Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome

Abbreviation of species names in each folder: Palb, P. alba; Pade, P. adenopoda; Pdav, P. davidiana; Ptra, P. tremula; Ptrs, P. tremuloides; Prot, P. rotundifolia; Pqio,P. qiongdaoensis.

1. FST
Relative divergence (FST) for pairwise species comparisons was calculated for all sites with 100 Kbp non-overlapping windows. 

2. dxy
Absolute divergence (dxy) was calculated for all sites with 100 Kbp non-overlapping windows. 

3. Nucleotide diversity
Nucleotide diversity (π) was calculated for all sites with 100 Kbp non-overlapping windows. 

4. Derived allele frequency
The derived frequencies of 4 different functional categories. Each folder contains seven Populus resluts

5. Derived_allele_statistics
The statistics of homozygous and  heterozygous derived alleles for loss of function, deleterious, tolerated and synonymous variants for each individual. The last two individuals in each file are outgroups 

6. dsuite-dinvestigate
The outputs of 10 trios using program Dinvestigate from Dsuite. The sliding window is 50 SNPs, and the step is 20 SNPs.

7. Recombination rate
The result of population-scaled recombination rate was calculated by LDhat v2.2.

8. Volcanofinder
Genome-wide scans of introgression sweeps within each species was implemented using VolcanFinder v.1.0 with the Model over 10 Kbp non-overlapping windows.

9. ihh12
phased SNPs were used to computed ihh12 by selscan v1.3.0. 

10 populus162.phased.recode.vcf.gz
SNPs were phased with Beagle v.4.1 for the 162 non-hybrid individuals.

11 populus227.snp.rm_indel.para_filter.biallelic.GQ30.max_miss20.bed.recode.vcf.gz 
The vcf of 227 Populus samples.