README-FILE

Description of data subfolders and their contained files:

In general, inside each folder you will find all relevant data and scripts to reproduce the contents of each Figure or Table, as well as general statistics given in the text.

It should be possible to run the various R scripts in each subfolder without changing path names if you uncompress the zip-file into your HOME-folder (path: ~/) on a MacOSX machine.
If the run fails, first adjust the locations of the necessary input files (they are all contained in each of the subfolders, respectively, and listed).

Subfolders:



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*SAMPLES:

 contains:
	
	# A tab-delimited text file that summarizes the sampling information for each individual (names, sampling locations, genotype information)
	**DATA	Sample_summary_table.txt


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*MANTEL:

 contains:
	
	# An R-Script to perform Mantel-tests(Mantel 1967) on both the whole dataset and each of the three clades (Fig. S1) separately from the listed DATA-files.
	**SCRIPT	MANTEL.R

	# Pairwise geographic distances (input for MANTEL.R)
	**DATA		ALL_GEOGRAPHY_rectangular.txt
	**DATA		CLADE1_GEOGRAPHY_rectangular_metric.txt
	**DATA		CLADE2_GEOGRAPHY_rectangular_metric.txt
	**DATA		CLADE3_GEOGRAPHY_rectangular_metric.txt

	# Pairwise genetic distances (input for MANTEL.R)
	**DATA		ALL_MCL_rectangular.txt
	**DATA		CLADE1_MCL_rectangular.txt
	**DATA		CLADE2_MCL_rectangular.txt
	**DATA		CLADE3_MCL_rectangular.txt
	
	# Output produced by the script
	**FIGURE	MANTEL.pdf


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*MOLECOL_KRAEMER_FIG2:

 contains:

	# An R-Script to sample pairwise genetic relatedness across geographic scales from a total of 147 individuals from the listed DATA-file. These are divided into 12 clone pairs at each of the five metric scales without replacement over the entire dataset, so that there are a total of 60 pairs (and N= 120 individuals), that are sampled only once over the entire dataset. This is to avoid staticial autocorrelation typical for pairwise genetic data comapred across spatial scales (for which a Mantel test is typically applied), which in turn  allows for rigorous, paramteric tests of signficance across geographic scales.
	**SCRIPT	Drawing_samples.Rmd
	**DATA		CloneDistances.txt

	# A spreadsheet that contains pairwise social compatibility derived through colony-merger-phenotyping assays on agar plates.
	**DATA		Phenotyping_data.xlsx
	
	# An R-Script to plot data of pairwise genetic and social compatibility to recapitulate Figures 2A+D from the two given DATA-files to produce the three output FIGURE-files.
	**SCRIPT	FIG2_PLOTTING.R
	**DATA		Input_FF_anova_metric_update_restrict.csv
	**DATA		Input_SK_anova_metric_update_restrict.csv
	**FIGURE	Fig2A.pdf
	**FIGURE	Fig2D.pdf
	**FIGURE	Fig2AD.pdf


----------------------
*MOLECOL_KRAEMER_FIG3:

 contains:

	# An R-script to plot geographic over genetic distance to recapitulate Figure 3 from the listed DATA-files. It also calculates the covariance statistic mentioned in the figure legend.
	**SCRIPT	FIG3_PLOTTING.R
	**DATA		Combined_metric.csv
	**DATA		CLADE1_GEOGRAPHY_rectangular_metric.txt
	**DATA		CLADE1_MCL_rectangular.txt
	**DATA		CLADE2_GEOGRAPHY_rectangular_metric.txt
	**DATA		CLADE2_MCL_rectangular.txt
	**DATA		CLADE3_GEOGRAPHY_rectangular_metric.txt
	**DATA		CLADE3_MCL_rectangular.txt
	**FIGURE	FIG3.pdf


----------------------
*MOLECOL_KRAEMER_FIGS1:

 contains:

	# Input file (*.phy) to infer the phylogenetic tree in PHYML for each sequence type.
	**DATA		FIGS1_PHYML_Input.phy

	# Output file (*.nwk) from PHYML to reproduce Fig. S1.
	**DATA		FIGS1_PHYML_tree.nwk


----------------------
*MOLECOL_KRAEMER_FIGS2:

 contains:

	# Input file (*.fas) to infer the phylogenetic tree in MEGA which was the basis for Fig. S2.
	**DATA		FIGSS2_INPUT.fas

	# Output file (*.nwk) from MEGA to reproduce Fig. S2.
	**DATA		FIGS2_tree.nwk


----------------------
*MOLECOL_KRAEMER_FIGS3:

 contains:

	# Input file (*.nex) to infer the phylogenetic network in SPLITSTREE which was the basis for Fig. S3.
	**DATA		FIGS3_SplitsTree_Input.nex

	# Output file (*.nex) from SPLITSTREE to reproduce Fig. S3.
	**DATA		FIGS3_SplitsTree_Output.nex

