Yuttapong Thawornwattana

PhD student, Mallet Lab

Department of Organismic and Evolutionary Biology, Harvard University, USA

📬 ythawornwattana[at]g.harvard.edu

Hi there 👋

🦟 Currently working on the phylogeny and evolution of malaria mosquitoes (Anopheles) in North America
🪰 Research areas: phylogenetics, computational statistics, evolutionary genomics
🐞 Publications, Google Scholar, NCBI Bibliography, ORCID, Web of Science
🐝 Currently learning: genome assembly, infectious disease epidemiology
🐛 Looking to collaborate on mosquito phylogeny and evolution, inference of gene flow and introgression
🪲 Ask me about phylogenetics and gene flow!
💬 Talks

Training & Research Experience

🔩 2024-2026. Research Fellow, UCL Department of Genetics, Evolution and Environment (GEE), UK (with Ziheng Yang)
🦋 2020-2024. PhD Organismic and Evolutionary Biology (OEB), Harvard University, USA (with James Mallet and Ziheng Yang)
🦠 2018-2020. Research assistant, Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Thailand
🧬 2014-2018. MPhil Genetics, Evolution and Environment, UCL GEE, UK (with Ziheng Yang)
🛠 2012-2013. MSc Computational Statistics and Machine Learning, UCL Computer Science , UK
🐛 2009-2012. BSc Biological Sciences, UCL GEE, UK

Publications

Google Scholar profile, NCBI Bibliography

Mallet J, Seixas FA, Thawornwattana Y (2024). Species, Concepts of. In Scheiner, S. M., editor, Encyclopedia of Biodiversity (Third Edition), 7:531-545. Elsevier. [doi:10.1016/B978-0-12-822562-2.00022-0] [RG]
Thawornwattana Y, Seixas FA, Yang Z, Mallet J. (2023) Major patterns in the introgression history of Heliconius butterflies. eLife. [doi:10.7554/eLife.90656] [data]
Thawornwattana Y, Huang J, Flouri T, Mallet J, Yang Z. (2023) Inferring the direction of introgression using genomic sequence data. Mol Biol Evol., 40(8):msad178. [doi:10.1093/molbev/msad178] [Heliconius data]
Huang J, Thawornwattana Y, Flouri T, Mallet J, Yang Z. (2022) Inference of gene flow between species under misspecified models. Mol Biol Evol., 39(12):msac237. [doi:10.1093/molbev/msac237]
Thawornwattana Y, Seixas FA, Yang Z, Mallet J. (2022) Full-likelihood genomic analysis clarifies a complex history of species divergence and introgression: the example of the erato-sara group of Heliconius butterflies. Syst Biol., 71(5):1159–1177. [doi:10.1093/sysbio/syac009] [data]
Aiewsakun P, Ruangchai W, Thawornwattana Y, Jaemsai B, Mahasirimongkol S, Homkaew A, Suksomchit P, Dubbs P, Palittapongarnpim P. (2022) Genomic epidemiology of Streptococcus agalactiae ST283 in Southeast Asia. Sci Rep., 12(1):4185. [doi:10.1038/s41598-022-08097-0]
Netikul T, Thawornwattana Y, Mahasirimongkol S, Yanai H, Maung HMW, Chongsuvivatwong V, Palittapongarnpim P. (2022) Whole-genome single nucleotide variant phylogenetic analysis of Mycobacterium tuberculosis lineage 1 in endemic regions of Asia and Africa. Sci Rep., 12(1):1565. [doi:10.1038/s41598-022-05524-0] [phylogeny: Asia/Africa/Oceania; phylogeny: global 1; phylogeny: global 2]
Netikul T, Palittapongarnpim P, Thawornwattana Y, Plitphonganphim S. (2021) Estimation of the global burden of Mycobacterium tuberculosis lineage 1. Infect Genet Evol., 91:104802. [doi:10.1016/j.meegid.2021.104802]
Thawornwattana Y, Dong HT, Phiwsaiya K, Sangsuriya P, Senapin S, Aiewsakun P. (2021) Tilapia lake virus (TiLV): Genomic epidemiology and its early origin. Transbound Emerg Dis., 68(2):435–444. [doi:10.1111/tbed.13693]
Thawornwattana Y, Mahasirimongkol S, Yanai H, Maung HMW, Cui Z, Chongsuvivatwong V, Palittapongarnpim P. (2021) Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 2. Microb Genom., 7(11):000697. [doi:10.1099/mgen.0.000697] [phylogeny: discovery; phylogeny: discovery+test]
Ajawatanawong P, Yanai H, Smittipat N, Disratthakit A, Yamada N, Miyahara R, Nedsuwan S, Imasanguan W, Kantipong P, Chaiyasirinroje B, Wongyai J, Plitphonganphim S, Tantivitayakul P, Phelan J, Parkhill J, Clark TG, Hibberd ML, Ruangchai W, Palittapongarnpim P, Juthayothin T, Thawornwattana Y, Viratyosin W, Tongsima S, Mahasirimongkol S, Tokunaga K, Palittapongarnpim P. (2019) A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing genotypes. Sci Rep., 9:13718. [doi:10.1038/s41598-019-50078-3]
Thawornwattana Y, Dalquen D, Yang Z. (2018) Coalescent analysis of phylogenomic data confidently resolves the species relationships in the Anopheles gambiae species complex. Mol Biol Evol., 35(10):2512–2527. [doi:10.1093/molbev/msy158]
Thawornwattana Y, Dalquen D, Yang Z. (2018) Designing simple and efficient Markov chain Monte Carlo proposal kernels. Bayesian Anal., 13(4):1037–1063. [doi:10.1214/17-BA1084]
dos Reis M, Thawornwattana Y, Angelis K, Telford MJ, Donoghue PC, Yang Z. (2015). Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Curr Biol., 25(22):2939–2950. [doi:10.1016/j.cub.2015.09.066] [data]

