README

Data and code for:

"Multiple source locations and long-distance dispersal explain the rapid spread of a recent amphibian invasion"

Submitted as an Article in Heredity





This upload contains 12 R scripts that collectively were used to analyse the generated SNP data. 


This upload also contains 25 input and output datasets. A brief summary of each dataset below:

- This upload contains five .vcf files.
	* BF_1701.recode.vcf: main vcf file obtained after bio-informatic processing
	* BF_1701_ExclFS.recode.vcf: vcf file with full-sibs removed
	* BF_1701_ExclFS_Tot.recode.vcf: vcf file with full-sibs removed, and only containing localities used for the paper
	* BF_1701_ExclFS_Cl1.recode.vcf: vcf file with full-sibs removed, and only containing localities from cluster 1 (obtained through STRUCTURE analysis)
	* BF_1701_ExclFS_Cl2.recode.vcf: vcf file with full-sibs removed, and only containing localities from cluster 2 (obtained through STRUCTURE analysis)

- BF_PCA_ExclFS.csv contains information for the principle coordinate analysis. It contains the:
	* ID of each locality (column B).
	* each individual sampled and sequences, expressed as .bam files (column E).
	* scores for each individual for each PcoA axis (column F-KC).

- Filtered2009Occurrences_POSTREVISION.csv contains cocurrence records used for geographic profiling.

- latlon_cl1.csv contains latitude and longitude (in WGS84) of each sampled individual in STRUCTURE cluster 1.

- latlon_cl2.csv contains latitude and longitude (in WGS84) of each sampled individual in STRUCTURE cluster 2.

- latlon_tot.csv contains latitude and longitude (in WGS84) of each sampled individual in STRUCTURE in all populations.

- Migration_Ratio.csv contains the imigration to emgiration ratio (RI/E) obtained through DivMigrate for each population included in the study.

- Pops_C1.csv contains ordered locality IDs for each individual in localities in STRUCTURE cluster 1.

- Pops_C2.csv contains ordered locality IDs for each individual in localities in STRUCTURE cluster 2.

- Pops_Tot.csv contains ordered locality IDs for each individual in all localities.

- Populations.csv contains summary information of all sampled locations and individuals, and what individuals/locations where used for what analysis.

- Pops_ExclFS.csv contains summary information of all sampled locations and individuals, and what individuals/locations where used for what analysis. Full-sibs were already removed.

- Pops_ExclFS_ExclARE.csv contains similar information as Pops_ExclFS.csv, but one population outside the Grote Nete river valley was removed.

- Ratios_Sources.csv contains information of Immigration, Emmigration, their Ratio, and coordinates of all localities included in the study. It also contains the coordinates of the source locations as predicted by geographic profiling.

- radiator_data_20240126@1738_genepop2.gen genepop file for analyses

-Populaties_SK_GBS_2_woareMN_ExclFS_converted.txt text-file containing for each individual the latitude and longitudes (in Belge Lambert 72 projected coordinate reference system)

- joblist_100000_240124.txt contains the joblist for STRUCTURE analysis on a High Performance Computer (related to R script: "Script_STRUCTURE_HPC.R)

- rivers_proj.shp: a shapefile containing the major rivers for calculating water way distances