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During adaptation, the strength of selection on a gene may vary in different individuals (cancer setting) or species (comparative genomic setting), two scenarios:
For example: species adaptation to cold environment. Both scenarios are possible: (1) In some environment, more fatty foods, and selection of more fat to adapt; in other environments, selection of more hair and furs. (2) Same environmental pressure, but selection on either hair/furs or fat. In either case, species may have different hair and fat.
Our goal is to identify genes that drive adaption given the environment or genes that adapting to environment through a certain phenotype. We consider one gene a time and test if it drives adaptation under certain environment or via the given the phenotype. Let \(S_i\) be the sequence (mutation) of individual/species \(i\), \(w_i\) be the selection coefficient on the gene in \(i\). \(E_i\) be the environment for \(i\). Our model is \(E_i \rightarrow w_i \rightarrow S_i\). When studying a certain phenotype of the individual \(P_i\), we treat the phenotype as a marker of selection and our model is \(P_i \rightarrow w_i \rightarrow S_i\). In both cases,\(P(S_i| w_i)\), and \(w_i = f(P_i)\) or \(w_i = f(E_i)\), where we can use \(dN/dS\) to model how the sequence/mutation depends on selection. For simplicity, use \(E_i\) to represent individual level selection (either environment of phenotype).
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
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[5] workflowr_1.6.2 R6_2.5.0 rlang_0.4.11 fansi_0.5.0
[9] stringr_1.4.0 tools_4.1.0 xfun_0.24 utf8_1.2.2
[13] git2r_0.28.0 htmltools_0.5.1.1 ellipsis_0.3.2 rprojroot_2.0.2
[17] yaml_2.2.1 digest_0.6.27 tibble_3.1.6 lifecycle_1.0.1
[21] crayon_1.4.2 later_1.2.0 vctrs_0.3.8 promises_1.2.0.1
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[29] stringi_1.7.3 compiler_4.1.0 pillar_1.6.4 httpuv_1.6.1
[33] pkgconfig_2.0.3