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Japan considered from the hypothesis of farmer/language spread

  • Chinese Academy of Sciences Institute of Vertebrate Paleontology and Paleoanthropology

Abstract and Figures

Formally, the Farming/Language Dispersal hypothesis as applied to Japan relates to the introduction of agriculture and spread of the Japanese language (between ca. 500 BC-AD 800). We review current data from genetics, archaeology, and linguistics in relation to this hypothesis. However, evidence bases for these disciplines are drawn from different periods. Genetic data have primarily been sampled from present-day Japanese and prehistoric Jomon peoples (14,000-300 BC), preceding the introduction of rice agriculture. The best archaeological evidence for agriculture comes from western Japan during the Yayoi period (ca. 900 BC-AD 250), but little is known about northeastern Japan, which is a focal point here. And despite considerable hypothesizing about prehistoric language, the spread of historic languages/dialects through the islands is more accessible but difficult to relate to prehistory. Though the lack of Yayoi skeletal material available for DNA analysis greatly inhibits direct study of how the pre-agricultural Jomon peoples interacted with rice agriculturalists, our review of Jomon genetics sets the stage for further research into their relationships. Modern linguistic research plays an unexpected role in bringing Izumo (Shimane Prefecture) and the Japan Sea coast into consideration in the populating of northeastern Honshu by agriculturalists beyond the Kanto region.
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Japan considered from the hypothesis of farmer/
language spread
Elisabeth de Boer1, Melinda A. Yang2, Aileen Kawagoe3and Gina L. Barnes4*
Faculty of East Asian Studies, Ruhr-Universität Bochum, Bochum, Germany,
Department of Biology, University of
Richmond, Richmond, Virginia, USA,
Department of Social Studies, New International School of Japan, Tokyo, Japan and
SOAS, University of London, London, UK
*Corresponding author. Email:
Formally, the Farming/Language Dispersal hypothesis as applied to Japan relates to the introduction of
agriculture and spread of the Japanese language (between ca. 500 BCAD 800). We review current
data from genetics, archaeology, and linguistics in relation to this hypothesis. However, evidence bases
for these disciplines are drawn from different periods. Genetic data have primarily been sampled from
present-day Japanese and prehistoric Jōmon peoples (14,000300 BC), preceding the introduction of
rice agriculture. The best archaeological evidence for agriculture comes from western Japan during the
Yayoi period (ca. 900 BCAD 250), but little is known about northeastern Japan, which is a focal
point here. And despite considerable hypothesizing about prehistoric language, the spread of historic lan-
guages/ dialects through the islands is more accessible but difficult to relate to prehistory. Though the lack
of Yayoi skeletal material available for DNA analysis greatly inhibits direct study of how the pre-agricul-
tural Jōmon peoples interacted with rice agriculturalists, our review of Jōmon genetics sets the stage for
further research into their relationships. Modern linguistic research plays an unexpected role in bringing
Izumo (Shimane Prefecture) and the Japan Sea coast into consideration in the populating of northeastern
Honshu by agriculturalists beyond the Kantōregion.
Keywords: Japanese language; Yayoi agriculture; Jōmon genetics; language/farming hypothesis; MumunYayoi migrations
Media summary: How Jōmon genetics, Mumun migrations, and Japanese dialect differences inform
farming/language spread hypothesis in Japan
The Jōmon period (see Figure 1) is one of the longest post-Palaeolithic archaeological periods in the
world, sustained by a huntinggatheringfishinghorticultural subsistence pattern (Habu, 2004). The
introduction of rice agriculture into the Genkai Bay area of North Kyushu (Figure 1) from around
1000 BC marks the beginning of the Yayoi period. Wet-rice technology was introduced by Mumun
(plain pottery) culture migrants from the southern Korean Peninsula relatively early, ca. 1000 BC,
in the Peninsulas Mumun period (1500300 BC). These migrants were not Yayoi, they were Mumun.
The term Yayoi has four uses, which can create much confusion. First, it is the designation of the
period beginning with the introduction of rice agriculture around 1000 BC until the advent of the
Mounded Tomb Culture in the third century AD. Yayoi is a period designation exclusive to Japan;
it includes both farmers and huntergatherers and entails the agricultural transition in a time-
transgressive and regionally disparate process. Second, Yayoi peoplemay refer to anyone living in
the Japanese Islands in the Yayoi period, or third, Yayoi may refer specifically to admixed people
© The Author(s), 2020. This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://crea-, which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original
work is properly cited.
Evolutionary Human Sciences (2020), 2, e13, page 1 of 20
(Mumun + Jōmon in varying in proportions and across great distances). Fourth, Yayoi may indicate
acculturation: the adoption of (rice) agriculture (and other continental material culture) by
Jōmon-lineage people in the Yayoi period. All of these conflicting aspects of Yayoi must be kept in
mind and clearly defined in any discussion.
Figure 1. Map of Japan: prefectures, districts, and placenames mentioned in the text, with Japanese archaeological periodizations.
Sources: Periodization from Barnes (2015), tables 1.6, 1.8. Map by TheOtherJesse [public domain], via Wikimedia Commons, modi-
fied by GLB []
2 Elisabeth de Boer et al.
Upon the Mumun migrantsarrival, it is assumed from artefactual, skeletal morphological, and
genetic evidence that many took partners from the resident Jōmon population, leading to mixed
descendants and to cultural transformation. These generational admixedfarmers then spread
out from North Kyushu into the rest of the Japanese Islands, meeting more local Jōmon-lineage peo-
ples with further admixing taking place. It is common in the literature to label the admixed farmers as
Yayoibecause they carried the new culture based on rice, while increasingly recognizing that
Jōmon-lineage peoples (distinguished as Epi-Jōmon in the north, but included within Yayoiin the
south) survived well into historical times without substantial admixture. The mixing of these two
populations is recognized as the Dual Structure Hypothesis of the modern mainland Japanese popu-
lation (Hanihara, 1991,2000).
The first section below reports on Jōmon genetics as a basis for further research on Yayoi admix-
tures. Despite the 13,000-year Jōmon history entailing multiple cultural formations and temporal
trends, archaeologists tend to treat the Jōmon as a homogeneous people unadmixed with mainland
East Asians and Austronesians since their separation from each other in the Palaeolithic. Genetic
research is disabusing us of that approach, revealing potential Jōmon contacts with coastal mainland
East Asians before the arrival of Mumun migrants; these data mirror archaeological evidence of con-
tact. This is enlightening for its own sake, particularly in tracing connections between the Jōmon and
continental peoples. However, in terms of investigating Yayoi admixtures, it makes the issue much
more complicated. As more Yayoi-period genomic data becomes available, we may then be able to
track the regional spread of continental genes through the Japanese archipelago. The addition of
new Yayoi-period genomic data is vital, as new waves of immigration from the Korean Peninsula in
the succeeding Kofun and Nara periods have enhanced the continental contribution in the modern
Japanese, making it difficult to use present-day genomes to effectively study population movement
and admixture in the Yayoi period.
The second section focusses on the spread of agriculture from west to east through the Japanese
Islands. The major topic of study in this spread has been the adoption of irrigated wet-rice agriculture.
It has been assumed that this technology was spread by admixed farmer-migrants. In contrast, new
studies are documenting instances of non-irrigated (swamp, dryland) rice and millet cultivation
that may be earlier (e.g. Nasu & Momohara, 2016; Shitara & Takashe [sic], 2014). These authors
assume that local Final Jōmon and Epi-Jōmon peoples were the cultivators, although some may
have become farmers of irrigated wet rice later. The relationships between cultivation technologies
and ethnic populations are often unclear, making the next step in the analysis, on language spread,
The third section deals with language spread. Prehistoric language as such is inaccessible, but the
fact that nowadays all languages on the islands except Ainu are related to Japanese makes it absolutely
clear that the population that brought wet-rice agriculture to Japan must have been speakers of
proto-Japanese. (Proto-Japanese is the ancestral language from which all modern varieties of
Japanese descended.) Proto-Japanese split into several dialects, and then Ryūkyūan split off from
the Kyūshūdialect. Evidence for the latter scenario has been growing in recent years. (For an overview
see De Boer 2017.) Although the Ryūkyūan varieties form independent languages now, their split from
the Kyūshūdialect makes them in origin dialects of Japanese.
Proto-Japanese is postulated to have developed on the continent (Whitman, 2011; Miyamoto,
2016; Robbeets, 2005,2017), and it is hypothesized to have had spread throughout the archipelago
with the admixed Yayoi people practising irrigated rice agriculture. This accords well with the farm-
ing/language dispersal hypothesis (Renfrew, 1987; Bellwood & Renfrew, 2002). Problems, however,
include exactly when and how this spread took place, whether it was indeed only associated with
rice agriculture or also with other grain crops, and what Jōmon or Epi-Jōmon language(s) might
have been replaced or pushed out by which dialect of Japanese. With the general lack of Yayoi
DNA and written linguistic data, it is difficult to match food production techniques, genomic iden-
tity and language type.
