Genomic analysis on pygmy hog reveals extensive interbreeding during wild boar expansion

Abstract

Wild boar ( Sus scrofa ) drastically colonized mainland Eurasia and North Africa, most likely from East Asia during the Plio-Pleistocene (2–1Mya). In recent studies, based on genome-wide information, it was hypothesized that wild boar did not replace the species it encountered, but instead exchanged genetic materials with them through admixture. The highly endangered pygmy hog ( Porcula salvania) is the only suid species in mainland Eurasia known to have outlived this expansion, and therefore provides a unique opportunity to test this hybridization hypothesis. Analyses of pygmy hog genomes indicate that despite large phylogenetic divergence (~2 My), wild boar and pygmy hog did indeed interbreed as the former expanded across Eurasia. In addition, we also assess the taxonomic placement of the donor of another introgression, pertaining to a now-extinct species with a deep phylogenetic placement in the Suidae tree. Altogether, our analyses indicate that the rapid spread of wild boar was facilitated by inter-specific/inter-generic admixtures.

DNA barcode approaches to reveal interspecies genetic variation of Indian ungulates

“…Pygmy hog (P. salvania) and wild boar (S. scrofa) population are sisters to each other. Recent findings of a genomic analysis on pygmy hog reveal extensive interbreeding of wild boar (Liu et al 2019). Indian spotted deer (A. axis) and hog deer populations are clustered together as sister species in clade 3 but paraphyletic with swamp and Sambar deer.…”

Ghost Introgression: Spooky Gene Flow in the Distant Past

“…While expanding out of Asia, this species probably interbred with several other taxa, potentially incorporating locally adapted loci from these taxa into its genome. [ 31 ] This would have facilitated expansion and establishment into new areas where the wild boar consequently outcompeted the local species. This hypothetical scenario is reminiscent of the expansion of humans out of Africa.…”

A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model

“…n the past few decades, with advanced sequencing technologies, huge volumes of omics data have been produced and used to interpret the underlying genetic mechanisms of biological processes. For example, genome resequencing data were used to study the domestication history of species [1][2][3] ; RNA-seq data were used to locate functional genes for specific tissues [4][5][6] ; and metagenomics data helped to interpret the molecular pathways that underlie the interactions between organisms and the microbial environment [7][8][9] . In addition, proteomics 10 , metabolomes 11 , methylation 12 , miRNA 13 , and other omics data have all participated in our understanding of the mechanisms of various biological processes 14 .…”