxonomic monograph (Amorim et al 2023). Images are also available from “Biodiversity of Singapore” (https://singapore.biodiversity.online/taxon/A-Arth-Hexa-Dipt-Mycetophilidae).…”

“…The first had 1,456 and the second, 1,567 specimens. The latter was sequenced after the cut-off date for the descriptive monograph (Amorim et al 2023). All specimens were sequenced for a 313-bp fragment of the cytochrome oxidase I gene ( COI ) given that such minibarcodes amplify better than the full- length barcode (Srivathsan et al 2021) and nevertheless yield similar species-level signal (Yeo et al 2020).…”

Towards holistic insect monitoring: species discovery, description, identification and traits for all insects

“…Resolving legacy issues in taxonomy is time-consuming, but this time only needs to be invested once per taxon and region. For example, once the described species of fungus gnats (Diptera: Mycetophilidae) in Southeast Asia had been evaluated based on descriptions and types, Amorim et al [38] were able to describe 115 of the 120 species of one set of Malaise trap samples from Singapore as new to science. When Meier et al, analysed a second set of samples, more than 90% of the specimens belonged to the species described based on the first set samples.…”

Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: a case study on beach meiofauna

“…A promising approach to mitigate this issue lies in the targeted collection, identification, and sequencing of a high number of specimens, followed by their addition to molecular reference databases. This method, sometimes implemented through taxonomic expert workshops, has been successfully employed across diverse taxonomic groups and ecosystems (Behrens-Chapuis et al, 2021; Creedy et al, 2020; De Souza Amorim et al, 2023; Dugal et al, 2022; Emerson et al, 2023; Zhou et al, 2011).…”