Evolutionary Human Sciences 3
Jōmon genetics
The transition from the Jōmon to the Yayoi periods marked a transition in the material culture of
Japan, with the appearance and increase of tools, artefacts and archaeobotanical remains associated
with agriculture. Studies have long associated this transition with the migration of Mumun people
through the Korean peninsula into the closest island in the Japanese archipelago, Kyushu
(Hammer & Horai, 1995; Hanihara, 1991). Early assessments using cranial and dental morphology
and genetics of humans and their commensals led to the Dual Structure model (Hanihara, 1991),
for which a key component is the argument that present-day Japanese are a mixture of populations
indigenous to Japan since the Palaeolithic and later migrants from mainland Asia. Many studies,
mostly using present-day genomes of indigenous populations in the archipelago (i.e. Ainu, Ryūkyū)
as a proxy for Jōmon-related ancestry, found genetic patterns that suggest that the present-day
Japanese populations are admixed, supporting that aspect of the Dual Structure model (Jeong,
Nakagome, & Di Rienzo, 2016a; Jinam et al., 2015; Nakagome et al., 2015).
Advances in DNA sequencing methods have allowed access to genetic material for studying popu-
lation demographic history in the Japanese archipelago. Uniparental markers were some of the earliest
used to infer population history; these include mitochondrial DNA (mtDNA), which exists outside the
nucleus, and the non-recombining portion of the Y-chromosome. The primary units considered when
studying these markers are haplogroups, which are variants of a DNA segment that derives from the
same common ancestor, and they can provide information on a populations genetic history.
Since uniparental transfer results in no recombination, it is straightforward to reconstruct
phylogenetic trees and assign a haplogroup to the mtDNA or Y-chromosome region (Haber,
Mezzavilla, Xue, & Tyler-Smith, 2016). Sets of haplogroups are now well annotated and easily iden-
tifiable in newly sequenced individuals using many tools and databases (e.g. ISOGG, 2019;
Weissensteiner et al., 2016). If they are identified to be at high frequency in a localized area but in
low frequency elsewhere, the origin of the haplogroup, or the common ancestor, can be inferred to
have derived from that region. While the lack of recombination allows simple haplogroup assignation,
it also means that it is a single data point representing population history, and stochastic events or
sex-biased migration patterns can lead to inaccurate inference of the true population history
(Nordborg, 1998; Rosenberg & Nordborg, 2002).
In contrast, the nuclear genome undergoes recombination, which means that small segments of
each chromosome have effectively independent histories. Study of a single diploid genome (i.e. the
23 pairs of chromosomes in the cell nucleus) can be interpreted as study of small portions of thou-
sands of different individuals, resulting in high statistical power for inferring the history of the popu-
lation(s) represented by those individuals. Thus, sampling genome-wide is imperative for assessing the
accuracy of the demographic relationships inferred from uniparental markers.
The ability to extract and sequence ancient DNA (aDNA) has revolutionized the study of human
prehistory, allowing direct sampling of past populations and revealing genetic variation no longer
observed today. Post-mortem degradation of DNA makes it very difficult to sequence aDNA, so
the greater numbers of mtDNA makes it much easier to extract and sequence. The earliest ancient
DNA studies in humans were for mtDNA (e.g. Krings et al., 1997), including from a Jōmon individual
as early as 1989 (Horai et al., 1989) and Yayoi individuals as early as 1995 (Oota, Saitou, Matsushita, &
Ueda, 1995). In fact, the majority of ancient DNA studies on Jōmon individuals have been on mtDNA
(Schmidt & Seguchi, 2014).
Only recently have ancient nuclear genomes been retrieved from individuals from Japan. Ancient
genomes have been published from human remains at different sites (Sanganji, Ikawazu, and
Funadomari associated with Jōmon material culture; Shimo-Motoyama associated with Yayoi material
culture; Figure 1). Two partial genomes sequenced from the Sanganji shellmound in Tōhoku were of
3000-year-old individuals (Kanzawa-Kiriyama et al., 2017). Genome-wide data have also been
retrieved for a 2700-year-old individual from Ikawazu (McColl et al., 2018) and two 3900-year-old
individuals from the Funadomori site in Hokkaido (Kanzawa-Kiriyama et al., 2019). Sampling of
4 Elisabeth de Boer et al.
nuclear genomes is still sparse, but a rough understanding of the ancestry associated with the Jōmon is
taking shape with each study.
Characterizing Jōmon-period ancestry is fundamental to understanding the genetic composition of
humans that lived during the Yayoi period, who ostensibly represent various degrees of mixture
between Jōmon and continental peoples. This in turn will improve our understanding of population
migration on the archipelago and its role in the spread of agriculture across the archipelago. Here, we
highlight some key features and emerging questions observed to date on Jōmon-related ancestry,
which allow us to better understand the challenges (and rewards!) in interpreting the genetics of
the Yayoi in future studies.
Analyses of both uniparental (Y and mtDNA) and nuclear DNA of present-day populations have
highlighted that ancestry persists in Japan that is deeply diverged from ancestry found in mainland
East Asian populations. The distribution of haplogroup frequencies across multiple populations is
often used to determine where haplogroups originated. For example, those that occur in high frequency
in present-day populations from Japan but low frequency elsewhere (e.g. N9b, M7a, G1b) were proposed
as candidate haplogroups of Jōmon origin (Adachi, Shinoda, Umetsu, & Matsumura, 2009; Adachi et al.,
2011; Kanzawa-Kiriyama, Saso, Suwa, & Saitou, 2013; Kivisild et al., 2002).
The most prominent of these is N9b, which is the most frequent mtDNA haplogroup assigned to
Jōmon individuals. An estimate of the time to the most recent common ancestor (t
) is ca. 22,000
years ago, which is older than the t
for several other haplogroups found in East Asians (Adachi
et al., 2011). The non-recombining region of the Y-chromosome has also been extensively studied in
Japan. Y-haplogroup D1b is exceptionally interesting as it is found in high frequency in the Japanese
archipelago and the Tibetan Plateau but not elsewhere (Hammer & Horai, 1995; Tajima et al., 2004;
Watanabe et al., 2019). The estimated t
for D1b is ca. 19,400 years ago (Hammer et al., 2006),
similar to that estimated for N9b mtDNA. These dates, if corresponding to the expansion of
Jōmon ancestry on the archipelago, suggest that Jōmon ancestry separated fairly early from mainland
East Asian ancestry.
One mtDNA haplogroup found in many Jōmon-associated individuals (e.g. Kanzawa-Kiriyama
et al., 2013; Adachi et al., 2011; Kim et al., 2010) as well as Yayoi-associated individuals (Igawa
et al., 2009) is D4, which is widespread in northern East Asia both in past and present-day populations
(e.g. Tanaka et al., 2004; Zhao et al., 2010; Hong et al., 2014; Jeong et al., 2018; Lan et al., 2019). Its
widespread presence, however, suggests that it was found in the common ancestral population of all
East Asians, making it difficult to evaluate its role in more recent migrations and interactions.
In genomic studies of ancient Asians, both a 40,000-year-old individual found in Tianyuan Cave,
Beijing, China (Fu et al., 2013; Yang et al., 2017) and 8000-year-old individuals from Southeast Asia
associated with Hòabìnhian foragers (McColl et al., 2018) show an early split time from other East
Asians, including from ancient Jōmon genomes (Kanzawa-Kiriyama et al., 2017,2019). Thus, we
denote them as basal Asians. In contrast, humans living in Southeast Asia, the eastern steppes of
Siberia and the southwest edges of the Tibetan Plateau from the Neolithic to historic periods (e.g.
Sikora et al., 2019; Jeong et al., 2016b) share a closer relationship to present-day East Asians than
the Jōmon individuals, confirming that Jōmon are distantly related to mainland East Asian ancestry
(Yang, MA and Fu, Q unpublished observations).
In fact, the Jōmon sampled thus far probably separated earlier than the split time of East Asians
and the early Asian population that contributed to Native Americans (Gakuhari et al., 2019;
Kanzawa-Kiriyama et al., 2017,2019). Estimates of when ancestral Native Americans separated
from the East Asian lineage is ca. 36,00025,000 years ago (Moreno-Mayar et al., 2018), and a direct
estimate of the split time between the Jōmon and mainland East Asians ranges from 38,00018,000
years ago (Kanzawa-Kiriyama et al., 2019). These estimates are broad, indicating there is still high
uncertainty as to the exact date. However, studies of both uniparental and nuclear markers all highlight
Jōmon ancestry separated from mainland East Asian ancestry in the Palaeolithic, with dates ranging
from 38,00018,000 years ago.
