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Genetic analysis reveals unique and enduring traits in Nara's famous deer: Nara University of Education led group uncover genotype that has thrived for over 1,000 years with human protection


A team of researchers, including Ayako Takano, a researcher, and Professor Harumi Torii from the Center for Natural Environmental Education at Nara University of Education, Ayako Murakami, a graduate student, and Professor Hidetoshi Tamate from Yamagata University's Graduate School of Science and Engineering, Toshihito Takagi, a graduate student, and Associate Professor Shingo Kaneko from Fukushima University's Graduate School of Symbiotic Systems Science and Engineering, have discovered that the population of Japanese sika deer in Nara Park has a unique genotype that sets it apart from the closely related surrounding populations. This conclusion was reached through a genetic analysis of the Japanese sika deer in Nara Park and throughout the Kii Peninsula. The team's study reveals that, although surrounding populations underwent periods of extinction, the population in Nara Park has been protected and maintained for more than 1,000 years. Its findings are expected to provide significant insights into the symbiotic relationship between nature and humans. The team's results were published in the January 30th issue of The American Society of Mammalogy.

The Japanese sika deer is a wild animal symbolic of Japan. It can be found widely throughout the country, from Hokkaido to the Nansei Islands. Although it has long been hunted, it has also been protected as an object of worship at Kashima Shrine and Kasugataisha Shrine. Populations are also believed to have been historically influenced by human activities. It is worth noting that during the modern era, the distribution of Japanese sika deer experienced a temporary decline due to overhunting and severe winters after the Meiji period (1868‐1912). However, the population recovered and expanded its distribution during the following 40 years.

Given the influence of historical human activities on wildlife, the research group aimed to examine the impacts on these deer in the Kii Peninsula — including in Nara Park, where they have long been protected — through genetic analysis.

The study used samples (muscle and blood) from 294 Japanese deer across 30 sites in 8 regions throughout the Kii Peninsula collected between 2000 to 2016. The researchers then conducted a lineage analysis using mitochondrial DNA D‐loop sequences.

The analysis identified 18 genotypes (haplotypes) within the Kii Peninsula. Types M1 to M6 were found over a wide area. However, types S1 to S12 were found only in specific areas. Of these genotypes, type S4 was found only in the Nara Park population and was unique. It differed from M1, a type widely distributed throughout the Kii Peninsula, by only one base. This finding indicates that S4 is native to the Kii Peninsula and may have remained only in Nara Park due to past population contractions.

The research team then analyzed the population structure using nuclear DNA SSRR regions. The genetic groups were broadly divided into Nara Park, the western peninsula, and the eastern peninsula. The western and eastern groups were found to be mixed in the central part of the peninsula. Only the Nara Park population was found to be unique, while the other areas had mixed populations due to individual movement.

After accumulating genetic variations, the team then estimated the time of divergence for each genetic group.

After comparing the genotypes with the assumed gene mutation rates, they found that the Nara Park Group first diverged from the Eastern Nara Peninsula Group in the 6th century (Kofun to Asuka Periods). It then diverged a second time from the Eastern Peninsula Group to the Western Peninsula Group in the 16th century (Muromachi to Sengoku Periods). These results indicate that changes occurred over a range of time periods and involved human activity.

The Japanese sika deer once inhabited the entire Kii Peninsula but were separated into groups due to isolation and extinction from human activities. The Nara Park population became isolated, so it likely became protected since at this point. The second divergence occurred during a period of warfare when distribution areas and populations declined. The population then recovered again, creating the current mixed population.

The team's research began around the year 2000, when Torii asked Tamate for help. The results have been made open access ( with support for graduate students provided through funding from Fukushima University.

Toshihito Takagi, one of the student participants in the study, stated, 'We believe that the findings of this study are essential for the future conservation management of deer in Nara and the surrounding areas. Currently, various problems are arising there, including the deteriorating health of the deer and injuries due to traffic accidents. I hope this paper will serve as a starting point for understanding their nature and formulating effective measures to protect and manage them.'

This article has been translated by JST with permission from The Science News Ltd. ( Unauthorized reproduction of the article and photographs is prohibited.

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