Talks

2023/09. “Inferring the direction of gene flow from genomic data” at Boston Evolutionary Genomics Supergroup Annual Retreat 2023, the Broad Institute (chalk talk)
2023/06. “Inferring phylogenies using full-likelihood multispecies coalescent with introgression” at Evolution conference (Albuquerque, New Mexico, USA) [slides, with builds]
2021/06. “Full-likelihood analysis of divergence and introgression in the erato-sara group of Heliconius” at Heliconius Seminar (now Lepinars) [slides]
2020/12. “Whole-genome sequencing for strain typing in practice” at CENMIG Workshop, Mahidol University [slides]
2020/11. “Population genomics of Mycobacterium tuberculosis” at the Department of Microbiology, Faculty of Science, Mahidol University [slides]
2020/07. “Population genomics of Mycobacterium tuberculosis” at MAEMOD journal club [slides]
2018/11. “Next generation phylogenetics: Building trees from whole genome data” at the Division of Medical Bioinformatics, Faculty of Medicine Siriraj Hospital, Mahidol University [slides]
2018/08. “Resolving the species relationships in the Anopheles gambiae species complex from whole genome data” at the Department of Microbiology, Faculty of Science, Mahidol University [slides]

On Github

make-3s-data: Phase multilocus data and sample 3 sequences per locus for 3s analysis
mtbtyper: Genotype strains of Mycobacterium tuberculosis isolates from whole-genome sequence data
group-specific-variants: Identify group-specific single-nucleotide variants from multiple sequence alignment
dvrcaller: Delect DVR (direct variable repeat) deletion pattern in the CRISPR region of Mycobacterium tuberculosis using whole-genome sequence data
snpplet: Nextflow pipeline for short variant calling (SNPs) from paired-end short-read genome sequencing data

Tutorials

Bayesian linear regression (2018) - slides
Dirichlet process mixture (DPM) model (2018) - slides
TensorFlow tutorial (2016)

Current projects

Phylogeny and evolution of Anopheles mosquitoes (Diptera: Culicidae: Anophelinae) in North America: specimens
Multispecies coalescent methods for inferring gene flow from genomic data
Bioinformatics pipeline for generating multilocus data from short-read sequencing data
Introgression histories in Heliconius butterflies (Lepidoptera: Nymphalidae: Heliconiinae: Heliconiini)
Taxonomic catalogue of Heliconiinae (Lepidoptera: Nymphalidae)