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Recent publications on molecular methods or data

Started by Martin Spies, October 10, 2015, 11:38:10 AM

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Martin Spies


Failla, A. J., Vasquez, A. A., Hudson, P., Fujimoto, M., Ram, J. L. (2015) Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae). Bull. entomol. Res. 106(1): 34-46.

Kranzfelder, P., Ekrem, T., Stur, E. (2015) Trace DNA from insect skins: a comparison of five extraction protocols and direct PCR on chironomid pupal exuviae. Mol. Ecol. Resources, Early View [First published online, DOI: 10.1111/1755-0998.12446]

Krosch, M. N., Bryant, L. M. (2015) A note on sampling chironomids for RNA-based studies of natural populations that retains critical morphological vouchers. CHIRONOMUS J. Chironomidae Res. 28: 4-11.

Tischler A., Egg, M., Füreder, L. (2015) Ethanol: A simple and effective RNA-preservation for freshwater insects living in remote habitats. Limnol. Oceanogr.: Methods [first publ. online, doi: 10.1002/lom3.10079 (xi.2015), 10 pp.].

Martin Spies


Augustyniak, M., Gladysz, M., Dziewięcka, M. (2016) The Comet assay in insects—Status, prospects and benefits for science. Mutation Res. – Revs Mut. Res. 767: 67-76.

Hambäck, P. A., Weingartner, E., Dalén, L., Wirta, H., Roslin, T. (2016) Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes. Ecology and Evolution 6(23): 8431-8439 + online suppl. info.

Kuncham, R., Thayumanavan, T., Reddy, G. V. S. (2016) Development of a modified mitochondrial DNA extraction method from chironomid larvae. J. Envir. Biol. 37(3): 473-478.

Meier, R., Wong, W. H., Srivathsan, A., Foo, M. S. (2016) $1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples. Cladistics 32(1): 100-110 + 6 online suppl. files.

Pramual, P., Simwisat, K., Martin, J. (2016) Identification and reassessment of the specific status of some tropical freshwater midges (Diptera: Chironomidae) using DNA barcode data. Zootaxa 4072(1): 39-60.

Song, C., Wang, Q., Zhang, R., Sun, B., Wang, X. (2016) Exploring the utility of DNA barcoding in species delimitation of Polypedilum (Tripodura) non-biting midges (Diptera: Chironomidae). Zootaxa 4079(5): 534-550.

Martin Spies


Bista, I., Carvalho, G. R., Walsh, K., Seymour, M., Hajibabaei, M., Lallias, D., Christmas, M., Creer, S. (2017) Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nature Communic. 8(14087), 11 pp. + suppl. material [publd online]

Kranzfelder, P., Ekrem, T., Stur, E. (2017) DNA barcoding for species identification of insect skins: a test on Chironomidae (Diptera) pupal exuviae. J. Insect Sci. 17(6, paper 111): 7 pp. + 2 suppl. tables [publd online xii.2017]

Krosch, M. N. (2017) Comparative analysis of larval transcriptomes from co-occurring species of Australian Cricotopus (Diptera: Chironomidae). Austral Ent. 56(4): 451-458 + online suppl. material.

Martin Spies


Carew, M. E., Kellar, C. R., Pettigrove, V. J., Hoffmann, A. A. (2018) Can high-throughput sequencing detect macroinvertebrate diversity for routine monitoring of an urban river? Ecol. Indicators 85: 440-450 + online suppl. data.

Elías-Gutiérrez, M., Valdez-Moreno, M., Topan, J., Young, M. R., Cohuo-Colli, J. A. (2018) Improved protocols to accelerate the assembly of DNA barcode reference libraries for freshwater zooplankton. Ecology and Evolution 8(5): 3002-3018 + 6 online suppl. files.

Lin, X.-L., Stur, E., Ekrem, T. (2018) Exploring species boundaries with multiple genetic loci using empirical data from non-biting midges. Zool. Scripta 47: 325-341 + online suppl. material.

Song, C., Lin, X.-L., Wang, Q., Wang, X.-H. (2018) DNA barcodes successfully delimit morphospecies in a superdiverse insect genus. Zool. Scripta 47: 311-324 + online suppl. material. [the genus treated is Polypedilum]

Srivathsan, A., Baloglu, B., Wang, W., Tan, W. X., Bertrand, D., Ng, A. H. Q., Boey, E. J. H., Koh, J. J. Y., Nagarajan, N., Meier, R. (2018) A MinIONTM-based pipeline for fast and cost-effective DNA barcoding. Mol. Ecol. Resources 18(5): 1035-1049 + online suppl. material.

