What are the evolutionary origins of glyphosate resistance in Lolium rigidum in Southeast Australia? What can we infer from genetic data alone? (and with how much accuracy?)
- data_filtering: Filtering and parsing of pileup to synchronized pileup (sync) using poolgen
- exploratory_analysis: Inference of pooled Lolium rigidum polymorphism data in Southeast Australia. Detection of characteristics of glyphosate resistance selection at the genomic level.
- gudmc_benchmarking.md: Benchmarking of gudmc (Genomewide Unbiased Discernment of Modes of Convergent evolution) using quantiNemo2 forward simulations
(extra) smooth_spline_windows: Implementing Beissinger et al. 2015 smooth spline windows to compute summary statistics with greater statistical power for gudmc.
Exploratory analysis python and rust code in src/
The data consists of 246 sequenced and phenotyped Lolium rigidum pools from across Southeast Australia. Glyphosate resistance is measured as the proportion of a tested sample still remaining after treatment.
Does not contain data (except plots) - analysis cannot be entirely replicated.