Dr.Amrita Srivathsan

Scientist

Amrita.Srivathsan@mfn.berlin+49 30 889140-8437
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Department:
Centre for Integrative Biodiversity Discovery

My research focuses on investigating biodiversity, species discovery, and species interactions across diverse ecosystems.

 

1) Development of cutting-edge bioinformatic tools and sequencing approaches for species discovery and integrative taxonomy. Publicly available tools include ONTbarcoder for large-scale nanopore-based DNA barcoding and IntegraTax for facilitating integrative taxonomic workflows.

 

2) Research on species interactions using metagenomics and metabarcoding to characterize ecological interactions from a wide range of environmental samples. These approaches enable the study of diet, parasites, microbiomes, and other ecological interactions, providing insights into the complex relationships between organisms and their environments.

Publications

Amorim, D.D.S., Oliveira, S.S., Balbi, M.I.P.A., Ang, Y., Torres, A., Yeo, D., Srivathsan, A., Meier, R. (2023). An integrative taxonomic treatment of the Mycetophilidae (Diptera: Bibionomorpha) from Singapore reveals 115 new species on 730km2 [Preprint]. bioRxiv. DOI: https://doi.org/10.1101/2023.09.02.555672

Srivathsan, A., Meier, R. (2024). Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing. In DeSalle, R. (Hrsg.), DNA Barcoding (223-238). New York, NY: Springer Nature. DOI: https://doi.org/10.1007/978-1-0716-3581-0_14

Hartop, E., Lee, L., Srivathsan, A., Jones, M., Peña-Aguilera, P., Ovaskainen, O., Roslin, T., Meier, R. (2024). Resolving biology’s dark matter: species richness, spatiotemporal distribution, and community composition of a dark taxon. BMC Biology, 22(1), 215. DOI: https://doi.org/10.1186/s12915-024-02010-zOpen Access

Caruso, V., Hartop, E., Chimeno, C., Noori, S., Srivathsan, A., Haas, M., Lee, L., Meier, R., Whitmore, D. (2024). An integrative framework for dark taxa biodiversity assessment at scale: A case study using Megaselia (Diptera, Phoridae). Insect Conservation and Diversity, 17(6), 968-987. DOI: https://doi.org/10.1111/icad.12762Open Access

Srivathsan, A., Ang, Y., Heraty, J.M., Hwang, W.S., Jusoh, W.F.A., Kutty, S.N., Puniamoorthy, J., Yeo, D., Roslin, T., Meier, R. (2023). Convergence of dominance and neglect in flying insect diversity. Nature Ecology & Evolution, 7(7), 1012-1021. DOI: https://doi.org/10.1038/s41559-023-02066-0Open Access

Andriienko, V., Buczek, M., Meier, R., Srivathsan, A., Łukasik, P., Kolasa, M.R. (2024). Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction [Preprint]. Microbiology. DOI: https://doi.org/10.1101/2024.04.30.591865

Srivathsan, A., Feng, V., Suárez, D., Emerson, B., Meier, R. (2023). ONTbarcoder 2.0: rapid species discovery and identification with real-time barcoding facilitated by Oxford Nanopore R10.4. Cladistics, 40(2), 192-203. DOI: https://doi.org/10.1111/cla.12566Open Access

Gygax, D., Ramirez‐Hincapie, S., Chibesa, M., Simpamba, T., Riffel, M., Riffel, T., Srivathsan, A., Nijland, R., Urban, L. (2025). Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries. PLoS ONE, 20(10), e0333994-e0333994. DOI: https://doi.org/10.1371/journal.pone.0333994Open Access

Srivathsan, A., Loh, R.K., Ong, E.J., Lee, L., Ang, Y., Kutty, S.N., Meier, R. (2023). Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community. Molecular Ecology, 32(23), 6418-6435. DOI: https://doi.org/10.1111/mec.16767Open Access

Meier, R., Srivathsan, A., Oliveira, S., Balbi, M., Y, A., Yeo, D., Kjærandsen, J., de Souza Amorim, D. (2025). “Dark taxonomy”: A new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment. Cladistics, 223–238. DOI: https://doi.org/10.1111/cla.12609Open Access

Srivathsan, A., Lee, L., Feng, V., Meier, R. (2025). Integrative Taxonomy: From FASTA Pain to Species Gain with the interactive “IntegraTax” [Preprint]. Zoology. DOI: https://doi.org/10.64898/2025.12.22.695429

Suárez, D., Arribas, P., Srivathsan, A., Meier, R., Emerson, B.C. (2024). Environmental heterogeneity, rather than stability, explains spider assemblage differences between ecosystems. Ecography, 2025(1), e07454. DOI: https://doi.org/10.1111/ecog.07454Open Access

Meier, R., Hartop, E., Pylatiuk, C., Srivathsan, A. (2024). Towards holistic insect monitoring: species discovery, description, identification and traits for all insects. Philosophical Transactions of the Royal Society B: Biological Sciences, 379(1904), 20230120. DOI: https://doi.org/10.1098/rstb.2023.0120Open Access

Torres, A., Lee, L., Srivathsan, A., Meier, R. (2025). UITOTO: a software for generating molecular diagnoses for species descriptions. Cladistics, n/a(n/a), cla.70023. DOI: https://doi.org/10.1111/cla.70023Open Access

Amorim, D.D.S., Oliveira, S.S., Balbi, M.I.P.D.A., Ang, Y., Torres, A., Yeo, D., Srivathsan, A., Meier, R. (2025). An integrative taxonomic treatment of the Mycetophilidae of Singapore reveals 115 new species from just 730 km2 (Diptera: Bibionomorpha). Integrative Systematics: Stuttgart Contributions to Natural History, 8(3), 1 – 318. DOI: https://doi.org/10.18476/2025.979589Open Access

Meier, R., Lawniczak, M.K., Srivathsan, A. (2024). Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics. Annual Review of Entomology, 70(2025), 185-204. DOI: https://doi.org/10.1146/annurev-ento-040124-014001Open Access

Vasilita, C., Feng, V., Hansen, A.K., Hartop, E., Srivathsan, A., Struijk, R., Meier, R. (2024). Express barcoding with NextGenPCR and MinION for species-level sorting of ecological samples. Molecular Ecology Resources, 24(3), e13922. DOI: https://doi.org/10.1111/1755-0998.13922Open Access

Hartop, E., Lee, L., Srivathsan, A., Jones, M., Peña-Aguilera, P., Ovaskainen, O., Roslin, T., Meier, R. (2024). Resolving Biology’s Dark Matter: Species richness, spatiotemporal distribution, and community composition of a dark taxon [Preprint]. Ecology. DOI: https://doi.org/10.1101/2024.05.07.592951

Pei, W., Feng, V., Hansen, A.K., Yan, L., Srivathsan, A., Xu, W., Sun, H., Yang, J., Zhang, X., Yang, N., Yuan, Q., Zhang, D., Meier, R. (2024). Megabarcoding reveals a tale of two very different dark taxa along the same elevational gradient [Preprint]. bioRxiv. DOI: https://doi.org/10.1101/2024.04.29.591578