Bottlenecks, drift and differentiation: the population structure and demographic history of sika deer (Cervus nippon) in the Japanese archipelago

AbstractThe Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

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Population dynamics in the Japanese Archipelago since the Pleistocene

10.21203/rs.3.rs-145519/v1 ◽

2021 ◽

Author(s):

Fuzuki Mizuno ◽

Jun Gojobori ◽

Masahiko Kumagai ◽

Hisao Baba ◽

Yasuhiro Taniguchi ◽

...

Keyword(s):

Demographic History ◽

Cultural Transition ◽

Rice Agriculture ◽

Hunter Gatherers ◽

Japanese Archipelago ◽

Mitogenome Sequence ◽

History Of ◽

Complete Mitogenome ◽

Genetic Continuity ◽

The Japanese Archipelago

Abstract The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome sequence from Palaeolithic human remains. We also obtained those of Neolithic (hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome is potentially an ancestral type of haplogroup M, suggesting it is not only connected to present-day Japanese but also present-day East Asians. There were no changes in the gene pool from the hunting-gathering (Jomon) to the farming cultures (Yayoi), and this is different from in Europe, where there was no genetic continuity between hunter-gatherers and farmers. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

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Habitat use and the coexistence of the sika deer and the Japanese serow, sympatric ungulates from Mt. Asama, central Japan

Mammalia ◽

10.1515/mammalia-2019-0150 ◽

2020 ◽

Vol 84 (6) ◽

pp. 503-511

Author(s):

Hayato Takada ◽

Riki Ohuchi ◽

Haruko Watanabe ◽

Risako Yano ◽

Risako Miyaoka ◽

...

Keyword(s):

Habitat Use ◽

Sika Deer ◽

Cervus Nippon ◽

Niche Differentiation ◽

Ecological Niches ◽

Dwarf Bamboo ◽

Central Japan ◽

Habitat Mosaic ◽

The Japanese Archipelago ◽

Japanese Serow

AbstractDifferential resource use allows for diverse species to specialize in ecological niches and thus coexist in a particular area. In the Japanese archipelago, increasing sika deer (Cervus nippon, Temminck 1836) densities have excluded the Japanese serow (Capricornis crispus, Temminck 1836), but in places where deer population densities are low, the two species coexist. We wanted to better understand their habitats and how these two ungulates manage to coexist. We evaluated the role of habitat use in the coexistence of these two sympatric ungulates on Mt. Asama, central Japan. Deer frequently used the dwarf bamboo-rich communities in autumn and winter, and their habitat use was not associated with topography. Serows frequently used deciduous broadleaf shrub-rich communities and steep slopes throughout the year. Consequently, their habitat use was significantly different in terms of vegetation and topography. Niche breadth suggests that deer tend to be generalists, whereas serows tend to be specialists. Niche differentiation in habitat use between deer and serows may make the coexistence of these similarly sized ungulates possible in Japanese mountainous zones. Therefore, the fine-grained habitat mosaic of different vegetation and topography areas might be the underlying feature that allows the coexistence of these two species.

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Population structure and demographic history of a tropical lowland rainforest tree speciesShorea parvifolia(Dipterocarpaceae) from Southeastern Asia

Ecology and Evolution ◽

10.1002/ece3.284 ◽

2012 ◽

Vol 2 (7) ◽

pp. 1663-1675 ◽

Cited By ~ 15

Author(s):

Hiroko Iwanaga ◽

Kosuke M. Teshima ◽

Ismael A. Khatab ◽

Nobuyuki Inomata ◽

Reiner Finkeldey ◽

...

Keyword(s):

Population Structure ◽

Demographic History ◽

Tropical Lowland ◽

History Of ◽

Lowland Rainforest ◽

Tropical Lowland Rainforest

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Reassessing the concept of the ‘Neolithic’ in the Jomon of Western Japan

Documenta Praehistorica ◽

10.4312/dp.34.1 ◽

2007 ◽

Vol 34 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Simon Kaner ◽

Takeshi Ishikawa

Keyword(s):

Large Scale ◽

Population Densities ◽

Neolithic Transition ◽

Japanese Archipelago ◽

History Of ◽

Western Japan ◽

The Japanese Archipelago ◽

Lower Population ◽

Late Palaeolithic

The concept of the Mesolithic/Neolithic transition is difficult to apply in the Japanese archipelago. The earliest pottery usage occurs in late Palaeolithic contexts. Holocene foragers lived in stable, permanent village settlements and constructed large scale monuments, and the first real ‘agriculture’ arrived as part of a cultural package which also included metallurgy. This paper will examine the use of the term ‘Neolithic’ in the history of Japanese archaeology, with particular emphasis on what happened in the western part of the archipelago in the latter part of the Jomon period (c. 5000 BC – c. 500 BC). Recent investigations in Kyushu and Western Honshu are leading to a re-assessment of the nature of Jomon culture and society in this region, traditionally considered to have ‘lagged behind’ the more developed societies of the eastern part of the archipelago, expressed in part through much lower population densities.

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