Evolutionary Human Sciences 5
Box: Three-way Analysis of Genetic Relationships
Figure 2. F4-tests surveying the relationship of populations with East Asian ancestry (on the x-axis, X)to
the Ikawazu Jōmon, relative to ancient Southeast Asian foragers (Hòabìnhian, HB), an ancient Tibetan
(Chokhopani, CH), and an inland ancient northern East Asian (Shamanka_EN, SH) (graphs by Melinda
Yang). Numerical values for the data visualized here can be found in Table S3. F4-statistics are tests of
symmetry of the form f4(Out, P1; P2, P3), where it is assumed that P2 and P3 form a clade with espect to
P1. Our statistics take the form (A) f4(Mbuti, HB; Ikawazu Jōmon, XEast Asians) or (B, C) f4(Mbuti,
Ikawazu Jōmon; CH or SH, XEast Asians), with the underlying tree structure verified by other genetic
analyses. Central African Mbuti were used as the outgroup (Out).
Key: tree models showing relationships of f4 values are placed to the right of the plot: f4 > 0
corresponds to the highest tree; f4 = 0 corresponds to the middle tree (clarified by dashed grey arrow);
and f4 < 0 corresponds to the lowest tree for each figure. The presence of gene flow in the model is
indicated by the red arrow. A significantly positive value highlights gene flow between the outgroup (P1)
and XEast Asians (P3). A significantly negative value highlights gene flow between the outgroup (P1) and
the other population in the tree (P2). Two standard errors are indicated by the thin grey bar, while one
standard error is indicated by the thick grey bar. Points are coloured (colour online) by region of origin,
with darker colours for ancient populations and lighter colours for present-day populations. East Asians
for whom all or part of their population live near coastal East Asia are shaded grey. *Ancient islanders
were sampled from Southeast Asian and Southwest Pacific islands, but were previously shown to share a
close relationship to present-day Austronesians (McColl et al., 2018; Skoglund et al., 2016).
Interpretation:inFigure 2A, 8000-year-old Hòabìnhian (HB) foragers from Laos and Malaysia are an
outgroup to the Ikawazu Jōmon individual and present-day and ancient populations of East Asian
ancestry. A connection between the Ikawazu Jōmon individual and the Hòabìnhians would result in a
6 Elisabeth de Boer et al.
A key aspect of the observed genome-wide patterns above is that these Jōmon individuals do not
share any relationship with sampled basal Asians. In admixture tests (Patterson et al., 2012), two
populations that form a clade (e.g. the Jōmon and mainland present-day East Asians) may sometimes
share excess ancestry with an outgroup population that potentially indicates partial shared demo-
graphic history, probably via a population closely related to the outgroup. However, Jōmon individuals
show no excess connection to basal Asians, including the Southeast Asian Hòabìnhians relative to
present-day East Asians, as indicated by the lack of significantly negative values in the Box (Figure 2A).
In particular, comparison of the Southeast Asian Hòabinhians from Laos and Malaysia with main-
land East Asians from East Asia and a Jōmon individual (Ikawazu) shows that the East Asians and
Jōmon ancestry are equidistant from Hòabìnhian ancestry (Figure 2A), indicating that the Jōmon do
not share a special relationship with Hòabìnhians as previously suggested (McColl et al., 2018). Tests
of genetic similarity do not show Hòabìnhians or the Jōmon sharing exceptionally high genetic similarity
with each other (Figure S1). Shared ancestry between present-day Japanese and recent Southeast Asians
are best explained by a common process gene flow from mainland East Asia, a phenomenon well-
characterized by tests of the Dual Structure model in Japan and by observations of gene flow into
Southeast Asia (Kanzawa-Kiriyama et al., 2017,2019; Lipson et al., 2018). In the future, individuals
from eastern Eurasia will almost certainly help to clarify how Jōmon ancestry first entered the
Japanese archipelago, but the current sampling has not yet shed light on who they might have been.
Connections do exist between the Jōmon and East Asians who live along the coast of East Asia. The
first Jōmon mtDNA sequenced in 1989, from the Early Jōmon Urawa-I site in the Kantōregion
(Figure 1), shared a close relationship to present-day Southeast Asians that suggests common ancestry
with Southeast Asians (Horai et al., 1989). This haplogroup, called E1a1a, is prevalent in
Austronesian-speaking populations of Taiwan and Southeast Asia who share a closer relationship to
East Asians than other Southeast Asians. A ca. 8000-year-old individual sampled from Liang Island
off the southeast coast of China in Fujian province also shares this haplogroup (Ko et al., 2014).
Study of the Liang Island individuals nuclear genome indicates a close genetic relationship to
Austronesians (Yang, MA and Fu, Q unpublished observations). Present-day Austronesians, such as
the Ami and Atayal from Taiwan (Mallick et al., 2016), share connections with the Ikawazu Jōmon
relative to more inland ancient East Asians (Figure 2B and C), potentially indicating admixture
between the Jōmon and southern East Asian populations. Comparisons with nuclear genomes from
Fujian in southern China show similar connections (Yang, MA and Fu, Q unpublished observations).
Thus, rather than Southeast Asian, the primary signal seems to be associated with Austronesians, who
derive from an East Asian population associated with southern China.
Siberian connections, particularly in Hokkaido, have also been a recurring theme of Jōmon-related
genetic studies. Several of the mtDNA haplogroups prevalent in the Japanese and Jōmon but rare in
mainland East Asians, especially G1b, can be found in southeastern Siberians, highlighting potential
contacts along the coast in northern East Asia as well (Sato et al., 2009; Adachi et al., 2011).
significantly negative statistic (f
< 0), which is not observed. In all cases, the Ikawazu Jōmon shows no
connection to Hòabìnhians (f
In Figure 2B, we compare against a 3100-year-old Tibetan (Chokhopani, CH), and in Figure 2C,we
compare against a 7500-year-old northern East Asian from the eastern steppe region of Siberia
(Shamanka_EN, SH). The Ikawazu Jōmon is an outgroup to all East Asians, including these ancient inland
East Asians. Thus, a significantly positive statistic (f
> 0) indicates that the Ikawazu Jōmon shares
connections with that East Asian (X) that the ancient inland East Asian Chokhopani or Shamanka_EN do
not possess. No connections are observed between the Ikawazu Jōmon and ancient inland East Asians,
which would be indicated by a significantly negative statistic (f
< 0). A symmetric relationship to Ikawazu
is observed when comparing with other non-coastal ancient and present-day East Asians (f
0). Coastal
East Asians from northern and southern East Asia tend to show significantly positive results (f
> 0),
indicating a connection to the Ikawazu Jōmon that ancient inland East Asians do not share.
Evolutionary Human Sciences 7
Pre-modern Ainu show similar mtDNA haplogroups to populations in the Lower Amur region of Siberia
and populations belonging to the early historic Okhotsk culture of Hokkaido (6001200 AD) (Adachi,
Kakuda, Takahashi, Kanzawa-Kiriyama, & Shinoda, 2018). Studies of nuclear DNA from Early
Neolithic populations in the Primorye region of Russia highlight that the Jōmon are an outgroup to all
mainland East Asians, including these more northern populations in Siberia (Sikora et al., 2019;de
Barros Damgaard et al., 2018). In the same comparisons set up for coastal southern East Asians above,
it can be shown that ancient and present-day coastal northern mainland East Asians dating up to 7700
years ago share connections with the Ikawazu Jōmon relative to more inland East Asians (Figure 2B,
C). Ancient northern Siberian ancestry prevalent during the Palaeolithic notable for both its closer relation-
ship with European-related rather than Asian-related ancestry and its impact on Native American ancestry
(Raghavan et al., 2014; Sikora et al., 2019) is not found in mainland East Asians or the Jōmon, which
emphasizes that the connections are specific to coastal mainland East Asians and the Jōmon.
One explanation for a connection between the Jōmon and coastal East Asians could be that the
Jōmon were not completely isolated from mainland East Asians. By 3900 years ago, the date of the
oldest Jōmon nuclear genome sampled (from Funadomari, Figure 1), Austronesians were rapidly
expanding into islands in the Pacific (Tsang, 1992; Spriggs, 2011). The main patterns observed
both in past mtDNA studies and in recent genome-wide studies of the Jōmon all seem to highlight
coastal connections, which may suggest that the Jōmon experienced gene flow with populations deriv-
ing from mainland East Asia prior to any contact associated with migration of Mumun immigrants
from the Korean peninsula. This is supported by archaeological studies that track artefact common-
alities resulting from trade and contact along the coast (Bausch, 2017), some of which date back to
the Palaeolithic (Morisaki, 2015). This is logical given that the Jōmon were inveterate deep-sea fishers
given their harpoon technology, and scores of dugout canoes have been excavated from archaeological
sites (Habu, 2010)although it is not clear how seaworthy they were.
