DNA barcoding and taxonomic classification of black flies in Southeast Asia

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Simulium mirum
Female, and two male forms of Simulium mirum sp. nov. discovered in Malaysia. Image from Takaoka H et al. (2016) (CC BY 4.0)

Black flies (Simuliidae) are one of the world's most medically significant groups of the blood-sucking insects. Females of certain species cause skin conditions like itching, rash and edema in humans and other animals and also serve as vectors of both human and zoonotic forms of river blindness, or onchocerciasis. At the same time, black flies are also an ideal freshwater bioindicator because immature stages can breed only in clean running rivers and streams.

Led by the world-renowned black fly taxonomist, Prof. Emeritus Dr. Hiroyuki Takaoka, the project team has carried out field surveys of black flies in seven Southeast Asian countries since 2010. The expeditions have discovered 145 new species from five subgenera of the genus Simulium (30 from Malaysia, 48 from Vietnam, 17 from Thailand, ten from Indonesia, three from Myanmar, two from the Philippines and one from Laos), bringing the total number of described Asian species in the family to 599.

Despite these advances in knowledge of Simuliidae diversity in Southeast Asia, the idenfification of black flies is challenging. The family is well-known as the most structurally uniform taxa, and the differences between species typically rely on subtle characteristics in one or two life stages. As such, research into black flies can benefit greatly from a DNA barcode library to facilitate rapid and accurate identification of known species while accelerating the pace of discovery by highlighting those morphologically similar but genetically distinct taxa (cryptic species) that may represent new species.

This project will digitize black flies from Southeast Asia and seek to address taxonomic issues via DNA barcoding and metabarcoding approaches, providing a way forward for establishing a DNA barcode library for the family Simuliidae and long-term improvements and additions to black fly information in Southeast Asia.

Project progress
At final reporting the project published to GBIF a dataset containing a total of 359 occurrence records from 109 black fly species with corresponding COI sequences from Malaysia (57 sequences from 22 species), Indonesia (86 sequences from 29 species), Thailand (81 sequences from 13 species) and Vietnam (135 sequences from 45 species).

The project reported that for best practices, the type specimens or specimens collected from type localities are the most reliable sources for DNA barcoding because they have already been verified by experienced taxonomists. The black flies specimens used in this project comprised type specimens, collected from type locations, and all samples have been identified by the world-renowned black fly’s taxonomist Prof. Dr. Hiroyuki Takaoka. This ensures the DNA barcodes generated from this study can be used globally for accurate identification and comparisons.

The project also completed PCR, sequencing and analysis of black fly species complexes such as members of Simulium asakaoe group based on multiple gene markers (BZF and ECP1 genes), though the performance was lower than the barcoding COI gene sequences.

During the project, two papers were presented at the International Conference of Medical Parasitology & Entomology 2022 (ICMPE 2022) held in August 2022, to promote the BIFA program and GBIF.

The project also aided to introduce GBIF to members of the Malaysian Society of Parasitology and Tropical Medicine (MSPTM), for which a seminar on the introduction to GBIF and data publishing was then organized by MSPTM and held in February 2023.

Post project progress
The following publications related to this project have been published:

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1 September 2021 - 28 February 2023
Project identifier
  • Chiang Mai University
  • University of Mataram
  • Ministry of Science and Technology, Viet Nam
Project lead
Universiti Malaya
Contact details

Van Lun Low
Universiti Malaya
Tropical Infectious Diseases Research and Education Centre
50603 Kuala Lumpur