About
The evolution of modern human populations has been accompanied by dramatic changes in environment and lifestyle. Positive selection, the driving force behind adaptive evolution, is the process whereby a genetic variant rapidly increases in frequency in a population due to the fitness advantage of one allele over the other.
Singleton density score (SDS) method was developed by Field et al. in 2016 to identify recent genetic natural selection over a timescale of the past 2,000-3,000 years (1). Integrated haplotype score (iHS) was another recent positive selection method on a timescale of tens of thousands of years, which was developed by Voight et al. in 2006 (2).
In our database RePos, we integrated SDS and iHS results from our own NyuWa dataset (3) as well as publicly available datasets UK10K (1), TOPMed (4), and 1KGP (5). As for population ancestry groups, we have gathered SDS results from Han Chinese (NyuWa), modern Britons (UK10K), European (TOPMed), African (TOPMed) and East Asian (TOPMed), and iHS results from Han Chinese (NyuWa) and 26 populations from 1KGP.
The website provides search of selection signal records by variants and gene regions. Genome browser JBrowse v2 (6) was utilized to visualize these selection data with gene and variant annotations. All data are also accessible in the download page.
1. Field, Y., Boyle, E.A., Telis, N., Gao, Z., Gaulton, K.J., Golan, D., Yengo, L., Rocheleau, G., Froguel, P., McCarthy, M.I., et al. (2016). Detection of human adaptation during the past 2000 years. Science.
2. Voight, B.F., Kudaravalli, S., Wen, X., and Pritchard, J.K. (2006). A Map of Recent Positive Selection in the Human Genome. PLOS Biology 4, e72. 10.1371/journal.pbio.0040072.
3. Zhang, P., Luo, H., Li, Y., Wang, Y., Wang, J., Zheng, Y., Niu, Y., Shi, Y., Zhou, H., Song, T., et al. (2021). NyuWa Genome resource: A deep whole-genome sequencing-based variation profile and reference panel for the Chinese population. Cell Reports 37, 110017. 10.1016/j.celrep.2021.110017.
4. Taliun, D., Harris, D.N., Kessler, M.D., Carlson, J., Szpiech, Z.A., Torres, R., Taliun, S.A.G., Corvelo, A., Gogarten, S.M., Kang, H.M., et al. (2021). Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature 590, 290–299. 10.1038/s41586-021-03205-y.
5. Johnson, K.E., and Voight, B.F. (2018). Patterns of shared signatures of recent positive selection across human populations. Nat Ecol Evol 2, 713–720. 10.1038/s41559-018-0478-6.
6. JBrowse 2: A modular genome browser with views of synteny and structural variation | bioRxiv https://www.biorxiv.org/content/10.1101/2022.07.28.501447v1.
