Current sika deer effective population size is near to reaching its historically highest level in the Japanese archipelago by release from hunting rather than climate change and top predator extinction

Abstract

Deer species were repeatedly overexploited and protected for their meat and fur and they had strong impacts on ecosystems and human society by damaging crops and planted trees, altering vegetation, deer vehicle collision, and increasing ticks that vector zoonosis. To accomplish appropriate population management, the historical demography and its main driver need to be clarified. In this study, we estimated the historical demography of effective population size ( Ne) of sika deer ( Cervus nippon Temminck) in Hokkaido and Hyogo Prefectures of the Japanese archipelago. We estimated Ne of >100 generations from present (2020) by folded single nucleotide polymorphisms (SNP) frequency spectra and, within 100 generations from present, by linkage disequilibrium between SNP. In Hokkaido, Ne drastically increased around 3.0 ky BP and decreased around 100–150 years ago with the assumption of their generation length as 4 or 9 years. The Ne decreased by a 10th before the recent bottleneck. In Hyogo, Ne increased around 80 and 1 ky BP and decreased around 100–250 years ago. Ne decreased by a 100th before the recent bottleneck. After these recent bottlenecks, Ne of both regions recovered and the current Ne has nearly reaches the highest level of the last 100 ky BP. Literature survey and paleoclimate indicates that the decrease and increase of Ne of sika deer in Japanese archipelago may be caused by variations in the hunting activity of humans rather than climate change or the top predator extinction.

An empirical test of the estimation of historical effective population size using Drosophila melanogaster

“…The method of Santiago et al (2020) has now been applied to different species, particularly in the last year, including insects, such as honeybees (Sang et al, 2022); birds, such as Black Robin (von Seth et al, 2022); fishes, such as turbot, seabream and seabass (Saura et al, 2021), Baltic herring (Atmore et al, 2022), pikeperch (De Los Ríos-Pérez et al, 2022, coho salmon (Martinez et al, 2022), catfish (Coimbra et al, 2023) and sailfish (Ferrette et al, 2023); wild mammals, such as grey wolf (Pacheco et al, 2022), killer whales (Kardos et al, 2023), sika deer (Iijima et al, 2023), scimitar-horned oryx (Humble et al, 2023) and gorilla (Alvarez-Estape et al, 2023); humans (Bird et al, 2023); domestic species, such as pigs (Krupa et al, 2022), cattle (Jin et al, 2022;Magnier et al, 2022), sheep (Djokic et al, 2023;Drzaic et al, 2022), horse (Criscione et al, 2022) and chicken (Gao et al, 2023;Liu et al, 2023); plants, such as walnut (Ding et al, 2022); crustaceans, such as Daphnia (Wersebe & Weider, 2023) and fungi (Singh et al, 2021). As suggested by Santiago et al (2020), the method is generally reliable for about 200 generations in the past, although…”

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

“…The low genetic diversity of sika deer in the protected area of Nara City probably results from multiple past population declines. Declines in the genetic diversity of Japanese sika deer in several areas of the Japanese archipelago have been attributed to population declines around the 19th century (Goodman et al, 2001; Iijima et al, 2023; Konishi et al, 2017; Nabata et al, 2004). The historical protected area in Nara City is no exception.…”

“…Conversely, to maintain the lineage of sacred deer, we must restore habitat gaps through intensive eradication around the sanctuary. Over the past several 100 years, hunting pressure has resulted in the decline and fragmentation of the distribution range of sika deer in the Japanese archipelago (Iijima et al, 2023; Tsujino et al, 2010). This has also affected the population dynamics of other species, for example, on the Kii Peninsula, the speciation of dung beetles ( Phelotrupes auratus ), which feed heavily on deer dung (Araki & Sota, 2023), coincided with the fragmentation of deer populations (Takagi et al, 2023).…”

Large ungulates will be present in most of Japan by 2050 owing to natural expansion and human population shrinkage

“…The distribution of large ungulates has continued to expand in recent years, especially in developed countries, and it is urgent to understand why (Carden et al 2011; Sales et al 2017; Cretois et al 2021; Iijima et al 2023). Factors related to their expansion include climate change (Ohashi et al 2016), land use change (Acevedo et al 2011; Carpio et al 2021), and hunting (Keuling et al 2008; Cromsigt et al 2013; Linnell et al 2020; Iijima et al 2023). Because global climate change is expected to continue, it may accelerate the expansion of their distribution (Ohashi et al 2016; Markov et al 2019).…”