Phylogenetic Relations and High-Altitude Adaptation in Wild Boar (Sus scrofa), Identified Using Genome-Wide Data.

Simple Summary: The genetic diversity and phylogenetic relationships among wild boars in major regions of the world were assessed using genome-wide data from the Qinghai–Tibet Plateau (QTP), southern and northern regions of China, Europe, Northeast Asia, and Southeast Asia. We clarified the close phylogenetic relationship of QTP wild boars with those in southern China. In addition, genome-wide selection signal analysis based on cross-population extended haplotype homozygosity, fixation index parameters, and run of homozygosity island recognition technology was performed to obtain a series of candidate genes related to the plateau adaptability of wild boar, such as TSC2, TELO2, VCP, SLC5A1, and SLC5A4. In particular, SLC5A1 and SLC5A4 are involved in glucose homeostasis and may be the key to the plateau adaptability of wild boars. This study enhances our understanding of the genetic mechanism of high-altitude adaptation in wild boars. The Qinghai–Tibet Plateau (QTP) wild boar is an excellent model for investigating high-altitude adaptation. In this study, we analyzed genome-wide data from 93 wild boars compiled from various studies worldwide, including the QTP, southern and northern regions of China, Europe, Northeast Asia, and Southeast Asia, to explore their phylogenetic patterns and high-altitude adaptation based on genome-wide selection signal analysis and run of homozygosity (ROH) estimation. The findings demonstrate the alignment between the phylogenetic associations among wild boars and their geographical location. An ADMIXTURE analysis indicated a relatively close genetic relationship between QTP and southern Chinese wild boars. Analyses of the fixation index and cross-population extended haplotype homozygosity between populations revealed 295 candidate genes (CDGs) associated with high-altitude adaptation, such as TSC2, TELO2, SLC5A1, and SLC5A4. These CDGs were significantly overrepresented in pathways such as the mammalian target of rapamycin signaling and Fanconi anemia pathways. In addition, 39 ROH islands and numerous selective CDGs (e.g., SLC5A1, SLC5A4, and VCP), which are implicated in glucose metabolism and mitochondrial function, were discovered in QTP wild boars. This study not only assessed the phylogenetic history of QTP wild boars but also advanced our comprehension of the genetic mechanisms underlying the adaptation of wild boars to high altitudes. [ABSTRACT FROM AUTHOR]