To address the relationship between population movement and the spread of farming in the
Japanese archipelago, Jōmon and Mumun ancestry must be well characterized. Here in this section,
we have briefly highlighted some key features of Jōmon ancestry using ancient mtDNA and nuclear
genomes. First, Jōmon ancestry diverged fairly early from that of mainland East Asians. Second,
they do not show notable connections to currently sampled basal Asians, such as the Tianyuan indi-
vidual or Hòabìnhians. Third, they share coastal connections with coastal populations in northern
and southern East Asia. This suggests that one of the major assumptions about the Jōmon may not
be true that they were genetically isolated since the first Palaeolithic migrations to the Japanese archi-
pelago until the Mumun migration at the end of the Jōmon period. If the Jōmon themselves are
already partially admixed, then characterizing increased gene flow from the mainland in populations
from the Yayoi or more recent historic periods will be substantially more complex.
Advances that utilize rare alleles or long haplotypes (Lawson & Falush, 2012; Schiffels et al., 2016)are
increasing the power of demographic analyses focused on more closely related populations, including in
Japan (Takeuchi et al., 2017), but these are still difficult to apply in the realm of ancient DNA where
obtaining data with high enough coverage is still rare. Present-day genomes are informative on recent
history (Takeuchi et al., 2017) but make it difficult to resolve questions about periods as early as the
Yayoi. Ancient genomes directly from the Yayoi are needed to clarify early population movement asso-
ciated with the spread of farming. Such sampling is just starting, where two nuclear genomes from the
Shimo-Motoyama rock shelter site in northwest Kyushu dating to the Terminal Yayoi show evidence of
admixture between Jōmon- and mainland East Asian-related ancestry, in a region where populations
were thought to be of unadmixed Jōmon-lineage (Shinoda et al., 2019). Characterizing the role admix-
ture played during the Yayoi requires understanding of the features of Jōmon ancestry described above to
help us understand how to contextualize these and future data.
The remaining parts of this paper focus on populations in the Yayoi to Nara periods, examining (1)
how archaeological shifts indicate a complex role for migration and admixture that was probably region-
specific and (2) how similarities in dialect types hint at prehistoric migration of admixed Yayoi popula-
tions along the Japan Sea coast, which only stresses the need for more data on ancient Yayoi DNA.
8 Elisabeth de Boer et al.
The coastal genetic connections proposed are not directly tied to the farmer/language spread
hypothesis because they are found in the Jōmon and thus would be prior to the spread of farming.
Instead, they are a cautionary point to understand farmer/language spread, we need to understand
who were the pre-existing populations (the Jōmon). If their ancestry is not as genetically isolated as has
been argued, then future studies need to account for that.
Agricultural transition in Japan
In dealing with this problem, first we must define agriculture. This is not as easy as it appears, since the
Jōmon were experienced at plant management, leading to several local domesticated species. Thus, they
can be called huntergathererfisherhorticulturalists. However, the plants that they domesticated or at
least managed soybeans, adzuki, Perilla, sweet chestnuts and Japanese millet (Echinochloa utilis)among
others were not suitable for intensive cultivation as carbohydrate sources to become staples (Crawford,
2011; Barnes, 2015:111112, and references therein). Crawford would rather discard the distinction
between horticulture and agriculture, preferring to deal with proportionalities in resource production,
which includes not only food but other strategic resources such as lacquer and hemp for fibres. Here,
we use agricultureto refer to the farming of major starch-grain crops: rice (Oryza sativa) and millets
(Setaria italica and Panicum miliaceum) in Early Yayoi, with barley and wheat added in later Yayoi.
The Jōmon subsistence system was interrupted by the importation of rice and millets from the Korean
Peninsula in the Mumun Period, heralding the start of the Yayoi period in the Japanese Islands. The begin-
nings of rice agriculture in each region of Japan have been meticulously tracked, first from its source on the
continent into North Kyushu (Miyamoto, 2017,2018,2019) and then eastwards through the archipelago
(Fujio, 2004,2009,2013,2014,2017). Proto-Japanese speaking Mumun migrants (Whitman, 2011) coming
into North Kyushu interacted with Jōmon peoples there, creating an initial admixed Yayoi population which
then spread throughout the Japanese islands as they occupied new lands for farming.
For each region, Fujio has identified a hazyperiod of possible cultivation capped by the clear
introduction of rice agriculture (Figure 3); he distinguishes this hazy period, however, from the
clear adoption of irrigated rice agriculture and the appearance of the continental cultivation toolkit,
moated settlements and moated burials. These elements have been treated as the Yayoi package
(Mizoguchi, 2013)orYayoi complex(Miyamoto, 2016,2019). Within most of western Honshu
Island, Fujio expects that grain cultivation (rice and particularly millets) preceded the formal package.
If we assume that the package was instituted by migrating farmers, the hazy periods and non-irrigated
rice-farming periods could represent the gradual conversion of Jōmon-lineage peoples to an agricul-
tural way of life. By 380 BC, however, the Yayoi packageentailing bronze and iron usage was fully
established west of the Waist of Honshu(between Wakasa Bay and Ise Bay, Figure 1).
Beyond the Waist of Honshu, the uptake of farming was far more diverse. Current research iden-
tifies phases of Jōmon pottery usage during the advent of agriculture in the Kinai, Chūbu central
mountains, and Kantōregions where cultivation of dry-field crops also preceded irrigated rice agricul-
ture (Shitara & Takashe, 2014; Shitara & Fujio, 2014, pp. 1213; Takase, 2014; Barnes, 2019). Thus,
some farmers in the Yayoi period might have been neither genetically admixed with Mumun
(being Jōmon-lineage) nor Japanese speakers. Rice agriculture was established in Hokuriku and
Tōhoku from 380 BC. However, settlements at the northern tip of Honshu failed by 100 BC, with
occupants reverting to a hunting and gathering lifestyle. Thus, North Tōhoku is included with
Hokkaido in the Epi-Jōmon period, which lasted to 700 AD, but we will refer to Jōmon-lineage people
in other parts of Tōhoku also as Epi-Jōmon.
According to Figure 3, irrigated rice agriculture was instituted by 380 BC in Hokuriku and 300 BC in
South Kantō, but not until 220 BC in Chūbu and 50 BC in eastern Tōkai. Interestingly, it reached North
and South Kantōvia different routes. The specific ceramic style accompanying the introduction of rice
into Gunma Prefecture in northwest Kantōhad its origin near the Japan Sea coast in Niigata Prefecture
(Baba, 2008). It most likely arrived there through diffusion along the Japan Sea coast from western
Honshu, a completely different route from that arriving in Kanagawa Prefecture along the Pacific seaboard.
Evolutionary Human Sciences 9
North of the Toné River, the essential elements of the Yayoi packageare mainly missing until ca.
150 AD (Fujio, 2013). Thus, it is assumed that cultivation techniques for rice and millet in South and
Central Tōhoku were previously borrowed by Epi-Jōmon peoples living in this area and the Japanese
language was spread by later movements of people in the Kofun period.
In the second and third centuries AD, state formation processes began with the widespread adop-
tion of mounded tomb building for those Yayoi elites who had risen to high status within the devel-
oping agricultural polities. The succeeding Kofun (old tomb) period (Barnes, 2007) witnessed the
establishment of a centralized Yamato state in the fifth-century Kinai region. This was also a century
of a second wave of immigration from the Korean Peninsula, stimulated by warfare among Peninsular
states. In the fifth and sixth centuries, migrations of elites from western Honshu augmented the Kantō
population and introduced equestrian culture.
The Nara period began when a national capital, Heijō(Figure 1), was built in todays Nara
Prefecture. At this point, however, the Yamato state was limited to the Kinai region, but alliances
were made with outlying chieftains in Kyushu and Kantō. By the mid-seventh century these figures
were integrated into a court hierarchy that represented an expanded Yamato state. However, this
state did not extend further north than Kantō; peoples who occupied the Tōhoku region were begin-
ning to be called emishi in court documents. The Nara state actively pursued military activities to bring
this region under court control, although they ultimately failed and the region remained under the rule
of prominent emishi.
Figure 3. Regional interfaces of expanding agriculture and Jōmon lifeways through phases IV of the Yayoi period, set against the
Mumun and Iron Age periods of the Korean Peninsula and the Shellmound periods of the RyūkyūIslands. Source: Fujio (2013), fig.
3, modified by GLB with permission. Key: 1, instances of bronze introduction and then rejection; 2, abandonment of bronze ritual
use; 3, use of bronze bells; 4, moated burials but not moated villages.
