Modelling of prehistoric dispersal of rice varieties in India point to a north-western origin

rice-dispersal

New paper (behind paywall), A tale of two rice varieties: Modelling the prehistoric dispersals of japonica and proto-indica rices, by Silva et al., The Holocene (2018).

Interesting excerpts (emphasis mine):

Materials

Our empirical evidence comes from the Rice Archaeological Database (RAD). The first version of this database was used for a synthesis of rice dispersal by Fuller et al. (2010), a slightly expanded dataset (version 1.1) was used to model the dispersal of rice, land area under wet rice cultivation and associated methane emissions from 5000–1000 BP (Fuller et al., 2011). The present dataset (version 2) was used in a previous analysis of the origins of rice domestication (Silva et al., 2015). The database records sites and chronological phases within sites where rice has been reported, including whether rice was identified from plant macroremains, phytoliths or impressions in ceramics. Ages are recorded as the start and end date of each phase, and a median age of the phase is then used for analysis. Dating is based on radiocarbon evidence (…)

Modelling framework

Our approach expands on previous efforts to model the geographical origins, and subsequent spread, of japonica rice (Silva et al., 2015). The methodology is based on the explicit modelling of dispersal hypotheses using the Fast Marching algorithm, which computes the cost-distance of an expanding front at each point of a discrete lattice or raster from the source(s) of diffusion (Sethian, 1996; Silva and Steele, 2012, 2014). Sites in the RAD database are then queried for their cost-distance, the distance from the source(s) of dispersal along the cost-surface that represents the hypothesis being modelled (see Connolly and Lake, 2006; Douglas, 1994; Silva et al., 2015; Silva and Steele, 2014 for more on this approach) and, together with the site’s dating, used for regression analysis. (…)

india-japonica-rice
Predicted arrival times of the non-shattering rice variety (japonica or the hybrid indica) across southern Asia based on best-fitting model H2. Included are also sites with known presence of non-shattering spikelet bases (see text).

Model and results

The ‘Inner Asia Mountain Corridor’ hypothesis (H2) therefore predicts japonica rice to arrive first in northwest India via a route that starts in the Yellow river valley, travels west via the well-known Hexi corridor, then just south of the Inner Asian Mountains and thence to India.

The results also show that the addition of the Inner Asia Mountain Corridor significantly improves the model’s fit to the data, particularly model H2 where rice is introduced to the Indian subcontinent exclusively via a trade route that circumvents the Tibetan plateau. This agrees with independent archaeological evidence that sees millets spread westwards along this corridor perhaps as early as 3000 BC (e.g. Boivin et al., 2012; Kohler-Schneider and Canepelle, 2009; Rassamakin, 1999) and certainly by 2500–2000 BC (Frachetti et al., 2010; Spengler 2015; Stevens et al., 2016), that is, in the same time frame as that predicted for rice in model H2. The arrival of western livestock (sheep, cattle) into central China, 2500–2000 BC (Fuller et al., 2011; Yuan and Campbell, 2009), and wheat, ca. 2000 BC (Betts et al., 2014; Flad et al., 2010; Stevens et al., 2016; Zhao, 2015), add evidence for the role of the Inner Asia Mountain Corridor for domesticated species dispersal in this period.

Conclusion

Through a combination of explicit spatial modelling and simulation, we have demonstrated the high likelihood that dispersal of rice via traders in Central Asia introduced japonica rice into South Asia. Only slightly less likely is a combination of introduction via two routes including a Central Asia to Pakistan/northwestern India route as well as introduction to northeastern India directly from China/Myanmar. However, there is a very low probability that current archaeological evidence for rice fits with a single introduction of japonica into India via the northeast. We have also simulated the minimum amount of archaeobotanical sampling from the Neolithic (to Bronze Age) period in the regions of northeastern India and Myanmar that will be necessary to strengthen support for the combined introduction (model H3) or a single Central Asian introduction (model H2).

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South-East Asia samples include shared ancestry with Jōmon

pca-south-east-asia-jomon

New paper (behind paywall) The prehistoric peopling of Southeast Asia, by McColl et al. (Science 2018) 361(6397):88-92 from a recent bioRxiv preprint.

Interesting is this apparently newly reported information including a female sample from the Ikawazu Jōmon of Japan ca. 570 BC (emphasis mine):

The two oldest samples — Hòabìnhians from Pha Faen, Laos [La368; 7950 with 7795 calendar years before the present (cal B.P.)] and Gua Cha, Malaysia (Ma911; 4415 to 4160 cal B.P.)—henceforth labeled “group 1,” cluster most closely with present-day Önge from the Andaman Islands and away from other East Asian and Southeast-Asian populations (Fig. 2), a pattern that differentiates them from all other ancient samples. We used ADMIXTURE (14) and fastNGSadmix (15) to model ancient genomes as mixtures of latent ancestry components (11). Group 1 individuals differ from the other Southeast Asian ancient samples in containing components shared with the supposed descendants of the Hòabìnhians: the Önge and the Jehai (Peninsular Malaysia), along with groups from India and Papua New Guinea.

