Postglacial population expansion of Japanese macaques (Macaca fuscata) inferred from mitochondrial DNA phylogeography

Abstract

We investigated the diversity and phylogeography of mitochondrial DNA (mtDNA) in Japanese macaques (Macaca fuscata), an endemic species in Japan that has the northernmost distribution of any non-human primate species. DNA samples from 135 localities representing the entire range of this species were compared. A total of 53 unique haplotypes were observed for the 412-bp partial mtDNA control region sequence, with length variation distinguishing the two subspecies. Clustering analyses suggested two putative major haplogroups, of which one was geographically distributed in eastern Japan and the other in western Japan. The populations in the east showed lower mtDNA diversity than those in the west. Phylogeographical relationships of haplotypes depicted with minimum spanning network suggested differences in population structure. Population expansion was significant for the eastern but not the western population, suggesting establishment of the ancestral population was relatively long ago in the west and recent in the east. Based on fossil evidence and past climate and vegetation changes, we inferred that the postulated population expansion may have taken place after the last glacial period (after 15,000 years ago). Mitochondrial DNA showed contrasting results in both variability and phylogenetic status of local populations to those of previous studies using protein variations, particularly for populations in the periphery of the range, with special inference on habitat change during the glacial period in response to cold adaptation.

The influence of climatic oscillations during the Quaternary Era on the genetic structure of Asian black bears in Japan

“…The study suggested that three populations, L, M and N (WNK, EC and WC, respectively, in Ishibashi and Saitoh's study), became isolated from the K population (ENK in Ishibashi and Saitoh's study) on the eastern side of the river, resulting in two populations that retreated to different refugia during the last glacial period. A similar phylogeographic pattern has been observed in other large mammal species such as the Japanese macaque (Kawamoto et al, 2007), Japanese wild boar (Sus scrofa; Watanobe et al, 2003) and sika deer (Cervus nippon; Tamate et al, 1998;Nagata et al, 1999), all of which exhibit two mtDNA lineages, with the distributions of the haplotypes of each lineage separated in the Kinki region. Given these data, Ishibashi and Saitoh (2004) suggested that the black bear would also have two Japanese lineages, separated at the Yura River.…”

“…The border between the Western and Eastern cluster areas of the black bear appears to be Lake Biwa, which is approximately 100 km east of the border that separates two major lineages identified in Japanese macaques (Kawamoto et al, 2007), Japanese wild boar (Watanobe et al, 2003) and sika deer (Nagata et al, 1999). The distinct lineages in wild boar are thought to have resulted from multiple migrations of the species from the Asian Continent to Japan across land bridges that repeatedly formed between the Korean Peninsula and Kyushu Island during past glacial periods (Watanobe et al, 2003).…”

“…For example, Japanese macaques (Macaca fuscata) exhibit remarkably lower variability in mitochondrial DNA (mtDNA) in northern than in southern Honshu (Kawamoto et al, 2007). This suggests that the macaques rapidly expanded their distribution into the northern area during the recovery of the broad-leaved forests after the end of the last glacial period.…”

Mitochondrial DNA Diversity among Three Subpopulations of Cynomolgus Macaques (Macaca fascicularis) Originating from the Indochinese Region

“…As an important genetic marker, maternally-inherited mitochondrial DNA (mtDNA) warrants special attention for genetic investigations such as intraspecies variation [35], population structure [10,12,13,20,34], phylo-, population structure [10,12,13,20,34], phylo- [10,12,13,20,34], phylo-, phylogeography [5,23,26,37], and demography [24] in ma- [5,23,26,37], and demography [24] in ma-, and demography [24] in ma- [24] in main macaque species. In particular, the mtDNA control (D-loop) region is composed of �00 to 1,000 base pairs (bp) and contains hypervariable segments 1 (HVI) and 2 (HVII).…”

“…Recently, sequence-based phylogenetic relationships and genetic structures in cynomolgus macaques were reported by analyzing 149 haplotypes on the mtDNA Dloop HVI segment [35] and 70 haplotypes on the HVII segment [5]. Kawamoto et al suggested that the Mauritian population, which originated from the island of Java in Indonesia, shows less genetic diversity than the other populations based on the HVII segment [13]. Genetic diversity analyses of the mtDNA have mainly been undertaken among geographically isolated populations from different regions, within single regional populations, and in different macaque species [5,13,35].…”