Development of paternally‐inherited Y chromosome simple sequence repeats of sika deer and their application in genetic structure, artificial introduction, and interspecific hybridization analyses

The effect of sex‐biased dispersal in mammalian ecology and evolution can be elucidated by focusing on maternally or paternally inherited DNA polymorphisms. In sika deer, the genetic structure of the maternal lineage has been clarified by studies based on mitochondrial DNA variation. However, the genetic structure of the paternal lineage has not been well analyzed due to the limited number of point mutations in Y chromosome sequences. In this study, we focused on mutations of highly polymorphic simple sequence repeats (SSRs) in the Y chromosome and developed 16 Y chromosome SSR markers to evaluate male‐biased dispersal in sika deer. In total, 55 alleles and 31 multi‐locus haplotypes were detected from these 16 loci, revealing clear genetic differentiation among populations (F′ST = 0.783). In particular, there were unique alleles for the native individuals on Tanegashima and Yakushima Islands and introduced exotic individuals from Taiwan. These markers are highly useful for evaluating not only historical male‐mediated dispersal, genetic structure, and demography of the native populations in Japan, but also the impact of artificial introductions on hybridization, especially the introgression of alleles from escaped farmed individuals to native populations. The YSSR markers developed in this study were shown to be robust markers capable of revealing variation between inter‐ and intra‐species lineages of sika deer. Population genetic analysis using these markers can provide important data about the role of historical male‐mediated dispersal in genetic structure and demography as well as the detection of male lineages in hybrids.