10 Elisabeth de Boer et al.
Emishiin the Nara period is understood to have been a word that designated people who lived in the
north beyond the reach of the state. It was neither an ethnonym nor referred to a way of life but was an
administrative term and so encompassed everyone living beyond state jurisdiction regardless of subsist-
ence, language, or genetic background. We assume that those emishi who practised rice agriculture spoke
Japanese, but Ainu place names surviving from Niigata and Fukushima northwards clearly indicate that
the Ainu language was being spoken by some emishi (see Hudson, 1994, fig. 1). Historical documents
record the need for interpreters at least once during the state expansion into the north (the Emishi
Wars 774811), which ended abruptly with the court abandoning its military campaigns (Friday, 1997);
the Epi-Jōmon included among the emishi were very likely speakers of an Ainu-related language, and
most linguists view Ainu as a relic Jōmon language. It is clear that evidence of the Ainu language predates
the emergence of the Ainu people in historical documents in the seventeenth century (Hudson, 1999).
Knowledge of the subsistence system of Tōhoku in the Kofun and Nara periods is not well devel-
oped. The Kantōbecame a prominent horse-breeding area, supplying the Court with horses and cav-
alry, leading to the development of the medieval samurai (Farris, 1992; Friday, 1997). Further north,
Epi-Jōmon, admixed Yayoi descendents and Kofun-period pioneers formed the emishi who opposed
the Nara Courts efforts at subjugation. By the ninth century, powerful local warlords from south-
western clans such as the Abe and Kiyohara ruled large territories in the north on behalf of the
Heian Court, and finally in the twelfth century, the Northern Fujiwara established their rule over
Tōhoku. It is significant that, despite the court origins of this family, the coffins of the first three
Northern Fujiwara rulers contained only a little rice and no continental millets, but large quantities
of barnyard millet (E. utilis) (Hudson, 1999, p. 76). This suggests that continental-type agriculture
was not a prominent feature of Tōhoku farming even into the Medieval period, with barnyard millet
harking back to Jōmon horticultural practices.
The languages of Japan
As in many other areas of the world, migrations in connection with the spread of agriculture in Japan
are thought to have led to large-scale replacement of the languages of indigenous huntergatherers
(Robbeets & Savelyev, 2017). The only remnant today of the many languages of huntergatherers
that must have been present in Japan in the Jōmon period is formed by Ainu, an (almost) extinct lan-
guage on the northeastern island of Hokkaidō. The presence of Ainu place names in Honshū,from
Niigata and Fukushima Prefectures northwards, indicates that this region too was once an area
where an Ainu-related language was spoken. All other languages in the archipelago now belong to
the Japanese language family.
It is likely that at least initially diversification in the language was low, as is often the case when a
group of migrants spreads out over a new territory. Dialect borders that later developed in Japan often
follow natural barriers such as mountain ranges that impede communication between neighbouring
areas. The best-known dialect border for instance, which divides the dialects up into an eastern
Japanese and a western Japanese dialect group based on differences in vocabulary and grammar, fol-
lows the Hida and Kiso mountain ranges in central Honshū. Most of these differences, for instance
those in grammar, do not go back further than the fourteenth century, and many are linked to linguis-
tic influence radiating out from the old capitals of Nara and Kyōto. Some other dialect borders, on the
other hand, may have links to the prehistoric migrations that spread agriculture through the islands.
The unexpected dialect type of the northeast
An example of such an unexpected dialect distribution is the fact that the phonology and tone system
of the Tōhoku dialect resemble those of Izumo, on the Japan Sea coast in the west of Honshū, more
than those of the adjacent Kantōregion.
The tone system of West Kantō, for instance, belongs to the so-called Chūrin or middle circletype,
in which the division of the words of the language in tone classes is different from that of the Tōhoku
Evolutionary Human Sciences 11
region, which has a so-called Gairin or outer circletype tone system. These names are derived from
the geographical positions of the types relative to each other (Figure 4). An earlier work (De Boer,
2010) analysed the Gairin-type merger pattern of the proto-Japanese tone classes as the result of an
innovation that other dialects lacked. As such, a Gairin-type system can develop multiple times inde-
pendently, as the tonal assimilations that gave rise to the Gairin system are natural (there are, for
instance, also two regions with Gairin A tone systems in Kyūshūand Shizuoka), but the agreements
between the dialects of Izumo and Tōhoku go deeper.
Within the innovative Gairin type, a further innovation occurred, resulting in a sub-type where high
tone shifts away from syllables that contain /i/ or /u/. It can be seen that this type (Gairin B in Figure 4)
developed in Izumo in the centre of the region, whereas the older Gairin type (Gairin A) was preserved
in the periphery. The Gairin B innovation is also found in the Tōhoku region, except in two areas far
removed from the Japan Sea coast. This distribution suggests that the Gairin B innovation was intro-
duced on the Japan Sea coast side, and spread eastward from there.
The vowel systems of both Izumo and Tōhoku have centralized /i/ and /u/ and raised /e/ and /o/ so
that these vowels are all close together and no longer maximally opposed to each other as they are in
other Japanese dialects. In central Izumo and in the Tōhoku region (except for a small area far
removed from the Japan Sea coast), this has resulted in mergers between vowels (Figure 5). This
Figure 4. Map of the Japanese tone systems. Adapted by EdB from Wurm and Hattori (1981): no page number.
12 Elisabeth de Boer et al.
geographical distribution, too, suggests that an innovation that originated in Izumo was introduced to
the northeast by way of the Japan Sea coast.
The East Kantōdialect (Figure S2) takes a somewhat intermediate position between the West Kantō
dialect and the Tōhoku dialect. Some centralization of /i/ and /u/ is present, and the fact that the tonal
distinctions have disappeared is most likely the result of a mixture of West Kantō(Chūrin) and
Tōhoku (Gairin) influences. From other areas in Japan it is known that confusion between adjacent
tone systems with different merger patterns of the tone classes can lead to collapse of the system.
The northeastern toneless zone includes not only the East Kantōdialect, but also the Pacific side of
southern Tōhoku (Figure 4). On the Japan Sea side of southern Tōhoku the reflexes are mixed
Chūrin and Gairin B, but the system has not collapsed.
What does the opposition between the West Kantōtone and vowel system and the northern
Tōhoku tone and vowel system and the intermediate zone between them mean for the way in
which the northeast was settled by Japanese-speaking farmers? There are a number of things to con-
sider. Vocabulary can be easily borrowed long distance from other dialects, as long as there is contact
(for instance through trade along the coast). Phonology, or the sound structure of a language, on the
other hand, usually spreads to adjacent areas, with which there is sustained contact. If it spreads to
distant areas, migration is the most likely cause, although it is possible for similarities in phonology
between far-flung regions to be the result of parallel independent development, if the innovations
are easily repeatable and cross-linguistically common.
The similarities between Izumo and Tōhoku (and to a lesser extent the Noto Peninsula) come in
shared sets (see Tables S1 and S2; and De Boer, forthcoming), which makes parallel independent
development unlikely. It suggests movement of people along the coast in at least two different periods:
first from Izumo to the area of the Noto peninsula (present-day Ishikawa and Toyama Prefectures),
spreading the set of features listed in Table S1; and later from Izumo to the Tōhoku coast, spreading
the set of features listed in Table S2.
Izumo in the Late Yayoi period
Although Izumo (Shimane Prefecture) is nowadays relatively poor and sparsely populated, this was not
always the case. Izumo was one of the most powerful confederacies of the Mid and Late Yayoi periods.
Figure 5. Map of vowel centralization of /i/ and /u/ and merger of /i/ and /u/ after coronal consonants. Adapted by EdB from
Kamei, Ko
̄no, and Chino (1989), p. 1760.
Evolutionary Human Sciences 13
It was the great rival of Yamato and the focal point of a wide maritime trade network that included the
Japan Sea coast, the Ryūkyūs, Kyushu, Korea and China (Torrance, 2016). Izumo formed alliances
with other adjacent regions along the Japan Sea coast; Watanabe (1995) speaks of an Izumo cultural
zonewhich he places in the Late Yayoi period.
The corner-projected mound burials typical for Izumo in this period are also found on the Noto
Peninsula and in Toyama Prefecture, where they stem from 100250 AD (Maeda, 2007, p. 6). This
makes it likely that the presence of the Izumo vowel system on the Noto Peninsula and in Toyama
dates back to the Mid to Late Yayoi period, suggested not only by the congruence of burial types
(Figure S3) but also the presence of the Izumo-style vowel mergers in Toyama (Figure 5). The
Izumo-style tone systems (Gairin A and Gairin B) had apparently not yet developed, as the tone sys-
tem of the Noto Peninsula does not share these innovations (Figure 4). Some other innovations have
occurred in the local tone systems since then, but not the same as those shared by Izumo and Tōhoku.
