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. 2011;6(6):e21509.
doi: 10.1371/journal.pone.0021509. Epub 2011 Jun 29.

Inferring the population expansions in peopling of Japan

Min-Sheng Peng  1 , Ya-Ping Zhang
Affiliations

Inferring the population expansions in peopling of Japan

Min-Sheng Peng et al. PLoS One. 2011.

Abstract

Background: Extensive studies in different fields have been performed to reconstruct the prehistory of populations in the Japanese archipelago. Estimates the ancestral population dynamics based on Japanese molecular sequences can extend our understanding about the colonization of Japan and the ethnogenesis of modern Japanese.

Methodology/principal findings: We applied Bayesian skyline plot (BSP) with a dataset based on 952 Japanese mitochondrial DNA (mtDNA) genomes to depict the female effective population size (N(ef)) through time for the total Japanese and each of the major mtDNA haplogroups in Japanese. Our results revealed a rapid N(ef) growth since ∼5 thousand years ago had left ∼72% Japanese mtDNA lineages with a salient signature. The BSP for the major mtDNA haplogroups indicated some different demographic history.

Conclusions/significance: The results suggested that the rapid population expansion acted as a major force in shaping current maternal pool of Japanese. It supported a model for population dynamics in Japan in which the prehistoric population growth initiated in the Middle Jomon Period experienced a smooth and swift transition from Jomon to Yayoi, and then continued through the Yayoi Period. The confounding demographic backgrounds of different mtDNA haplogroups could also have some implications for some related studies in future.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. BSP of female effective population size (Nef) through time for total Japanese mtDNA lineages.
The bold black line represents the median population size estimate from Bayesian posterior distribution. The grey lines delimit the 95% highest posterior density (HPD) boundaries, accounting for uncertainty in the reconstructed phylogeny and substitution model parameters. Nef is plotted on a log scale and assumes a generation time of 20 years . All the lines were drawn within the lower 95% HPD boundary of the maximum time to the coalescent age.
Figure 2
Figure 2. Phylogeny and BSPs of female effective population size (Nef) through time for the major Japanese mtDNA haplogroups.
The percentage of each haplogroup is indicated in the brackets. For detailed information, please refer the legend of Figure 1.
See this image and copyright information in PMC

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