Nat. Selection (Pond) Track Settings
 
Natural selection analysis from Sergei Pond's research group   (All Variation and Repeats tracks)

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 Negative Selection  Sites of negative selection implicated in data from Sergei Pond's research group   Schema 
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 Positive Selection  Sites of positive selection implicated in data from Sergei Pond's research group   Schema 


updated Note: Updated May, 2021

Description

This track shows data from Sergei Pond's research group, updated several times between 2020 and 2022, with results published in 2022. The current dataset is from February 2022 and is scheduled to be updated soon. Contact us or Sergei if you believe that the data shown is too outdated for your analyses.

The authors use several statistical techniques to identify selection sites of interest in SARS-CoV-2 data from GISAID.

Display Conventions and Configuration

This track has two subtracks:

Positive Selection: "On average along interior tree branches, this site has a dN/dS>1 is accumulating non-synonymous changes (some of which might have a functional impact, but most probably don't) faster relative to synonymous changes than would be expected under neutral evolution."

Negative Selection: "On average along interior tree branches, this site has a dN/dS<1, meaning that it is conserved, i.e. non-synonymous changes might be selected against. Note that sites with no changes (i.e. perfectly conserved sites) cannot be detected by dN/dS based methods"

Methods

The CSV used to generate the genomic coordinates of selection sites was parsed and the position, gene, site_in_gene, score, and type fields were used to generate the resulting fields provided for each site in the data.

References

Pond et al, 2020 "Natural selection analysis of SARS-CoV-2/COVID-19"

Pond et al, 2020 "Natural selection analysis of SARS-CoV-2/COVID-19, V2"

Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P et al. Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function. Mol Biol Evol. 2022 Apr 11;39(4). PMID: 35325204; PMC: PMC9037384