These are the source files for our paper on Celtis genetic diversity using SSRs. Note that final formatting and additional edits were applied directly to the submitted manuscript in Word doc format. Those changes aren't reflected here.

File List

• celtis.Rmd: The manuscript source, in RMarkdown (plain text) format
• plantarum.json: My bibliography database, required only to insert citations into the compiled manuscript.
• data_prep.R: The main script used to read and process the data
• systematic-botany.csl: The Systematic Botany citation format specification. Needed only to format citations and the literature cited section of the manuscript.
• celtis.pdf: The manuscript, compiled into a pdf for easier reading.
• data/:
  • cssr2018-09-06.txt: microsatellite raw data, in tab-delimited format. Sample.Name: code for each sample; Marker: locus; Allele.1-4: size of each allele at that locus.
  • flow.csv: raw flow cytometry data as generated from flowPloidy. channel: filename, including sample name. countsA, countsB: cell counts in each histogram peak. sizeA, sizeB: mean/location of each peak. cvA, cbB: coefficient of variation for each peak. rcs: residual Chi Square. linearity: linearity parameter for NLS model. pg: estimated nuclear DNA content in picograms. ploidy: individual ploidy level (blank = diploid).
  • popTable.csv: metadata for each individual. sample: individual code. population: population code. species: field ID (not to be trusted!). ploidy (ploidy from flow cytometry analysis). Genotype (not used). Latitude/Longitude: coordinates of population.
  • dipAssign.csv: Admixture assignments from STRUCTURE, in tab-delimited format. sample: sample code. pop1, pop2: estimated admixture from each population. population: which of the two populations the sample was assigned to (i.e., had > 0.7 admixture proportion from that species). "mix" indicates hybrids.
  • struc-out.csv: STRUCTURE probabilities for identifying optimal K value.
  • celtis_morph.csv: morphological data. Some of the variables are coded in differenet ways in different columns. See the code in data_prep.R for the correct way to import it
  • maps/: directory for maps. Most of the map data is downloaded directly in from the internet by running this script. At least until the raster package is deprecated, then all bets are off.
    • greatlakes.shp: a vector layer for plotting the outline of the great lakes on my maps.
• ssr-screening/:
  • ssr-screening.pdf: Our manuscript describing primer development for this project. APPS no longer publishes primer notes, so we don't have somewhere to publish it.
• structure-all: directory for files associated with the STRUCTURE analysis of the complete (mixed ploidy) data.
  • celtis-structure.org: Details of the STRUCTURE analysis. This is an orgmode file. This is a plain text format, you can open and read it in any text editor. If that editor is Emacs, you'll have extra feature available to you, but this is not necessary to read the text and review the code.
  • mainparams and extraparams: run options for STRUCTURE
  • structure.sh: the script used to run STRUCTURE, looping over all the replicates for each K value.
  • all2_1.csv, all3_1.csv and all4_1.csv: The admixture/assignment results for one replicate of the STRUCTURE runs for K = 2, 3, and 4.
  • ksummary.csv: "Estimated Ln Prob of Data", extracted from STRUCTURE output and used to calculate Evanno's Delta values.