We welcome contributions from any individual, whether code, documentation, or issue tracking. All participants are expected to follow the code of conduct for this project.
Authors and Contributions:
- Bethany A. Zumwalde (BAZ)- co-led the writing, provided mentoring and advising, performed several analyses, led revisions after peer review
- Bailie Fredlock Munoz (BFM)- performed lab work, wrote first draft of manuscript
- Ross A. McCauley (RM)- field sampling and discussions
- Drew Duckett (DD)- field sampling, contributed to lab work, discussions, assisted with writing
- Emma Suzuki Spence (ESS)- performed some lab work, provided mentoring and advising
- Emily Beckman Bruns (EBB)- performed the geospatial analysis, contributed to writing and revisions
- Sean Hoban (SH)- project lead, field work, performed analysis and created figures, co-led the writing and revisions
All .gen files are genpop files that contain the genetic data. The differences among the .gen files are just different subsets of the data or different ways of combining populations, described as follows. File list:
- QH_total_garden_by_pop.gen contains all the genotypes ex situ and in situ. Each population is separated by POP. The East populations come first, and the West populations come next, and then the garden populations
- QH_total_garden_by_pop_E.gen contains all the genotypes from the in situ populations and all the ex situ samples from East populations. Each population is separated by POP. The East populations come first, and the West populations come next, and then the garden populations
- QH_total_garden_by_pop_W.gen contains all the genotypes from the in situ populations and all the ex situ samples from West populations. Each population is separated by POP. The East populations come first, and the West populations come next, and then the garden populations
- QH_total_garden_for_FST.gen contains all the genotypes ex situ and in situ. The only difference from "garden_by_pop" is that all the East populations are merged under one POP and all the West populations are merged under one POP. Each garden population is separated by POP. (The purpose of this was to calcualte FST between each garden and the East and West.) As with the others, the East populations come first, and the West populations come next, and then the garden populations
- QH_wild.gen contains only genotypes from wild populations (for subsampling) There are also several .txt files
- samples_in_gardens.csv lists all the garden samples, and which populations, regions and maternal trees they come from
- reduced_prop_capture_lm.txt is the proportion of alleles captured in each allele category by each botanic garden (reduced means only considering alleles with >2 copies in the dataset)
- all_prop_capture_lm.txt is the proportion of alleles captured in each allele category by each botanic garden (all means considering all alleles no matter the number of copies)
- ex_vs_in_situ_11_species.csv and ex_vs_in_situ_dr_0_11_species.csv are the results of allele capture of the 11 species analyzed in Hoban et al 2020 (Proceedings B)
- Folders for each of the species analyzed in Hoban et al 2020 contain the subsampling results from these 11 species (note these are large files!)