The fact that the Izumo tonal innovations are today present in the northern Tōhoku region, and in
a mixed form along the southwestern Tōhoku coast, means that migrations from Izumo to these areas
must have taken place after the Gairin B innovations developed. The presence of both Gairin A and
Gairin B in the northeast may indicate migrations in different periods. It may also be related to
different points of departure from Izumo, as political and economic prominence in Izumo fluctuated
historically between the eastern and western parts (Piggott, 1989; Torrance, 2016). The Gairin B tonal
innovation is most advanced in western Izumo (Hirako, 2017), meaning that it most likely started
there and only gradually spread to eastern Izumo. In the Tōhoku region too, the Gairin B system
was most likely present in a smaller area in earlier times. The tone shifts typical of this system continue
to spread to adjacent areas: recent fieldwork (Boiko, 2018) has shown that, by now, the Gairin A area
on the Shimokita Peninsula has disappeared, and instead, the Gairin B tone shifts have been adopted.
Looking for the time of the migrations
Exploring the similarity of the Izumo and Tōhoku dialects, it is necessary to examine opportunities for
migration of Izumo dialect speakers into the northeast. Although the very first forays of rice farmers
from western Japan to the northern tip of Honshūalready took place in the Middle Yayoi period, these
settlements were later abandoned. The full Yayoi packagereached the coastal areas of Ishikawa,
Toyama and western Niigata as early as 300 BC. It is possible that rice farmers settling along the
coast departed from Izumo, but there is no direct evidence for this. Clear evidence of influence
from Izumo is more recent: the Izumo-style corner-projected burial mounds in Ishikawa and
Toyama date from 100250 AD. While the full Yayoi packageappeared briefly in the central moun-
tains (Figure 3: #1, Chūbu district), it also intruded into western Gunma Prefecture at this time. The
ceramics accompanying the irrigated-rice culture package derived from the Jōetsu Basin in western
Niigata and spread through the river valleys of Nagano Prefecture into western Gunma (Baba, 2008).
It is unlikely that the rice farmers who moved inland from western Niigata spoke a dialect with the
features typical of Izumo. Linguistic influence from Izumo in the form of migration was not only later,
it also may have been initially limited to Ishikawa (i.e. the Noto Peninsula) and Toyama, as
Izumo-style mound burials have not been found in Niigata. If there was already some Izumo influence
on the dialect of Niigata at the time when rice farmers moved inland to Gunma, it would have been on
the vowel system only. The tonal innovations in the Izumo dialect had not yet occurred, judging from
the fact that these are not present in the dialects of Ishikawa and Toyama. What applies to the dialect
of Niigata also applies to Nagano (Chūbu) and Gunma (West Kantō), which was settled from Niigata,
and to Tochigi and Ibaraki (East Kantō), which were all settled overland. If the Tōhoku region was
entirely settled overland from these areas, the similarities with the Izumo dialect remain unexplained.
Can migration of Izumo dialect speakers into Tōhoku in later periods explain the similarities
between the dialects? Piggott (1989) examined the history of Izumo throughout the Late Yayoi and
Kofun periods, distinguishing between eastern and western Izumo. Izumos unique mound-burial cul-
ture of Late Yayoi gave way to cultural and political inroads from Kibi to the south and Yamato itself,
14 Elisabeth de Boer et al.
first into western Izumo. The chieftains of eastern Izumo maintained trade relations with northern
Koshi (western Niigata) into the sixth century, but by the 540s the Izumo chieftains had all allied
with Yamato (Piggott, 1989, pp. 5960). Torrance (2016, p. 4), on the other hand, argues that
Izumo remained an important and independent presence along the Japan Sea coast, at least until
the late sixth or early seventh century.
Under the circumstances it is possible that groups from Izumo, avoiding Yamato pressure, would
migrate northward along the Japan Sea coast. Diffusion into Tōhoku through mountain basins and
over passes could have taken place, but were the numbers enough for linguistic change throughout
Tōhoku? The mixed nature (and collapse) of the tone systems in south and central Tōhoku suggest
that there was some influence but not enough to determine the dialect. The linguistic influence in nor-
thern Tōhoku, however, was much stronger.
Hudson (2017) mentions that until the fifth century the pottery types of the northern Tōhoku
region and Hokkaidōwere identical. From the fifth to the seventh centuries, however, this pottery
type starts to disappear from northern Tōhoku, and is from then on restricted to Hokkaidōonly.
This development has been taken to mean that the Epi-Jōmon population among the emishi who,
from the evidence of place-names, must have spoken an Ainu-related language, moved away from nor-
thern Honshūinto Hokkaidōin that period. According to Matsumoto (2018, p. 158), after the late
fifth century there are no traces of habitation in the northern Tōhoku for about a century, after
which a new population arrives in the late sixth century. The new arrivals were archeologically indis-
tinguishable from Kofun cultures elsewhere in Japan (Matsumoto, 2018, p. 159).
If the people arriving in the late sixth century were from Izumo, then northern Tōhoku would have
been sparsely populated at that time, as the Epi-Jōmon population had for a large part moved away.
That means that the new population could rapidly spread out over the entire area, which would explain
why the Izumo-style tone system was preserved well there, in contrast to the situation in south and
central Tōhoku. In south and central Tōhoku there was interference not only from other dialects
but most likely also from languages of the local Epi-Jomon population, who were no longer
huntergatherers but settled farmers by then. The relatively low internal diversity of the Tōhoku dia-
lects may be attributed to the overall later spread of Japanese to the northeast compared with other
areas of mainland Japan (Inoue, 1992).
Migration of people from Izumo to the northeast may even have left a genetic trace. Saitō(2017,
p. 127) uses a principal component analysis (PCA), in which nuclear DNA from modern Tōhoku
individuals is compared with nuclear DNA from modern Ainu, Ryūkyūan and mainland Japanese
individuals (Figure S4). A PCA simplifies complex datasets, creating summaries that emphasize the
components explaining the maximum amount of variance. In population genetics, this method is
often a quick and useful tool to examine population relationships, as the maximum amount of vari-
ance is often attributed to shared population history. However, it is not a formal test of shared
Saitōconcludes that, in contrast to Ryūkyūans, the Tōhoku population has very low traces of
Ainu-related ancestry, which was used as a proxy for Jōmon-related ancestry. He also includes a
PCA showing the position of Izumo individuals relative to Okinawan and Kantōindividuals (Saitō,
2017, p. 155), and he remarks upon the fact that these individuals occupy the same relative position
as the Tōhoku individuals (Figure S4), namely they are to the lower right of the average Mainland
Japanese individual.
It is better to be cautious in drawing conclusions until more detailed comparisons from different
areas of Japan are available, but the initial results are definitely interesting in light of the dialectal simi-
larities between Izumo and the Tōhoku region.
Concluding remarks
Confronted with the Yayoi farmers and their new mode of subsistence, the different ethnic groups that
were already present in Japan could react in different ways: assimilation and adoption of the new
Evolutionary Human Sciences 15
techniques, specialization in products with which to trade with the new farming populations, resist-
ance or withdrawal. The available options differed per region and per period, influencing the way
in which the Japanese language spread.
The present-day dialect distribution in northern Honshūsuggests that a considerable part of the
early historic emishi population were speakers of an Izumo-type dialect. There certainly will have
been Epi-Jomon people speaking an Ainu-related language among the emishi ranks, but what
seems clear is that the Izumo-type dialect of Tōhoku must have already had a strong foothold in
the northeast before the period of the Emishi Wars of the late eighth century. That dialect is proposed
to have spread either with the introduction of rice agriculture by admixed Yayoi peoples in Mid to Late
Yayoi, or in the expansion of the mounded tomb culture in the Kofun period.
This study has highlighted a strong need to bring Japanese scholarship on the history and archae-
ology of Tōhoku into consideration with the farming/language dispersal hypothesis. The complexity of
population movements in this area is illustrated by Hakomori (2013). Also needed is ancient DNA
sequencing at fine temporal and geographic scales. With increasingly sophisticated techniques for
quantifying genetic admixtures (cf. Chikhi, Nichols, Barbujani, & Beaumont, 2002; Dupanloup,
Bertorelle, Chikhi, & Barbujani, 2004; Wollstein & Lao 2015), maybe Yayoi- to Nara-period skeletal
material from the Kantōand Tōhoku regions will enlighten us on the interactions between indigenous
peoples and migrants in the spread of agriculture to the northeast. The deep ancestry associated with
the Jōmon will aid in highlighting changing proportions of different types of Asian-related ancestry in
these different regions, although it behooves us to be alert to Jōmon continental interaction prior to
the Yayoi period.
Acknowledgements. We would like to thank Qiaomei Fu for allowing us to cite unpublished work on ancient human
genetics of Neolithic East Asia.
