2
Initial Movements of Modern Humans
in East Eurasia
Naruya Saitou, Timothy A. Jinam, Hideaki Kanzawa-Kiriyama
and Katsushi Tokunaga

This contribution discusses three topics touching on the initial movements of modern humans in East
Eurasia using genetic data:
1.
2.
3.

The emergence of modern humans including the establishment of the ‘Sahulian’ inhabitantsof the Pleistocene continent of Australia and adjacent islands.
Negritos as remnants of the initial dispersal to the Southeast Asian region.
The descendants of ancient human migration to the Japanese Archipelago.

From the emergence of modern humans to the establishmentof Sahulians
Anatomically modern humans (AMH) are now distributed all over the inhabited planet, andare genetically divided into six major groups: African, West Eurasian, East Eurasian, Sahulian,Northern American, and Southern American (Saitou 1995). It has now been established that
AMH originated in Sub-Saharan Africa. Nei and Roychoudhury (1974) estimated the divergencetimes of three human populations (African, East Eurasian, and West Eurasian) as ca. 120,000 BP
for the African and Eurasian split and ca. 55,000 BP for the East Eurasian–West Eurasian
divergence. Later, Nei and Ota (1991) obtained essentially the same divergence time estimatesfrom the allele frequency data of 181 loci.
More recently, Gronau et al. (2011) estimated somewhat different divergence times froma comparison of six personal genomes; 38,000–64,000 BP years for African and Eurasian
divergence, and 31,000–40,000 BP for West Eurasian and East Eurasian divergence. Although
the rooted tree topology is the same, the divergence time estimates between Africans and nonAfricans based on classic markers and genome data are rather different. Gronau et al. (2011)
also estimated the divergence time of San (bushman) and Yoruba in Nigeria as ca. 150,000 BP
when the human–chimpanzee divergence was assumed as 7.6 Mya, and migration between thesetwo populations after their divergence was surmised. If this estimate of human–chimpanzee
divergence is a close approximation then the emergence of modern humans would also date toat least ca. 150,000 BP.

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New Perspectives in Southeast Asian and Pacific Prehistory

Human movements during the ‘Out-of-Africa’ dispersal possibly started via coastal routes(e.g. Macaulay et al. 2005). If we connect the coastlines in present-day Tanzania and the northernreaches of Australia, the total length across land is less than 40,000 km. If AMH migrated along
this coastal route using raft-like boats, they could have arrived at present-day Australia within
110 years, assuming an average forward movement of 1 km per day. If they encountered any reason
to halt progressive movement and abandon the fringes of occupied territory, they could have
simply backtracked to their homeland by following the same coastline. The adventurous colonists
who continued to move south and east would have passed down the Thai-Malay Peninsula andoverland across ‘Sundaland’ as far as Borneo and Bali, and then traversed the islands of eastern
Indonesia before eventually settling in Sahul. Their descendants became Australian Aborigines
and Melanesians (including some of the present-day inhabitants of New Guinea, the islands of
the Bismarck and Solomon archipelagos, Australia and Tasmania).

Negritos as remnants of secondary dispersal within the
Indo‑Pacific Ocean area
Until the Holocene (starting ca. 11,000 BP), the present-day islands of Sumatra, Java andBorneo were joined together with the Asian mainland, forming a landmass known as Sundaland(Bellwood and Glover 2004). Sundaland was separated from Sahulland by multiple islands
referred to as Wallacea. Several human populations with characteristic morphological featuresin the Andaman Islands, the Philippines, and Peninsular Malaysia are collectively known as‘Negritos’. These Negritos may be remnants of early AMH dispersals within Island Southeast
Asia postdating the initial colonisation of Sahulland.
Omoto and his collaborators studied Philippine Negritos using classic genetic polymorphism
markers such as blood groups, red cell enzymes, and serum proteins (Omoto et al. 1978;
Omoto 1981, 1985). A phylogenetic tree shown in Omoto (1981) suggests that the Philippine
Negritos diversified after the Sahulians split off from Eurasians but before the majority of East
Eurasian lineages diversified. Omoto (1985) also demonstrated that the Mamanwa, a Negrito
population found on Mindanao Island, appear to be quite different from other Negrito groups
in the Philippines. We are now conducting genome-wide SNP data analysis of these Philippine
Negritos typed by one of us (Katsushi Tokunaga) as well as those for Malaysian and Andamanese
Negritos, and have found some shared components among these populations (Jinam et al. 2013).
Jinam et al. (2012) conducted a genetic analysis of Southeast Asian populations using SNP
data from PASNP (HUGO Pan-Asian Consortium 2009) and HGDP-CEPH panel database(www.cephb.fr/), together with newly generated complete mitochondrial DNA (mtDNA)
sequences in four indigenous Malaysian groups, and compared them with other populations.
These include three Austronesian groups (Temuan, Seletar, and Bidayuh) and a Negrito group(Jahai). Negritos in the Thai-Malay Peninsula currently speak Austro-Asiatic languages, but
this is attributed to ‘language switch’ following the mid-Holocene incursion of early AustroAsiatic populations into the Peninsula. Complete mtDNA sequences were newly determinedfrom 86 individuals (24 Jahai, 18 Temuan, 21 Seletar and 23 Bidayuh). These sequence data
are available from the DDBJ/EBA/GenBank International Nucleotide Sequence Databases
accession nos AP012346–AP012431. All individuals were assigned to specific haplogroups
belonging to M and N macro-haplogroups by following the nomenclature in these databases(www.phylotree.org).
Principal Component Analysis (PCA) was performed using haplogroup frequencies from thisstudy and from selected populations available in the literature. The PCA plot shown in Figure 2 ofJinam et al. (2012) shows that Negrito populations (Jahai, Kensiu, Batek and Mendriq) and one

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2. Initial Movements of Modern Humans in East Eurasia

45

non-Negrito population in the Thai-Malay Peninsula (Temuan) are clearly separated from other
Southeast Asian populations in terms of their PC1 coordinates. Interestingly, the population
closest to this ‘Peninsula Negrito’ cluster is Papuan. This suggests some level of shared ancestry
between Peninsula Negritos and Papuans. Five other (non-Papuan) populations, which are close
to the ‘Peninsula Negrito’ cluster, are non-Negrito populations in the Thai-Malay Peninsula andthe Philippine Negrito Mamanwa. This result also suggests some level of shared ancestry between
Peninsula and Philippine Negrito populations.
Phylogenetic trees of M and N mtDNA macro-haplogroups are shown in Figures 3A and 3B of
Jinam et al. (2012), and the coalescence time estimates of selected haplogroups based on mtDNA
coding-region sequences are shown in Table 3 of Jinam et al. (2012). These results show thatthe mtDNA lineages of all three populations living in the Thai-Malay Peninsula coalesce with
mtDNA sequences found from other geographical areas, and their coalescence time estimates areolder than 10,000 years ago.
Jinam et al.’s (2012) study included the first description of mtDNA diversity in four indigenous
Thai-Malay Peninsula populations using complete sequence data from all sampled individuals.
This is in contrast to most studies in which complete mtDNA sequencing was performed only
on selected haplotypes based initially on control region diversity. Such biased sampling can leadto exaggerated results in some analyses as demonstrated by Gunnarsdottir et al. (2011).
Jinam et al. (2012) also analysed genome-wide (~50,000 SNP) data for 17 human populations
that are mainly located in Southeast Asia. Those data were retrieved from the Pan-Asian
SNP database (www4a.biotec.or.th/PASNP) based on the paper by HUGO Pan-Asian SNP
Consortium (2009). PC1 of the PCA plot shown in Figure 4A of Jinam et al. (2012) clearly
separates Melanesian from the other populations. The Alorese in east Indonesia are closest
to Melanesian, suggesting some gene flow between them if we consider their geographicalpropinquity. Philippine Negritos lie between Alorese and other populations, and this suggests
some degree of shared common ancestry. Thai-Malay Peninsula Negritos are quite different
from all other populations in terms of PC2 coordinates. When these four outlier populations(Melanesians, Alorese, Philippine Negritos, and Peninsula Negritos) are eliminated fromcomparison, the remaining 13 populations are now well scattered in a circular structure as shownin Figure 4B of Jinam et al. (2012). The Bidayuh in Borneo and the Temuan in the Thai-Malay
Peninsula both show a ‘comet-like’ pattern (named by Jinam et al. 2012), which suggests recent
admixture with surrounding populations. The locations of the other 11 populations on this PCA
plot are as follows (counter-clockwise): Indigenous Taiwanese, Filipino, Mentawai, Sulawesi,
Sumatran, Malay, Dayak, Javanese, Cambodian, Thai, and South Chinese. This constellation of
populations is more or less consistent with the ‘Out-of-Taiwan’ model for the origins of people
who speak Austronesian languages (Bellwood 2005, 2007).
A phylogenetic network of 17 human populations mainly from Southeast Asia, which was
drawn by using Neighbor-Net (Bryant and Moulton 2004), is shown in Figure 2.1 (modified
from Figure 5B of Jinam et al. 2012). Consistent with the PCA plot (Figure 4A of Jinam et al.
2012), Melanesians fall well apart from all other populations, although Alorese are closest to
Melanesians because they are separated from the other 15 populations at split ‘a’. Interestingly,
split ‘b’ links Melanesians and Philippine Negritos. Splits ‘a’ and ‘b’ are incompatible witheach other, and a parallelogram is formed to represent the reticulated structure. These splits
suggest different types of shared ancestry or outcomes of recent Alorese-Melanesian admixture
and Philippine Negrito-Melanesian admixture. Splits ‘c’ and ‘d’ are also incompatible, as theformer indicates genetic similarity between the Temuan and Peninsula Negritos, while the latterterra australis 45

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New Perspectives in Southeast Asian and Pacific Prehistory

clusters Peninsula Negritos, Philippine Negritos, Alorese, and Melanesians. The dichotomy of
populations suggested by split ‘d’ may correspond to two major waves of human dispersals to
Southeast Asia and Oceania.
The paper by Jinam et al. (2013), which was included in the special Human Biology issue on
Negritos (Endicott 2013), analysed admixture patterns between two Peninsula Negrito groups(the Jahai and Kensiu) and surrounding populations. It found traces of recent admixture in both
Negrito populations, particularly the Jahai. It also identified significantly differentiated nonsynonymous SNPs and haplotype blocks related to intracellular transport, metabolic processes,
and detection of stimulus. These results highlight the different levels of admixture experienced
by the two Malaysian Negrito populations.
If we examine external edge lengths for each population in Figure 2.1, most of the populations
with large population size have short lengths, such as Southern Chinese, Thai, Javanese, Malays
and Filipinos. In contrast, populations with small population sizes tend to have long exterioredge length, such as Aboriginal Taiwanese, Mentawai in Sumatra, Dayak and Bidayuh in Borneo,
Temuan in Malay Peninsula, and Peninsula and Philippine Negritos. A possible exception is
Cambodians; although they have a large population size, their exterior edge length is quite
long. This suggests a unique history of the Cambodian population. It should also be notedthat populations who experienced admixture in the past, such as the Japanese of Japan’s central
islands, also tend to have short external edge lengths, as indicated by the Japanese Archipelago
Human Population Genetics Consortium (2012).
MentawaiTaiwanese

Sumatran
Aloreseb
Malay

Filipino
Torajac

Dayak
BidayuhJavanesedThai
S-Chinese

MelanesianaP-Negrito

TemuanM-Negrito
CambodianFigure 2.1 A phylogenetic network of 17 human populations based on genome-wide SNP data.
Source: Modified from Jinam et al. 2012.

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Descendants of ancient human migrants to the JapaneseArchipelago
After modern humans initially migrated into Sundaland and then Sahulland, their movements
northward reached the Japanese Archipelago, which has been populated for more than 40 Kya(Imamura 1996). The Jomon people were Neolithic hunter-gatherers who inhabited the JapaneseArchipelago from ca. 16,000 BP to 3000 BP (Harunari and Imamura 2004). The Jomon
culture is defined by the presence of cord-marked (‘jomon’ in Japanese) pottery, and ranged
geographically from Hokkaido to the Okinawa islands, stretching over 4,000 km from north tosouth. The archipelago was essentially disconnected from continental East Eurasia, by the end of
the last glacial period, from ca. 12,000 BP. The Jomon people were probably genetically isolated
from continental East Eurasians after that time. Craniofacial data suggests that the ancestorsof the Jomon came from somewhere in Southeast Asia (Hanihara 1991), while classic genetic
marker data (Omoto and Saitou 1997) and mtDNA sequence data (Adachi et al. 2011) suggest
a northern origin. Interestingly, the so-called Jomon mtDNA haplotypes (M7a and N9b) arerarely observed in other modern East Eurasians (Adachi et al. 2011). Therefore, the origins of the
Jomon people and their genetic relationship with other modern humans are still unclear.
Kanzawa-Kiriyama et al. (2013) determined the mtDNA haplotypes of four individuals excavatedfrom the Sanganji shell mound in Fukushima, Tohoku district, Japan, dating to the late and final
Jomon Period, between 4000–2500 BP. The haplogroup frequencies were 50 per cent for N9b
and 50 per cent for M7a2. Haplogroup N9b had previously been observed at high frequencies
in other Tohoku Jomon fossils and Hokkaido Jomon fossils, as well as the Okhotsk and Ainu
peoples, whereas its frequency is reported to be low in Kanto Jomon fossils and the modern
Japanese of the central islands. Sub-haplogroup M7a2 has previously been reported in Hokkaido
Jomon fossils, and the Okhotsk and modern Udegey peoples, but not amongst Kanto Jomon
fossils, or the Ainu or Ryukyu peoples.
Kanzawa-Kiriyama et al. (2013) also compared mtDNA haplogroup frequencies of Jomon
fossils from three areas (Tohoku, Hokkaido, and Kanto) and 15 present-day East Asians. The
phylogenetic network using Neighbor-Net (Bryant and Moulton 2004) based on Fst values isshown in Figure 2.2 (from Figure 4 of Kanzawa-Kiriyama et al. 2013). Interestingly, the Tohoku
and Hokkaido Jomon populations appear to be closely related, while the Kanto Jomons are
obviously distinct. The Udegey of Southern Siberia, who live near the Japan Sea, are relatively
closer to Tohoku and Hokkaido Jomon. The reticulation suggests that the Udegey represent an
admixture of southern Siberian populations and the northern Jomon people.
It should be noted that mtDNA is a single locus, and its genetic information is very limited even
if its complete genomic sequence is obtained. We have therefore proceeded to determine nuclear
DNA sequences that are much larger than mtDNA. The results (Kanzawa-Kiriyama et al. 2017)
clearly indicate that the present-day Japanese have inherited the DNA of Jomon people, as best
represented by the Ainu who are direct descendants of the Jomon. This confirms Hanihara’s(1991) dual structure model and the conclusion of Japanese Archipelago Human Population
Genetics Consortium (2012).

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New Perspectives in Southeast Asian and Pacific Prehistory
Tohoku Jomons
Hokkaido Jomons
0.1

UdegeyKanto Jomons

Ulchi

Nivkhi

Ryukyuan

Ainu

Mainland Japanese

Okhotsk
NegidalKorean

Northern Chinese
Yangtze River region ChineseSouthern Chinese

Kamchatkan

Northern
SiberianTaiwanese Aboriginals

Figure 2.2 A phylogenetic network of three ancient Jomon populations and 15 present-day
populations based on mtDNA haplotype frequencies. Scale bar represents the genetic distance
between populations based on mitochondrial DNA haplotype frequencies.
Source: From Kanzawa-Kiriyama et al. 2013; published with the permission of the Anthropological Society of Nippon.

Acknowledgements
This study is supported by a SOKENDAI strategic research grant given to Naruya Saitou and inpart by a Grant-in-Aid in 2011–2015 (no. 23247040) and 16H02527 (P.I. of both grants are
Hirobumi Matsumura) from the Japan Society for the Promotion of Science.
Authors are grateful to Dr Hirofumi Matsumura who gave us the opportunity to contribute
this paper to this book.

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This text is taken from New Perspectives in Southeast Asian and Pacific Prehistory,edited by Philip J. Piper, Hirofumi Matsumura and David Bulbeck, published 2017by ANU Press, The Australian National University, Canberra, Australia.