Revision of the genus Dichaetophora Duda (Diptera: Drosophilidae), part I: DNA bar-coding and molecular phylogenetic reconstruction

Katoh, T. K.; Chen, J.-M.; Yang, J.-H.; Zhang, G.; Wang, L.; Suwito, A.; Toda, M. J.; Zhang, Y.-P.; Gao, J.-J.

doi:10.1101/2021.05.28.446102

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bioRxiv · 10.1101/2021.05.28.446102

Revision of the genus Dichaetophora Duda (Diptera: Drosophilidae), part I: DNA bar-coding and molecular phylogenetic reconstruction

Katoh, T. K.·Chen, J.-M.·Yang, J.-H.·Zhang, G.·Wang, L.·Suwito, A.·Toda, M. J.·Zhang, Y.-P.·Gao, J.-J.

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Abstract

The genus Dichaetophora is currently comprised of 67 formally described species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. In the present study, we challenged to delimit species from a huge amount of samples of Dichaetophora and allied taxa (the genus Mulgravea and the subgenus Dudaica of Drosophila) collected from a wide range of the Oriental and east Palearctic regions. We first sorted all specimens into morpho-species, which were tentatively classified into the species groups of Dichaetophora, Mulgravea and Dudaica based on the morphological diagnoses for these supraspecific taxa. Then, we selected representative specimen(s) for each morpho-species and subjected them to barcoding of COI (the cytochrome c oxidase subunit I gene) sequences. The applied ABGD (automatic barcode gap discovery) algorithm estimated a total of 222 MOTUs (molecular operational taxonomic units). Although most of the morpho-species were recognized as individual MOTUs, some others were divided into multiple MOTUs or combined into a single MOTU, suggesting the existence of cryptic sibling species, subspecies or intraspecific genetic varieties. Out of the 222 MOTUs, 88 representing the supraspecific taxa of Dichaetophora, Mulgravea and Dudaica were selected, along with 33 species from major genera and subgenera of Drosophila in the tribe Drosophilini, as in-group (four species from the tribe Colocasiomyini as out-group) for phylogenetic reconstruction. We analyzed a dataset of concatenated nucleotide sequences of 12 nuclear gene markers by the maximum likelihood and Bayesian inference methods. As a result, the three focal taxa (i.e., Dichaetophora, Mulgravea and Dudaica) formed a clade, which we called the "pan-Dichaetophora". Within this large clade, the agbo, tenuicauda, sinensis and trilobita groups of Dichaetophora, Mulgravea and Dudaica were recovered as monophyletic groups, but Dichaetophora and its acutissima group were regarded as paraphyletic. In addition, two clusters were recognized among ungrouped MOTUs of Dichaetophora. Thus, the present study has uncovered some problems in the taxonomy of the pan-Dichaetophora. Solving such problems will be challenged in Part II of this serial work.

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Katoh, T. K., Chen, J.-M., Yang, J.-H., Zhang, G., Wang, L., Suwito, A., Toda, M. J., Zhang, Y.-P., Gao, J.-J.. 2021-05-30. Revision of the genus Dichaetophora Duda (Diptera: Drosophilidae), part I: DNA bar-coding and molecular phylogenetic reconstruction. https://doi.org/10.1101/2021.05.28.446102

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