Herding dogs exhibit a distinct constellation of behaviors marked by inherent instinct and motor skills that manipulate and guide livestock in response to instructive commands and cues. Comparison of the whole-genome sequences of herding and nonherding breeds reveals signatures of positive selection associated with pathways underlying social interaction and cognitive functions. Of the strong selective sweep signals, haplotypes within ephrin type-B receptor 1 ( EPHB1 ), which is linked to locomotor hyperactivity and spatial memory, show evidence of segregation within breed lineages for the conformation versus working lines of border collies and introgression with a genetically and geographically distant herding breed of Entlebucher mountain dogs. We show that a working line–specific haplotype of EPHB1 is associated with elevated levels of chase-bite motor patterns based on a well-validated behavior survey. These findings indicate that functional selection has shaped the genetic architecture of herding breeds, which may relate to their proficiency in addressing diverse tasks and challenges in maintaining control over the herd.

This study explores the phylogeny of Korean native black goats through analysis of their complete mitochondrial DNA. The National Institute of Animal Science has gathered genetic material on purebred goats from isolated regions such as Tongyeong, Dangjin, and Jangsu, and is actively breeding them on a national level. These populations, however, are small and exhibit high inbreeding rates, highlighting the urgent need to preserve genetic diversity. The haplotype diversity within this native group is 0.659, with 39 haplotypes identified. By contrast, including international breeds in the analysis increases the overall haplotype diversity to 0.925 with 203 haplotypes identified, highlighting the limited genetic diversity among native black goats. For phylogenetic assessment, a neighbor-joining tree and median-joining network were constructed using identified haplogroups (A, B, C, D, G, and F) from prior studies. The results pinpoint the native black goats as closely related to, but distinct from, Haplogroup A with a bootstrap value of 98, establishing them as a separate clade (A’). This supports the notion of a shared ancestry with various global populations. This research provides essential data on the origins and evolutionary history of Korean native black goats, supporting conservation and breeding efforts aimed at enhancing genetic diversity.

Selective sweep approaches are widely used in livestock population genomics to identify genomic regions associated with positive selection, adaptation, and breed-specific evolutionary history. With the increasing availability of genome-wide SNP genotype data, various population genomic approaches have been applied to investigate genetic structure, genomic differentiation, haplotype diversity, and homozygosity patterns in domestic animals. However, integrated and reproducible workflows for selective sweep studies using livestock SNP genotype data remain limited. In this protocol, we introduce a step-by-step workflow for population genomic characterization and selective sweep studies using publicly available goat SNP genotype data. Representative goat breeds were used to demonstrate procedures for genotype quality control, linkage disequilibrium pruning, principal component analysis (PCA), ancestry estimation using ADMIXTURE, fixation index (FST), cross-population extended haplotype homozygosity (XP-EHH), and runs of homozygosity (ROH). This workflow provides practical guidance for livestock population genomic studies using genome-wide SNP genotype data and can be applied to various livestock and companion animal populations.