Supplementary Material. The supplementary material for this article can be found at
Author contributions. Gina Barnes designed the project and wrote the Introduction and Agriculture section; Elisabeth de
Boer contributed the Language section; Melinda Yang contributed the section on Jōmon genetics; all three contributed com-
ments and revisions to the main text and Conclusions; Aileen Kawagoe acted as researcher and discussant, with many of her
comments incorporated herein.
Financial support. The linguistic part of this project has received funding from the European Research Council under the
European Unions Horizon 2020 research and innovation programme under grant agreement no. 677317.
Publishing ethics. As a review article, elements of our individual research and previous publications have been included in
the wider scholarly context.
Conflicts of interest. None of the authors have conflicts of interest to declare.
Research transparency and reproducibility. The genetic data shown are all previously published, as described in Table S5.
Data in Table S5 are presented in a format that can be read by the software Admixtools (version 412; Patterson et al., 2012)
where genotyped data are available for the 1240KSNP panel and can be found in a publicly available database: v42.4, David
Reich Lab Harvard University (Reich, 2020). Data used to visualize Figures 2 and S1 are reproduced in Tables S3 and S4.
Scripts used to conduct the genetic analyses and visualize the data can be made available upon request to
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20 Elisabeth de Boer et al.
... Like Longlin, they are more closely related to 9,000-4,000-year-old East Asians from coastal China than to Tianyuan or Hòabìnhians, but are an outgroup of these northern and southern East Asians. Some have argued for the presence of excess connections to Hòabìnhians by fitting the data to a graph that includes admixture with a Hòabìnhian-related population and finding different f4 patterns for Hòabìnhians compared to younger Southeast Asians in comparisons to a Jōmon individual [63]; however, alternative admixture graphs and f4-statistic comparisons do not show evidence for this connection [68,85,86]. ...
... Using Treemix and f4-ratio analyses (Box 1), Adachi et al. [64] found that present-day Japanese populations had 10% Jōmon ancestry. This finding broadly supports a core tenet of the dual structure hypothesis for the population history of Japan, wherein migrants from mainland Asia, likely through the Korean peninsula, moved to the Japanese archipelago starting 3,000 years ago, and mixed with indigenous Jōmon populations [86,95]. Adachi et al. also estimated that present-day Korean and Ulchi populations in northeast Asia show 5%-8% Jōmon ancestry [64]. ...
... Adachi et al. also estimated that present-day Korean and Ulchi populations in northeast Asia show 5%-8% Jōmon ancestry [64]. Furthermore, in f4-statistics, Jōmon individuals show connections to present-day Austronesians and 8,000-7,000-year-old individuals from coastal southern East Asia and Siberia [85,86]. These ties to coastal and island populations suggest that the Jōmon may not have been completely isolated after their migration into the Japanese archipelago ( Figure 2). ...
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L.L. Cavalli-Sforza spearheaded early efforts to study the genetic history of humans, recognizing the importance of sampling diverse populations worldwide. He supported research on human evolutionary genetics in Asia, with research on human dispersal into Asia and genetic distances between present-day East Asians in the late 20th century. Since then, great strides have been made in understanding the genetic history of humans in Asia, through large-scale genomic sequencing of present-day humans and targeted sequencing of DNA from ancient humans. In this review, I survey the genetic prehistory of humans in Asia, based on research using sequence data from humans who lived in Asia as early as 45,000 years ago. Genetic studies comparing present-day Australasians and Asians show that they likely derived from a single dispersal out of Africa, rapidly differentiating into three main lineages: one that persists partially in South Asia, one that is primarily found today in Australasia, and one that is widely represented across Siberia, East Asia, and Southeast Asia. Studies of ancient DNA from human remains in Asia dating from as far back as 45,000 years has greatly increased our understanding of the population dynamics leading to the current Asian populations. Based on "Jin L, Underhill PA, Doctor V, Davis RW, Shen P, Cavalli-Sforza LL, Oefner PJ. Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations. Proc Natl Acad Sci U S A. 1999;96(7):3796-3800”.
... The 1st millennium BCE is a defining period within the Japanese islands triggered by a major demic and cultural diffusion event that led to profound and long-lasting social, economic, cultural, and biological changes [56][57][58]. Archaeologically this moment is marked by the transition from the so-called Jomon period (ca 14,000 -early 1 st millennium BCE), characterised predominantly (but not exclusively) by a hunting and gathering economy, to the Yayoi period (early 1st millennium BCE-ca 250 CE), typically associated with the introduction of wet-rice farming brought in by migrant communities from the Korean peninsula in northern Kyushu during the first few centuries of the 1st millennium BCE. From a genetic standpoint, the subsequent admixture between the migrant and the incumbent groups is recognised as the origin of the modern Japanese population [59,60]. ...
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Large sets of radiocarbon dates are increasingly used as proxies for inferring past population dynamics and the last few years, in particular, saw an increase in the development of new statistical techniques to overcome some of the key challenges imposed by this kind of data. These include: 1) null hypothesis significance testing approaches based on Monte-Carlo simulations or mark permutations; 2) non-parametric Bayesian modelling approaches, and 3) the use of more traditional techniques such as correlation, regression, and AIC-based model comparison directly on the summed probability distribution of radiocarbon dates (SPD). While the range of opportunities offered by these solutions is unquestionably appealing, they often do not consider the uncertainty and the biases arising from calibration effects or sampling error. Here we introduce a novel Bayesian approach and nimbleCarbon , an R package that offers model fitting and comparison for population growth models based on the temporal frequency data of radiocarbon dates. We evaluate the robustness of the proposed approach on a range of simulated scenarios and illustrate its application on a case study focused on the demographic impact of the introduction of wet-rice farming in prehistoric Japan during the 1st millennium BCE.
... Recently, however, archaeobotanical research identifying northeast China as a centre of millet domestication has enabled linguists to propose the West Liao basin as the Neolithic homeland of a barley (Hordeum vulgare) and wheat (Triticum aestivum) developed in Korea by 1300 BC (Ahn, 2010;Kwak et al., 2017;Kim et al., 2019;Lee, , 2017a. Although Japanese archaeologists had earlier suggested that rice had been introduced to Korea from Japan, by the 1970s it was accepted that rice had moved to the peninsula from northeast China (Kim, 1982) and that Bronze Age agriculture spread from Korea to Japan after 1000 BC (Crawford, 2018;de Boer et al., 2020;Li et al., 2020;Miyamoto, 2014Miyamoto, , 2016Leipe et al., 2020). ...
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While earlier research often saw Altaic as an exception to the farming/language dispersal hypothesis, recent work on millet cultivation in northeast China has led to the proposal that the West Liao basin was the Neolithic homeland of a Transeurasian language family. Here, we examine the archaeolinguistic evidence used to associate millet farming dispersals with Proto-Macro-Koreanic, analysing the identifica- tion of population movements in the archaeological record, the role of small-scale cultivation in language dispersals, and Middle–Late Neolithic demography. We conclude that the archaeological evidence is con- sistent with the arrival and spread of Proto-Macro-Koreanic on the peninsula in association with millet cultivation in the Middle Neolithic. This dispersal of Proto-Macro-Koreanic occurred before an apparent population crash after 3000 BC, which can probably be linked with a Late Neolithic decline affecting many regions across northern Eurasia. We suggest plague (Yersinia pestis) as one possible cause of an apparently simultaneous population decline in Korea and Japan.
Recognized worldwide as an unusual “overlap” syndrome, Parkinsonism and motor neuron disease, with or without dementia, is best exemplified by the former high-incidence clusters of Amyotrophic Lateral Sclerosis and Parkinsonism-Dementia Complex (ALS/PDC) in Guam, USA, in the Kii Peninsula of Honshu Island, Japan, and in Papua, Indonesia, on the western side of New Guinea. Western Pacific ALS/PDC is a disappearing neurodegenerative disorder with multiple and sometime overlapping phenotypes (ALS, atypical parkinsonism, dementia) that appear to constitute a single disease of environmental origin, in particular from exposure to genotoxins/neurotoxins in seed of cycad plants (Cycas spp.) formerly used as a traditional source of food (Guam) and/or medicine (Guam, Kii-Japan, Papua-Indonesia). Seed compounds include the principal cycad toxin cycasin, its active metabolite methylazoxymethanol (MAM) and a non-protein amino acid β-N-methylamino-L-alanine (L-BMAA); each reproduces components of ALS/PDC neuropathology when individually administered to laboratory species in single doses perinatally (MAM, L-BMAA) or repeatedly for prolonged periods to young adult animals (L-BMAA). Human exposure to MAM, a potent DNA-alkylating mutagen, also has potential relevance to the high incidence of diverse mutations found among Guamanians with/without ALS/PDC. In sum, seven decades of intensive study of ALS/PDC has revealed field and laboratory approaches leading to discovery of disease etiology that are now being applied to sporadic neurodegenerative disorders such as ALS beyond the Western Pacific region. This article is part of the Special Issue "Parkinsonism across the spectrum of movement disorders and beyond" edited by Joseph Jankovic, Daniel D. Truong and Matteo Bologna.
