Amrita Srivathsan

Tasks

Researcher in bioinformatics for species discovery and species interactions

Research

My research focuses on investigating species interactions and biodiversity in various ecosystems. (1) I develop bioinformatic tools and employ cutting-edge technologies such as Nanopore for species discovery. A key focus has been to develop user friendly tools for large scale NGS barcoding projects, such as ONTbarcoder to obtain accurate consensus barcodes using nanopore sequencing. (2) I furthermore use metagenomics and metabarcoding to characterize species interactions using different types of environmental samples. This allows us to study the diet, parasites and microbiomes and provide valuable insights into the complex relationships between species and their surrounding environment.

Publications (Selection)

Srivathsan A, Ang Y, Heraty JM, Hwang WS, Jusoh WFA, Kutty SN, Puniamoorthy J, Yeo D, Roslin T, Meier R (2023). Convergence of dominance and neglect in flying insect diversity. Nature Ecology and Evolution 7: 1012-1021 doi: 10.1038/s41559-023-02066-0

Srivathsan A, Loh RK, Ong EJ, Lee L, Ang Y, Kutty SN, Meier (2022). Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community. Molecular Ecology doi: 10.1111/mec.16767.

Srivathsan A, Lee L, Katoh K, Hartop E, Kutty SN, Wong J, Yeo D, Meier R (2021). ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biology 19: 217. doi: 10.1186/s12915-021-01141-x

Ang A, Roesma DI, Nijman V, Meier R, Srivathsan A, Rizaldi (2020). Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species. Scientific Reports 10(1): 9396. doi: 10.1038/s41598-020-66007-8

Srivathsan A, Hartop E, Puniamoorthy J, Lee WT, Kutty SN, Kurina O, Meier R (2019). Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing. BMC Biology 17: 96. doi: 10.1186/s12915-019-0706-9

Srivathsan A, Nagarajan N, Meier R (2019). Boosting natural history research via metagenomic clean-up of crowdsourced feces. PLoS Biology 17(11): e3000517. doi: 10.1371/journal.pbio.3000517

Srivathsan A, Baloğlu B, Wang W, Tan WX, Bertrand D, NG AHQ, Boey EJH, Koh JJY, Nagarajan N, Meier R (2018). A MinION™‐based pipeline for fast and cost‐effective DNA barcoding. Molecular Ecology Resources 18(5): 1035-1049. doi: 10.1111/1755-0998.12890

Srivathsan A, Ang A, Vogler AP, Meier R (2016). Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate. Frontiers in Zoology 13: 17. doi: 10.1186/s12983-016-0150-4

Srivathsan A, Sha JCM, Vogler AP, Meier R (2015). Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf‐feeding monkey (Pygathrix nemaeus). Molecular Ecology Resources 15(2): 250-261. doi: 10.1111/1755-0998.12302

Srivathsan A, Meier R (2012). On the inappropriate use of Kimura‐2‐parameter (K2P) divergences in the DNA‐barcoding literature. Cladistics 28(2): 190-194. doi: 10.1111/j.1096-0031.2011.00370.x

For more see Amrita Srivathsan on Google Scholar