Theissinger, K., Kästel, A., Elbrecht, V., Makkonen, J., Michiels, S., Schmidt, S. I., Allgeier, S., Leese, F., Brühl, C. A. (2018) Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. Metabarcoding and Metagenomics 2: e21060; 13 pp. + online suppl. material. [publd online (i.2018); DOI: 10.3897/mbmg.2.21060]

Wang, W. Y., Srivathsan, A., Foo, M., Yamane, S. K., Meier, R. (2018) Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: Validating a reverse workflow for specimen processing. Mol. Ecol. Resources 18(3): 490-501. [no chironomid content; posted here for method info.]

Martin Spies


Czechowski, P., Stevens, M. I., Madden, C., Weinstein, P. (2019) Steps towards a more efficient use of chironomids as bioindicators for freshwater bioassessment: Exploiting eDNA and other genetic tools. Ecol. Indicators 110: 11 pp. + online suppl. material. [first publd online (20.xi.2019)]

Gajski, G., Žegura, B., Ladeira, C., Pourrut, B., Del Bo', C., Novak, M., Sramkova, M., Milic, M., Gutzkow, K. B., Costa, S., Dusinska, M., Brunborg, G., Collins, A. (2019) The comet assay in animal models: From bugs to whales – (Part 1 Invertebrates). Mutation Res. / Revs Mutation Res. 779: 82-113.

McCulloch, G. A., Purcell, M. F., Harms, N. E., Grodowitz, M. J., Zhang, J., Hong, S.-H., Walter, G. H. (2019) Molecular screening of herbivorous flies collected from Hydrilla verticillata across China and Korea – setting up hypotheses for further exploratory surveys and tests. Biol. Control 138(paper 104051): 6 pp. + online suppl. material.

Morinière, J., Balke, M., Doczkal, D., Geiger, M. F., Hardulak, L. A., Haszprunar, G., Hausmann, A., Hendrich, L., Regalado, L., Rulik, B., Schmidt, S., Wägele, J., Hebert, P. D. (2019) A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring. Mol Ecol Resour.: 29 pp. + online suppl. material. [first publd online (12.iv.2019);]

Weigand, H., Beermann, A. J., Čiampor, F., Costa, F. O., Csabai, Z. et al. [41 authors in total, incl. several chironomid researchers] (2019) DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. Sci. Total Envir. 678: 499-524 + online suppl. material.

Martin Spies


Finch, G., Nandyal, S., Perretta, C., Davies, B., Rosendale, A. J., Holmes, C. J., Gantz, J. D., Spacht, D. E., Bailey, S. T., Chen, X., Oyen, K., Didion, E. M., Chakraborty, S., Lee Jr, R. E., Denlinger, D. L., Matter, S. F., Attardo, G. M., Weirauch, M. T., Benoit, J. B. (2020) Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability. Scientific Reports 10(item 19791): 27 pp. + online suppl. material.

Kotrba, M. (2020) The DNA barcoding project on German Diptera: An appreciative and critical analysis with four suggestions for improving the development and reliability of DNA-based identification. Eur. J. Entomol. 117: 315-327. [publd online 28.vii.2020]

Zhang, L., Yang, J., Li, H., You, J., Chatterjee, N., Zhang, X. (2020) Development of the transcriptome for a sediment ecotoxicological model species, Chironomus dilutus. Chemosphere 244(paper 125541): 12 pp. + online suppl. material.

Martin Spies


Krosch, M. N., Silva, F. L., Ekrem, T., Baker, A. M., Bryant, L. M., Stur, E., Cranston, P. S. (2021) A new molecular phylogeny for the Tanypodinae (Diptera: Chironomidae) places the Australian diversity in a global context. Mol. Phyl. Evol. 166(item 107324): 11 pp. + online suppl. material. [first publd online 8.x.2021]

Park, K., Kwak, L.-S. (2021) Multi-level gene expression in response to environmental stress in aquatic invertebrate chironomids: Potential applications in water quality monitoring. Reviews envir. Contamin. Toxicol. 259: 77-122 + online suppl. material. [publd online 19.x.2021]

Martin Spies


Huang, J., Miao, X., Wang, Q., Menzel, F., Tang, P., Yang, D., Wu, H., Vogler, A. P. (2022) Metabarcoding reveals massive species diversity of Diptera in a subtropical ecosystem. Ecol. Evol. 12(1): 13 pp. + online suppl. material. [publd 12.i.2022]

Kjærstad, G., Majaneva, M., Falahati-Anbaran, M., Topstad, L., Finstad, A. G., Arnekleiv, J. V., Ekrem, T. (2022) DNA metabarcoding of preservative ethanol reveals changes in invertebrate community composition following rotenone treatment. Frontiers envir. Sci. 10(paper 872739): 14 pp. + online suppl. material. [publd]

Kodama, A., Maruta, R., Saito, H., Kawai, K. (2022) Molecular phylogeny of Japanese marine Tanytarsini chironomids (Chironomidae: Chironominae). Genetica: 10 pp. [publd online 13.viii.2022]

Krueger, T. A., Cross, A. T., Hübner, J., Morinière, J., Hausmann, A., Fleischmann, A. (2022) A novel approach for reliable qualitative and quantitative prey spectra identification of carnivorous plants combining DNA metabarcoding and macro photography. Scientific Reports 12(Article 4778): 11 pp. + online suppl. material.

