# Potato_nichediversity_drivers
Data and code applicable to "Interactions between specific breeding system and ploidy play a critical role in increasing niche adaptability in a global food crop"


This submisssion includes 11 files. 



1) README.md --this is the read me file
2) CPFull_32sp_unaligned_Solanum.fas -- this file includes the full fasta alighment of all the taxa used to create the phylogeny used in the phylogentic regression
3) MAFFT_MaxiterateAligned_Solanum.fas -- this is the alignment of all the taxa used to creat the phylogeny in the manuscript. 
4) SolanumMaxiterate_MrBayes --This is the tree file of the phylogeny
5) Koeppen-Geiger-ASCII.txt -- This file includes the latitute and longitude and Koeppen Geigher climate for each occurance point used in the analysis
6) evol_drivers.csv -- this file contains all the species used in the study as rows, as columns it includes 
MS_PL -mating system and ploidy
ID - incompatible diploid	
CD - self-compatible diploid	
CP - self -compatible polyploid	
AD - asexual diploid	
AP - asexual polyploid	
outcrossing	
selfcompatible	
diploid	
triploid	
tetraploid	
pentaploid	
hexaploid	
polyploid	
one.EBN	- endosperm balance number of one
two.EBN	- endosperm balance number of two
four.EBN - endosperm balance number of four	
six.EBN	- endosperm balance number of six
mean.elev	
sd.elev	
mean.lat	
sd.lat	
mean.long	
sd.long	
Cls.cnt	-number of climates the species is present in 
Cls.mjr - the climate the majority of occurance point is in
7) evol_drivers_phylo2.csv -- This file contains all the species present in the phylogenetic regression 
MS_PL -mating system and ploidy
ID - incompatible diploid	
CD - self-compatible diploid	
CP - self -compatible polyploid	
AD - asexual diploid	
AP - asexual polyploid	
outcrossing	
selfcompatible	
diploid	
triploid	
tetraploid	
pentaploid	
hexaploid	
polyploid	
one.EBN	- endosperm balance number of one
two.EBN	- endosperm balance number of two
four.EBN - endosperm balance number of four	
six.EBN	- endosperm balance number of six
mean.elev	
sd.elev	
mean.lat	
sd.lat	
mean.long	
sd.long	
Cls.cnt	-number of climates the species is present in 
Cls.mjr - the climate the majority of occurance point is in
8) intersection_ploidy_matingsystem.Rmd -- R-markdown script to make the figures and conduct analysis
9) molclock_vcov_matrix.csv -- molecular clock variance covariance matrix for creating the dated phylogney
10) potato_ci.csv -- This file contains the occurance for each speceis as well as information of the extent of the distributions, include mean, max, min and variances of elelveation, latitde, longitude. 
11) potato_cwr_elev.csv -- This file contains all raw occurance data for the accession used in this study, including latitude, longidue and elevation
