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Abstract High‐throughput sequencing has changed many aspects of population genetics, molecular ecology and related fields, affecting both experimental design and data analysis. The software packageangsdallows users to perform a number of population genetic analyses on high‐throughput sequencing data.angsduses probabilistic approaches which can directly make use of genotype likelihoods; thus,SNPcalling is not required for comparative analyses. This takes advantage of all the sequencing data and produces more accurate results for samples with low sequencing depth. Here, we presentangsd‐wrapper, a set of wrapper scripts that provides a user‐friendly interface for runningangsdand visualizing results.angsd‐wrapper supports multiple types of analyses including estimates of nucleotide sequence diversity neutrality tests, principal component analysis, estimation of admixture proportions for individual samples and calculation of statistics that quantify recent introgression.angsd‐wrapper also provides interactive graphing ofangsdresults to enhance data exploration. We demonstrate the usefulness ofangsd‐wrapper by analysing resequencing data from populations of wild and domesticatedZea.angsd‐wrapper is freely available fromhttps://github.com/mojaveazure/angsd-wrapper. 

Many SNPs are predicted to encode deleterious amino acid variants. These slightly deleterious mutations can provide unique insights into population history, the dynamics of selection, and the genetic bases of phenotypes. This is especially true for domesticated species, where a history of bottlenecks and selection may affect the frequency of deleterious variants and signal a “cost of domestication”. Here, we investigated the numbers and frequencies of deleterious variants in Asian rice (Oryza sativa), focusing on two varieties (japonica and indica) and their wild relative (O. rufipogon). We investigated three signals of a potential cost of domestication in Asian rice relative to O. rufipogon: an increase in the frequency of deleterious SNPs (dSNPs), an enrichment of dSNPs compared with synonymous SNPs (sSNPs), and an increased number of deleterious variants. We found evidence for all three signals, and domesticated individuals con- tained 􏰚3–4% more deleterious alleles than wild individuals. Deleterious variants were enriched within low recombin- ation regions of the genome and experienced frequency increases similar to sSNPs within regions of putative selective sweeps. A characteristic feature of rice domestication was a shift in mating system from outcrossing to predominantly selfing. Forward simulations suggest that this shift in mating system may have been the dominant factor in shaping both deleterious and neutral diversity in rice.