Lin, X.-L., Liu, Zh., Yan, L.-P., Duan, X., Bu, W.-J., Wang, X.-H., Zheng, Ch.-G. (2022) Mitogenomes provide new insights of evolutionary history of Boreheptagyiini and Diamesini (Diptera: Chironomidae: Diamesinae). Ecol. Evol. 12(5, item e8957): 13 pp. + online suppl. material. [publd 24.v.2022]

Pfenninger, M., Foucault, Q., Waldvogel, A.-M., Feldmeyer, B. (2022) Selective effects of a short transient environmental fluctuation on a natural population. Mol. Ecol.: 15 pp. + online suppl. material. [publd online 25.x.2022]

Qi, Y., Duan, X., Jiao, K.-L., Lin, X.-L. (2022) First complete mitogenome of Axarus fungorum (Albu, 1980) from Guizhou Province, China (Diptera, Chironomidae). Mitochondrial DNA Part B 7(10): 1807-1809. [publd online 17.x.2022]

Shen, M., Li, Y., Yao, Y., Fu, Y. (2022) Complete mitochondrial genome of Chironomus nipponensis, new record from China (Diptera: Chironomidae). Mitochondrial DNA Part B 7(6): 1163-1164.

Vasquez, A. A., Bonnici, B. L., Yusuf, S. H., Cruz, J. I., Hudson, P. L., Ram, J. L. (2022) Improved chironomid barcode database enhances identification of water mite dietary content. Diversity [Basle] 14(2, paper 65): 20 pp. + online suppl. material. [publd online 19.i.2022]

Xiao, Y.-L., Xu, Z.-G., Wang, J.-X., Fang, X.-L., Fu, Y. (2022) Complete mitochondrial genome of a eurytopic midge, Polypedilum nubifer (Diptera: Chironomidae). Mitochondrial DNA Part B 7(11): 1936-1938. [publd online 11.xi.2022; open access at]

Yoshida, Y., Shaikhutdinov, N., Kozlova, O., Itoh, M., Tagami, M., Murata, M., Nishiyori-Sueki, H., Kojima-Ishiyama, M., Noma, S., Cherkasov, A., Gazizova, G., Nasibullina, A., Deviatiiarov, R., Shagimardanova, E., Ryabova, A., Yamaguchi, K., Bino, T., Shigenobu, S., Tokumoto, S., Miyata, Y., Cornette, R., Yamada, T. G., Funahashi, A., Tomita, M., Gusev, O., Kikawada, T. (2022) High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance. NAR Genomics and Bioinformatics 4(2): 12 pp. + online suppl. material. [publd online 5.iv.2022]

Zheng, Ch.-G., Liu, Zh., Zhao, Y.-M., Wang, Y., Bu, W.-J., Wang, X.-H., Lin, X.-L. (2022) First report on mitochondrial gene rearrangement in non-biting midges, revealing a synapomorphy in Stenochironomus Kieffer (Diptera: Chironomidae). Insects 13(1, item 115): 12 pp. + online suppl. material. [publd online 21.i.2022]

Martin Spies


Di, X., Lei, T., Mou, K., Song, Ch., Qi, X. (2023) Complete mitochondrial genome of the non-biting midge Polypedilum henicurum Wang, 1995 (Diptera: Chironomidae). Mitochondrial DNA Part B 8(8): 908-911 + online suppl. material. [publd online 25.viii.2023]

Fang, X., Wang, X., Mao, B., Xiao, Y., Shen, M., Fu, Y. (2023) Comparative mitogenome analyses of twelve non-biting flies and provide[sic!] insights into the phylogeny of Chironomidae (Diptera: Culicomorpha). Scientific Reports [London] 13(1, Article 9200): 13 pp. + online suppl. material. [first publd online]

Han, W., Tang, H., Wei, L., Zhang, E. (2023) The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases. Ecology and Evolution 13(2, paper e9849): 14 pp. + online suppl. material. [publd online 27.ii.2023]

Song, Ch., Wang, L., Lei, T., Qi, X. (2023) New color-patterned species of Microtendipes Kieffer, 1913 (Diptera: Chironomidae) and a deep intraspecific divergence of species by DNA barcodes. Insects [Basle] 14(3, paper 227): 27 pp. + online suppl. material. [publd online 24.ii.2023]

Zhang, D., He, F.-X., Li, X.-B., Aishan, Zh., Lin, X.-L. (2023) New mitogenomes of the Polypedilum generic complex (Diptera: Chironomidae): Characterization and phylogenetic implications. Insects [Basle] 14(3, paper 238): 14 pp. + online suppl. material. [publd 27.ii.2023]

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