Data and code from: African suid genomes provide insights into the local adaptation to diverse African environments

The contents of this dataset has been generated and used in the project and the paper "African suid genomes provide insights into the local adaptation to diverse African environments".In this study, we assembled high-quality genomes of a common warthog (Phacochoerus africanus), a red river hog (Potamochoerus porcus), as well as an East Asian Diannan small-ear pig (Sus scrofa). We conducted whole genome alignment (WGA) to identify orthologous genes and uses them to perform phylogenetic tree, divergence time, and positive selection analyses.

The WGA, the 14,221 original protein-coding sequnce alignments, the 10,969 resulted maximum likelihood trees, and the alignment of four-fold degenerate sites of 10,969 orthologous genes that were used for gene tree construction were included in this dataset. Based on these data, we constructed the phylogeny for the Suidae family, and we detected species-specific variations and selective signals in the African wild suids.