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The origins of people in the Japanese archipelago are of long-standing interest among anthropologists, archeologists, linguists, and historians studying the history of Japan. While the ‘dual-structure’ model proposed by Hanihara in 1991 has been considered the primary working hypothesis for three decades, recent advances in DNA typing and sequencing technologies provide an unprecedented amount of present-day and ancient human nuclear genome data, which enable us to refine or extend the dual-structure model. In this review, we summarize recent genome sequencing efforts of present-day and ancient people in Asia, mostly focusing on East Asia, and we discuss the possible migration routes and admixture patterns of Japanese ancestors. We also report on a meta-analysis we performed by compiling publicly available datasets to clarify the genetic relationships of present-day and ancient Japanese populations with surrounding populations. Because the ancient genetic data from the Japanese archipelago have not yet been fully analyzed, we have to corroborate models of prehistoric human movement using not only new genetic data but also linguistic and archeological data to reconstruct a more comprehensive history of the Japanese people.
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In 1981, Okumura Mitsuo reported that the dialect of Izumo Taisha in western Japan had preserved remnants of the separate tone class 2.5, which until then had only been found in dialects in central Japan. His discovery proved that this tone class had formed part of proto-Japanese, but the phonetic realization in Izumo and in central Japan was totally different. The article offers a reconstruction of the proto-system of the Izumo region, as well as an explanation of how class 2.5 came to be (partly) preserved in Izumo. It is argued that this was through a series of rightward shifts of the /H/ tone. These shifts radiated out from the northwestern part of the region. In the period, when the shifts were active, a contour tone on the second syllable of class 2.5 blocked rightward /H/ tone shift in this class. In this way, the contour tone, although later lost, left a trace in the modern dialects.
Advances in ancient genomics are providing unprecedented insight into modern human history. Here, we review recent progress uncovering prehistoric populations in Eastern Eurasia based on ancient DNA studies from the Upper Pleistocene to the Holocene. Many ancient populations existed during the Upper Pleistocene of Eastern Eurasia—some with no substantial ancestry related to present-day populations, some with an affinity to East Asians, and some who contributed to Native Americans. By the Holocene, the genetic composition across East Asia greatly shifted, with several substantial migrations. Three are southward: an increase in northern East Asian-related ancestry in southern East Asia; movement of East Asian-related ancestry into Southeast Asia, mixing with Basal Asian ancestry; and movement of southern East Asian ancestry to islands of Southeast Asia and the Southwest Pacific through the expansion of Austronesians. We anticipate that additional ancient DNA will magnify our understanding of the genetic history in Eastern Eurasia.
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During my attendance at the ‘Transeurasian Millets and Beans, Words and Genes’ conference in Jena (January 2019), Martine Robbeets invited me to comment on the articles that are published in this Special Collection in the journal Evolutionary Human Sciences . My comments are focused on the seven articles that deal with the ‘Farming/Language Dispersal Hypothesis’, one of the key theoretical constructs discussed during the conference. I consider how the hypothesis might aid an understanding of the prehistory and early history of the Transeurasian language family.
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In this special collection, we address the origin and dispersal of the Transeurasian languages, i.e. Japonic, Koreanic, Tungusic, Mongolic and Turkic, from an interdisciplinary perspective. Our key objective is to effectively synthesize linguistic, archaeological and genetic evidence in a single approach, for which we use the term 'triangulation'. The 10 articles collected in this volume contribute to the question of whether and to what extent the early spread of Transeurasian languages was driven by agriculture in general, and by economic reliance on millet cultivation in particular.
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Background: Profiling of mitochondrial DNA is surely to provide valuable investigative clues for forensic cases involving highly degraded specimens or complex maternal lineage kinship determination. But traditionally used hypervariable region sequencing of mitochondrial DNA is less frequently suggested by the forensic community for insufficient informativeness. Genome-wide sequencing of mitochondrial DNA can provide considerable amount of variant information but can be high cost at the same time. Methods: Efficiency of the 60 mitochondrial DNA polymorphic sites dispersing across the control region and coding region of mitochondrial DNA genome was evaluated with 106 Mongolians recruited from the Xinjiang Uyghur Autonomous Region, China, and allele-specific PCR technique was employed for mitochondrial DNA typing. Results: Altogether 58 haplotypes were observed and the haplotypic diversity, discrimination power and random match probability were calculated to be 0.981, 0.972, and 0.028, respectively. Mitochondrial DNA haplogroup affiliation exhibited an exceeding percentage (12.26%) of west Eurasian lineage (H haplogroup) in the studied Mongolian group, which needed to be further verified with more samples. Furthermore, the genetic relationships between the Xinjiang Mongolian group and the comparison populations were also investigated and the genetic affinity was discovered between the Xinjiang Mongolian group and the Xinjiang Kazak group in this study. Conclusion: It was indicated that the panel was potentially enough to be used as a supplementary tool for forensic applications. And the matrilineal genetic structure analyses based on mitochondrial DNA variants in the Xinjiang Mongolian group could be helpful for subsequent anthropological studies.
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The Jomon and the Yayoi are considered to be the two major ancestral populations of the modern mainland Japanese. The Jomon people, who inhabited mainland Japan, admixed with Yayoi immigrants from the Asian continent. To investigate the population history in the Jomon period (14,500–2,300 years before present [YBP]), we analyzed whole Y-chromosome sequences of 345 Japanese males living in mainland Japan. A phylogenetic analysis of East Asian Y chromosomes identified a major clade (35.4% of mainland Japanese) consisting of only Japanese Y chromosomes, which seem to have originated from indigenous Jomon people. A Monte Carlo simulation indicated that ~70% of Jomon males had Y chromosomes in this clade. The Bayesian skyline plots of 122 Japanese Y chromosomes in the clade detected a marked decrease followed by a subsequent increase in the male population size from around the end of the Jomon period to the beginning of the Yayoi period (2,300 YBP). The colder climate in the Late to Final Jomon period may have resulted in critical shortages of food for the Jomon people, who were hunter-gatherers, and the rice farming introduced by Yayoi immigrants may have helped the population size of the Jomon people to recover.
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Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
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Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.
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Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300–2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380–975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups.
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The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
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The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyze 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after but not at the time of Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.
The chapter starts with an overview of the history of dialect classification in Japan. A puzzling aspect of the distribution pattern of the Japanese dialects is the fact that many features, which cannot all be explained as retentions or simplifications, recur in geographically distant areas. These similarities have been commonly but unsatisfyingly regarded as the result of parallel independent developments. Phonological (including tonal), morphological, and lexical features are selected to illustrate the splits that result in the different branches of Japonic. Based on shared innovations, the new classification at the end of the chapter proposes a Izumo-Tōhoku branch, as well as a Kyūshū-Ryūkyū branch.
The Funadomari Jomon people were hunter-gatherers living on Rebun Island, Hokkaido, Japan c. 3500–3800 years ago. In this study, we determined the high-depth and low-depth nuclear genome sequences from a Funadomari Jomon female (F23) and male (F5), respectively. We genotyped the nuclear DNA of F23 and determined the human leukocyte antigen (HLA) class-I genotypes and the phenotypic traits. Moreover, a pathogenic mutation in the CPT1A gene was identified in both F23 and F5. The mutation provides metabolic advantages for consumption of a high-fat diet, and its allele frequency is more than 70% in Arctic populations, but is absent elsewhere. This variant may be related to the lifestyle of the Funadomari Jomon people, who fished and hunted land and marine animals. We observed high homozygosity by descent (HBD) in F23, but HBD tracts longer than 10 cM were very limited, suggesting that the population size of Northern Jomon populations were small. Our analysis suggested that population size of the Jomon people started to decrease c. 50000 years ago. The phylogenetic relationship among F23, modern/ancient Eurasians, and Native Americans showed a deep divergence of F23 in East Eurasia, probably before the split of the ancestor of Native Americans from East Eurasians, but after the split of 40000-year-old Tianyuan, indicating that the Northern Jomon people were genetically isolated from continental East Eurasians for a long period. Intriguingly, we found that modern Japanese as well as Ulchi, Korean, aboriginal Taiwanese, and Philippine populations were genetically closer to F23 than to Han Chinese. Moreover, the Y chromosome of F5 belonged to haplogroup D1b2b, which is rare in modern Japanese populations. These findings provided insights into the history and reconstructions of the ancient human population structures in East Eurasia, and the F23 genome data can be considered as the Jomon Reference Genome for future studies.
Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from eighteen Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100–1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants.