Jomon: Paleolithic Contingent in Modern Japanese

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Jomon: Paleolithic Contingent in Modern Japanese Sept 29, 2021 3:20:17 GMT

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Post by Admin on Sept 29, 2021 3:20:17 GMT

Upper Paleolithic northern migration route
The oldest samples providing the genetic evidence of the
northern migration route come from a high-coverage genome
sequence of individuals excavated from the Yana RHS
site in northeastern Siberia (Figure 2), which is about 31600
years old (Sikora et al., 2019). A wide range of artifacts,
including bonecrafts of wooly rhinoceros and mammoths,
were excavated at the site (Pitulko et al., 2004). The analysis
of genome sequences showed that the samples were deeply
diverged from most present-day East Asians and more closely
related to present-day Europeans, suggesting that the
population reached the area through a route different to the
southern route. A 24000-year-old individual excavated near
Lake Baikal (Figure 2), also known as the Mal’ta boy, and
17000-year-old individuals from the Afontova Gora II site
(Afontova Gora 2 and 3) showed similar genetic features to
the Yana individuals (Raghavan et al., 2014; Fu et al., 2016;
Sikora et al., 2019). Interestingly, genetic data suggested that
Yana individuals received a large amount of gene flow from
the East Asian lineage (Sikora et al., 2019; Yang et al.,
2020). A similar tie between early Western Eurasians and
East Asians was also reported by Lipson and Reich (Lipson
and Reich, 2017). In addition, Sikora et al. (2019) used an
admixture graph analysis to model the Mal’ta individual
(MA-1) as descendants of a population split from the ancestral
Yana, with a minor contribution from Late Paleolithic
hunter-gatherers in Caucasus after the split (Sikora et al.,
2019). Using our dataset, we confirmed that Yana individuals
shared more genetic drift with East Asian populations
than present-day Europeans do, and MA-1 shared more genetic
drift with present-day Europeans than Yana individuals
did (Supplementary Table 1). The populations of early migrants
to Northeast Asia, represented by Yana, Mal’ta, and
Afontova Gora individuals, are labeled as Ancient North
Siberians (Sikora et al., 2019), although we do not yet have
a complete picture of this population.

Last Edit: Sept 29, 2021 4:25:30 GMT by Admin

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Jomon: Paleolithic Contingent in Modern Japanese Sept 29, 2021 4:54:07 GMT

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Post by Admin on Sept 29, 2021 4:54:07 GMT

Around 20000 years ago (the time estimate has a broad
range, probably between 25000 and 15000 years ago (Sikora
et al., 2019)), Ancient North Siberians admixed with the
people who took the southern route, at least, for the second
time. The relatively high-coverage genome from a 9800-year-old
Kolyma individual (Kolyma1, Figure 2) was closely related to
present-day East and Northeast Asians, but also had
a significant amount of gene flow from Ancient North Siberians.
Interestingly, the Kolyma individual showed a stronger genetic
affinity to the Mal’ta than to the Yana individuals.
This observation is consistent with the archeological evidence
that shows a discontinuity in human occupation at
Yana for about 10000 years, meaning that genetic components
specific to Yana did not directly contribute to any
present-day populations. The Kolyma individual was genetically
close to present-day ethnic groups in the Chukchi and
Kamchatka regions and to Native Americans, but the shared
ancestry with Ancient North Siberians was more pronounced
in the Native Americans than in the Kolyma individual
(Sikora et al. 2019). Using a maximum composite likelihood
method, they estimated the divergence time of Kolyma and
Native American lineages as around 24000 years ago and
postulated that these lineages received gene flow from Ancient
North Siberians after their split (Sikora et al., 2019).
The above observation indicates that the ancestral population
of the Kolyma people and Native Americans independently received
gene flow from Ancient North Siberians.
When and how did the admixture take place? Studies of
mitochondrial and autosomal genomes from ancient and
present-day Alaskans and Native Americans suggest that the
ancestral populations for all Native Americans were isolated
in the Beringia regions during the Last Glacial Maximum
(LGM) from 25000 to 15000 years ago and spread to the
New World after that. This is referred to as the standstill
model (Bonatto and Salzano, 1997; Tamm et al., 2007;
Hoffecker et al., 2016; Moreno-Mayar et al., 2018). Under
this model, we are able to assume that the admixture between
a population from the southern route and Ancient
North Siberians occurred around 25000 years ago. It might
be reasonable to assume that the admixture of populations
occurred at refugia during the LGM; however, genetic data
alone do not indicate the location of any actual refugium.
Sikora et al. (2019) performed a paleoclimate reconstruction
to find potential regions for such refugia during the LGM
and showed southern Beringia could potentially have been
the one.

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Jomon: Paleolithic Contingent in Modern Japanese Sept 29, 2021 12:59:35 GMT

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Post by Admin on Sept 29, 2021 12:59:35 GMT

Paleolithic population history in Southeast and East Asia
After reaching Sundaland, some populations that had taken
southern route migrated further northward. Fossil remains of
anatomically modern Homo sapiens appeared as
early as 40000 years ago in several places in China, such as
Zhoukoudian Upper Cave and Tianyuan Cave (Figure 2)
(Kaifu and Fujita, 2012; Shelach-Lavi, 2015). A partial genome
sequence of the Tianyuan individual was determined
by Fu et al. (2013). Studies showed the Tianyuan lineage at
the root of all East and Northeast Asian populations (Fu et
al., 2013; Yang et al., 2017); however, mixed results have
been obtained when trying to determine whether the lineage
of the Tianyuan split from ancestors was before or after the
split of the early Asians such as Papuans and Negritos (Fu et
al., 2013; Yang et al., 2017; McColl et al., 2018; Kim et al.,
2020). We performed a meta-analysis with f4 statistics to
confirm the genetic relationship of the Tianyuan individual
to other East Asian populations. f4 statistics with a configuration
of f4(W, X; Y, Z) measure the amount of shared genetic
drift between W and Y, or X and Z. If we fix the population
W as the outgroup population that did not experience recent
gene flow with X, Y, and Z, then positive and negative f4
values indicate the gene flow between X and Z, and between
X and Y, respectively. Throughout this article, we fix the
Yoruba population as the W. Here we present the results
fixing the Dai population as the Z and selecting various ancient
and present-day Southeast, East, and Northeast Asian
populations as the Y in Supplementary Tables 2 and 3. Most
Southeast, East, and Northeast Asian populations, including
Jomon, are nearly equally distant from the Tianyuan individual,
supporting the hypothesis that the Tianyuan population
are diverged from the lineage basal to all East and Northeast
Asians. The Tianyuan individual was significantly more
closely related to the Dai population than to the Jehai,
Kusunda, and Papuan populations (Supplementary Table 3).

However, a further f4 analysis showed that the Tianyuan individual
would be placed to more basal position of Asians
than the Kusunda and Jehai, as the deviation of f4 statistics is
considerably smaller in f4(Yoruba, Tianyuan; Kusunda/
Jehai, Dai) than in f4(Yoruba, Kusunda/Jehai; Tianyuan, Dai)
(Supplementary Table 3). The reason why the Tianyuan individual
is more closely related to the Dai population than to
the Kusunda/Jehai populations is not clear, but might be due
to the Kusunda and Jehai genomes containing some genetic
component derived from relatively distant populations. For
example, we found that the Kusunda population is more
closely related to Europeans (CEU, Utah residents with
Northern and Western European ancestry) than the Dai population
is (Z = –3.06, Supplementary Table 3). Such unknown bias would
make it difficult to define basal populations by presenting a
tree-shaped population relationship. In
contrast, the Papuan population showed only marginal deviation
of f4(Yoruba, Papuan; Tianyuan, Dai) value (Z = 2.26),
supporting the hypothesis that the population related to the
Tianyuan individual diverged after the split of the Papuan
population (Supplementary Table 3).
Interestingly, previous studies showed that the Tianyuan
individual showed some genetic similarity to a 35000-yearold
ancient West Eurasian individual (GoyetQ116-1) and
some specific native South Americans (Surui) (Yang et al.,
2017). In addition, Sikora et al. (2019) presented data showing
that the Yana samples have substantially more genetic
affinity to the Tianyuan individual than to other early Western
hunter-gatherers (Sikora et al., 2019), indicating the
early contact between the populations passing along the
southern and northern routes. A similar pattern was also
shown by Yang et al. (2020).
Several lineages, such as Jehai, Kusunda, and Jomon,
form basal populations to all East and Northeast Asian populations.
These populations and a population related to the
Tianyuan, seem to have spread to widely across South,
Southeast, and East Asia. In addition to these populations, a
recent ancient-genome sequencing of Hoabinhian hunter-gatherers
from Laos and Malaysia (~5800–2300 BCE)
showed that these hunter-gatherers were genetically close to
Andamanese Negritos (Onge) and admixed with populations
from southern China in the Neolithic era (McColl et al.,
2018). In addition, the Hoabinhian individuals showed a
statistically significant genetic relationship with a Jomon
individual from Ikawazu demonstrating the southern-route
origin of the Jomon people (McColl et al., 2018; Gakuhari et
al., 2020; but also see de Boer et al., 2020 for a different result).

