A historic religious sanctuary may have preserved ancestral genetics of Japanese sika deer (Cervus nippon)

Abstract

Deer have been a major resource for human populations for thousands of years. Anthropogenic activities, such as hunting, have influenced the genetic structure and distribution of deer populations. In Japan, wild Japanese sika deer (Cervus nippon) have been hunted since ancient times but have also been historically protected as sacred animals in several sanctuaries. Sika deer have been protected for over a thousand years in the religious sanctuary around the Kasuga Taisha Shrine on the Kii Peninsula, located in the center of Japan. Here, we used short sequence repeats (SSR) and mitochondrial DNA (mtDNA) to investigate the genetic diversity, population structure, and demography of Japanese sika deer inhabiting the Kii Peninsula, Japan, and discuss possible anthropogenic influences. Using SSR, three distinct genetic groups were distinguished on the Kii Peninsula: an Eastern genetic group, a Western genetic group, and an isolated genetic group with individuals in the religious sanctuary of Kasuga Taisha Shrine in Nara city. The isolated genetic sanctuary group had only the mtDNA haplotype S4. The SSR genotype data suggested a newer divergence time of the genetic groups of the religious sanctuary than would have occurred as a result of Late Quaternary climate change. This time scale coincided with the establishment of the sanctuary with Kasuga Taisha Shrine. Thus, the religious protection conserved genetic variation over a thousand years.

The sacred deer conflict of management after a 1000‐year history: Hunting in the name of conservation or loss of their genetic identity

“…The present analysis revealed the existence of genetically heterogeneous populations in the protected area of Nara Park and the management area surrounding it. In the protected area, only the S4 mtDNA haplotype was found, a haplotype identified as unique to the sacred deer population in previous study (Table 1) (Takagi et al, 2023). The nuclear SSR results indicated lower genetic variation in the protected area compared to management areas (Table 1).…”

“…The mtDNA‐CR sequences excluding TRs (683 bp) were determined from 135 individuals, and a total of seven haplotypes (M1, M2, M4, S4, S5, S7, and S11) were identified across all areas (Table 1). These haplotypes were also detected in the comprehensive analysis of Kii Peninsula populations by (Takagi et al, 2023). In the protected area, all individuals sampled had only one haplotype, S4.…”

“…The nuclear SSR results indicated lower genetic variation in the protected area compared to management areas (Table 1). The low level of genetic diversity in the protected area compared to other populations on the Kii Peninsula is likely due to the spatial isolation of the population and repeated bottlenecks, discussed below (Takagi et al, 2023). In protected areas, all individuals had a high proportion of assignment to cluster 1 (Figures 4 and 5).…”

“…To determine the multi locus genotypes of nuclear SSR loci, we used 14 markers described in a previous study (Takagi et al, 2020, 2023): ABS12 (Pfister‐Genskow et al, 1995); BL42, BMC1009, BM203, BM888, BM4107, BM6438, and RM095 (Bishop et al, 1994); BOVIRBP (Abernethy, 1994. ); CSSM019 (Moore et al, 1994); ETH225 (Steffen et al, 1993); IDVGA29 (Mezzelani et al, 1995); OarFCB193 (Buchanan & Crawford, 1993); and TGLA127 (Georges & Massey, 1992).…”

“…6.12.03 (Rozas et al, 2017). The naming convention for mtDNA‐CR haplotypes follows that of (Takagi et al, 2023). The haplotype diversity ( h ) and nucleotide diversity ( π ) for each sub‐population or area were calculated using Arlequin ver.…”