INTRODUCTION

The wild African harlequin quail (Coturnix delegorguei delegorguei ) is endemic to Eastern and Southern Africa and is commonly found in grassland areas with scattered bush cover (Lewis & Pomeroy, 1989). For generations, rural smallholder farmers in Kenya have hunted quail for consumption as a complementary source of poultry protein (Urban et al., 1986, Ogada et al., 2022). However, in addition to continuous and uncontrolled harvesting, breeding attempts by rural farmers, climate change, habitat destruction by humans, migration, population bottlenecks, and inbreeding are among the main challenges facing wild African harlequin quail in Kenya (Wamuyu et al., 2017; Ogada et al., 2021). These factors interfere with the normal evolutionary processes experienced by wild African harlequin quails and may influence natural, artificial, or sexual selection (Allendorf & Hard, 2009).
In contrast, commercial quail breeds, such as the domestic Japanese quail, have become the most commonly consumed quail species globally since their domestication in the late 19th century and early 20th century (Nishibori et al., 2001). The domestic Japanese quails have undergone intense selection pressure since their domestication through modern breeding methods aimed at increased egg and meat production (Mills et al., 1997; Lukanov & Pavlova, 2020). The domestication and artificial selection of the Japanese quail have brought about genetic variation changes, altering its phenotype and increasing its size and number of eggs laid (Lukanov & Pavlova, 2020).
The main differences between wild and domestic quail species lie in the morphological, behavioral, and productivity characteristics (Chang et al., 2009). In our previous study, the wild African harlequin quail meat and eggs were found to contain higher protein content and minerals (zinc, potassium, calcium, and iron) when compared to domestic Japanese quail, helmeted guinea fowl, indigenous and commercial chickens (Chepkemoi et al., 2017). Therefore, understanding the genetic architecture of the wild African harlequin quail, among other factors, could help elucidate this finding, among other observed traits.
Genomic regions affected by selection pressures tend to develop signatures such as high allele frequencies, substantial linkage disequilibrium, increased homozygous genotypes, and long haplotypes (Nielsen, 2005; Qanbari & Simianer, 2014). Signatures of selection tests are crucial for understanding genomes as they can provide an accurate and deep understanding of the processes that affect population diversity and trait selection in the genome (Oleksyk et al., 2010; Ma et al., 2015). This study used the composite likelihood ratio test (CLR) and integrated haplotype score (iHS) methods to detect selection signatures. The CLR method uses site frequency spectrum (SFS) patterns of single-nucleotide polymorphisms (Williamson et al., 2007). In contrast, the iHS test examines the homozygosity of extended haplotypes generated by a selective sweep (Voight et al., 2006).
Quails are increasingly becoming an essential source of poultry protein in developing countries, thus helping to ensure food security (Jeke et al., 2018). At present, there is no information on the impacts of selection on the wild African harlequin quail. Furthermore, wild and domestic quails are exposed to different selection pressures; thus, it is important to investigate the effects of natural and artificial selection on the quail genome. Gaining knowledge about the selection signatures in quail genomes will form the basis for comprehending the underlying mechanisms that influence their key traits.