The impact of habitat fragmentation on genetic structure of the Japanese sika deer (Cervus nippon) in southern Kantoh, revealed by mitochondrial D‐loop sequences

Abstract

In southern Kantoh, Japanese sika deer (Cervus nippon) are distributed discontinuously due to large urban areas and developed road networks. To assess the impact of habitat fragmentation on sika deer subpopulations, we examined mitochondrial D-loop sequences from 435 individuals throughout southern Kantoh. About 13 haplotypes were detected, and their distributions revealed spatial genetic structure. Significant genetic differentiation was observed among seven of eight subpopulations. We found no significant correlation between pairwise F ST and geographical distance among subpopulations. Genetic diversity indices suggested that seven of eight subpopulations had probably experienced population bottlenecks in the recent past. Therefore, and in the light of the results of a nested clade analysis of these haplotypes, we conclude that recent fluctuations in population size and the interruption of gene flow due to past and present habitat fragmentation have played major roles influencing the spatial genetic structure of the sika deer population. This is the first evidence of spatial genetic population structure in the highly fragmented sika deer population in Honshu, Japan.

Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey

“…Nonetheless, comparisons with results from studies conducted at a similar geographical scale indicate that Scottish Highland red deer are more diverse than Japanese Sika deer in Kantoh (average h ¼ 0.37; Yuasa et al, 2007) and white-tailed deer (Odocoileus virginianus) from the coastal plain of Georgia and South Carolina (average h ¼ 0.41; Purdue et al, 2000). The low genetic diversity found in these two studies in comparison to our study can be attributed to the impact of severe habitat fragmentation in Sika deer in the Kantoh (Yuasa et al, 2007) and to overharvesting of white-tailed deer from the coastal plain of Georgia and South Carolina in the early nineteenth century (Purdue et al, 2000). Genetic diversity found in Scottish Highland red deer was within the range of that found in other genetic surveys of European populations of deer conducted at larger geographical scales (for example, Hartl et al, 2003 andFeulner et al, 2004 for red deer; Vernesi et al, 2002 andRoyo et al, 2007 for roe deer).…”

Effects of time and environmental conditions on the quality of DNA extracted from fecal samples for genotyping of wild deer in a warm temperate broad-leaved forest

“…For wild ungulate species, most genetic research so far has relied on tissue samples from hunted individuals (Tamate et al 1998;Tamate et al 2000;Schettler et al 2006;Yamada et al 2007;Yuasa 2007;Yuasa et al 2007;Henry-Roitberg 2008;Pérez-Espona et al 2009;Barbosa and Carranza 2010).…”

Evaluation of the genetic structure of sika deer (Cervus nippon) in Japan's Kanto and Tanzawa mountain areas, based on microsatellite markers

“…These studies focused on the southern Kanto area (Yuasa 2007;Yuasa et al 2007), Nikko National Park (Fukui et al 2001), and the island of Kinkazan (Tamate et al 2000). These studies focused on the southern Kanto area (Yuasa 2007;Yuasa et al 2007), Nikko National Park (Fukui et al 2001), and the island of Kinkazan (Tamate et al 2000).…”

“…The sika deer of the Japanese archipelago include six subspecies (Ohtaishi 1986), which can be clearly separated into two different groups based on mitochondrial DNA D-loop region analysis: those inhabiting northern and southern Japan (Nagata et al 1999). The mitochondrial D-loop region has been used in many studies for analyzing phylogenetic relationships among Japanese sika deer (Nagata et al 1999;Yamada et al 2006;Yuasa et al 2007;Yoshio et al 2008;Takiguchi et al 2012;Terada et al 2013), but analysis of this DNA only yields information about maternal inheritance. Microsatellites are more powerful tools for analyzing genetic population structures (Yuasa 2007;Olano-Marin et al 2014;Hoffmann et al 2016;Zachos et al 2016) because these markers are located at multiple chromosomal loci and are rich in polymorphisms.…”

“…Several previous studies have explored the genetic features of sika deer using various DNA markers. These studies focused on the southern Kanto area (Yuasa 2007;Yuasa et al 2007), Nikko National Park (Fukui et al 2001), and the island of Kinkazan (Tamate et al 2000). However, the detailed genetic structure of sika deer inhabiting the overall Kanto area remains poorly understood.…”