Last Edit: Sept 29, 2021 21:25:27 GMT by Admin

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Jomon: Paleolithic Contingent in Modern Japanese Sept 29, 2021 21:24:02 GMT

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Post by Admin on Sept 29, 2021 21:24:02 GMT

Neolithic population history in East Eurasia
Neolithic population history in Southeast Asia
As shown in the previous section, a population split from
Tianyuan became the major ancestral root of all present-day
populations in East and Northeast Asia. In a principal component a
nalysis (PCA) plot including a wide-range of
Southeast, East, and Northeast Asian populations presented
by Yang et al. (2020), two major genetic clines were observed: a
south-to-north genetic cline and a Han-to-Tibetan
genetic cline. Figure 3 shows our PCA plot of East and
Northeast Asians with projections of several ancient individuals
in East Asia. Note that we focus here on the East Asian
populations and do not include Tibetan-related populations,
because our primary dataset did not contain many Tibetan-related
individuals. In the plot, we can see Southeast Asian
populations such as Cambodians, Dai people, and Kinh
Vietnamese are placed on the southernmost side of the cline.
In southern China, Neolithic populations lived around 7500
BCE in the Middle and Lower Yangtze River basin and
rice-farming became prevalent as early as 5000 BCE
(Bellwood, 2004; Shelach-Lavi, 2015). Recent studies of
ancient genomes mostly support the scenario where southward movements
of rice-farming Neolithic people from
southern China greatly influenced the current genetic architecture of
Southeast Asians, Melanesians, Micronesians, and
Polynesians (Lipson et al., 2018a; McColl et al., 2018; Yang
et al., 2020). The pattern is also consistent with the distribution
of diverse languages spoken in the area and provides
examples of how human migration in the Late Neolithic era
can explain the current distribution of various languages
(Diamond and Bellwood, 2003; Bellwood, 2004).

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Jomon: Paleolithic Contingent in Modern Japanese Sept 30, 2021 3:05:01 GMT

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Post by Admin on Sept 30, 2021 3:05:01 GMT

The best-known example of migration patterns linking to
linguistic patterns is the case of the Austronesian-speaking
Neolithic population’s expansion to Micronesia, Melanesia,
and Polynesia through the island of Taiwan, which has been
supported by both archeological and linguistic data (Gray
and Jordan, 2000; Diamond and Bellwood, 2003; Bellwood,
2004). The expansion was estimated to start around 3000
BCE, arrive at the Bismarck Archipelago around 1000 BCE
(Sheppard et al., 2015), and finally reach the eastern part of
the Polynesian islands by 1000 AD. The migration process is
also well reflected by the genetic data of present-day
Polynesians (Wollstein et al., 2010; Ko et al., 2014; Lipson et al.,
2014). The ancient-genome sequences of Vanuatu (~1100–
700 BCE) and Tonga (~700–300 BCE) populations revealed
a detailed but complex migration history from New Guinea
to remote Oceania (Skoglund et al., 2016; Lipson et al.,
2018b). The unsolved question is: if the migration started
from southern China, what were the genetic features of the
original migrants? A very recent study of ancient-genome
sequencing from southern China, including approximately
5000-year-old samples from the island of Taiwan and Fujian
province, revealed that the Late Neolithic people (~3000–
2000 BCE) in the southern coastal regions of China were
genetically very close to present-day Austronesian-speaking
people, even closer than the Early Neolithic people in these
regions were (Skoglund et al., 2016; Yang et al., 2020).
The migration of Neolithic rice-farmers to mainland (continental)
Southeast Asia has also been reinforced by many
present-day and ancient genome studies (Lipson et al.,
2018a; McColl et al., 2018; Liu et al., 2020). Mainland
Southeast Asia is home to people speaking diverse languages,
including Austronesian, Austroasiatic, Tai-Kadai (KraDai),
Sino-Tibetan (including Tibeto-Burman), and HmongMien languages.
All these different languages are considered
to have spread with Neolithic farmers from the north.
Ancient-genome studies showed that Neolithic/Bronze Age/
Iron Age people in this area were admixed with populations
related to the first-layer hunter-gatherers, such as the
Hoabinhian hunter-gatherers. Most Neolithic samples were
genetically very similar to present-day Southeast Asians,
indicating that the Neolithic migrants rapidly admixed with
indigenous populations, or already admixed with the
first-layer people before reaching these regions (Lipson et
al., 2018a; McColl et al., 2018). A more recent study examining
present-day Vietnamese individuals with diverse languages showed
that the Austroasiatic group was the first to
enter the regions and admix with indigenous people. People
speaking Austronesian, Tai-Kadai, Hmong-Mien, and SinoTibetan
migrated to the area after the Austroasiatic-speaking
people (Liu et al., 2020). This study also revealed cultural
interaction among people speaking different language groups
at a later stage with or without gene flow.

Last Edit: Sept 30, 2021 3:06:20 GMT by Admin