We also find a distinctive relationship between the group 1 samples and the Ikawazu Jōmon of Japan (IK002). Outgroup f3 statistics (11, 16) show that group 1 shares the most genetic drift with all ancient mainland samples and Jōmon (fig. S12 and table S4). All other ancient genomes share more drift with present-day East Asian and Southeast Asian populations than with Jōmon (figs. S13 to S19 and tables S4 to S11). This is apparent in the fastNGSadmix analysis when assuming six ancestral components (K = 6) (fig. S11), where the Jōmon sample contains East Asian components and components found in group 1. To detect populations with genetic affinities to Jōmon, relative to present-day Japanese, we computed D statistics of the form D(Japanese, Jōmon; X, Mbuti), setting X to be different presentday and ancient Southeast Asian individuals (table S22). The strongest signal is seen when X=Ma911 and La368 (group 1 individuals), showing a marginally nonsignificant affinity to Jōmon (11). This signal is not observed with X = Papuans or Önge, suggesting that the Jōmon and Hòabìnhians may share group 1 ancestry (11).

jomon-japanese-migrations
Model for plausible migration routes into SEA. This schematic is based on ancestry patterns observed in the ancient genomes. Because we do not have ancient samples to accurately resolve how the ancestors of Jōmon and Japanese populations entered the Japanese archipelago, these migrations are represented by dashed arrows. A mainland component in Indonesia is depicted by the dashed red-green line. Gr, group; Kra, Kradai.

(…) Finally, the Jōmon individual is best-modeled as a mix between a population related to group 1/Önge and a population related to East Asians (Amis), whereas present-day Japanese can be modeled as a mixture of Jōmon and an additional East Asian component (Fig. 3 and fig. S29)

Interesting in relation to the oral communication of the SMBE O-03-OS02 Whole genome analysis of the Jomon remain reveals deep lineage of East Eurasian populations by Gakuuhari et al.:

Post late-Paleolithic hunter-gatherers lived throughout the Japanese archipelago, Jomonese, are thought to be a key to understanding the peopling history in East Asia. Here, we report a whole genome sequence (x1.85) of 2,500-year old female excavated from the Ikawazu shell-mound, unearthed typical remains of Jomon culture. The whole genome data places the Jomon as a lineage basal to contemporary and ancient populations of the eastern part of Eurasian continent, and supports the closest relationship with the modern Hokkaido Ainu. The results of ADMIXTURE show the Jomon ancestry is prevalent in present-day Nivkh, Ulchi, and people in the main-island Japan. By including the Jomon genome into phylogenetic trees, ancient lineages of the Kusunda and the Sherpa/Tibetan, early splitting from the rest of East Asian populations, is emerged. Thus, the Jomon genome gives a new insight in East Asian expansion. The Ikawazu shell-mound site locates on 34,38,43 north latitude, and 137,8, 52 east longitude in the central main-island of the Japanese archipelago, corresponding to a warm and humid monsoon region, which has been thought to be almost impossible to maintain sufficient ancient DNA for genome analysis. Our achievement opens up new possibilities for such geographical regions.

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Complex history of dog origins and translocations in the Pacific revealed by ancient mitogenomes

remote-oceania-vanuatu-lapita

Open access Complex history of dog (Canis familiaris) origins and translocations in the Pacific revealed by ancient mitogenomes, by Creig et al., Scientific Reports (2018).

Abstract:

Archaeological evidence suggests that dogs were introduced to the islands of Oceania via Island Southeast Asia around 3,300 years ago, and reached the eastern islands of Polynesia by the fourteenth century AD. This dispersal is intimately tied to human expansion, but the involvement of dogs in Pacific migrations is not well understood. Our analyses of seven new complete ancient mitogenomes and five partial mtDNA sequences from archaeological dog specimens from Mainland and Island Southeast Asia and the Pacific suggests at least three dog dispersal events into the region, in addition to the introduction of dingoes to Australia. We see an early introduction of dogs to Island Southeast Asia, which does not appear to extend into the islands of Oceania. A shared haplogroup identified between Iron Age Taiwanese dogs, terminal-Lapita and post-Lapita dogs suggests that at least one dog lineage was introduced to Near Oceania by or as the result of interactions with Austronesian language speakers associated with the Lapita Cultural Complex. We did not find any evidence that these dogs were successfully transported beyond New Guinea. Finally, we identify a widespread dog clade found across the Pacific, including the islands of Polynesia, which likely suggests a post-Lapita dog introduction from southern Island Southeast Asia.

canis-familiaris
A map of Southeast Asia and the Pacific showing the source location of the specimens and associated haplogroups (assignment to haplogroup follows Duleba and colleagues) and the median-joining network. The boundary between Near and Remote Oceania is also shown. Symbols identify the type of sequence: filled circle, ancient mitogenome; half circle, partial ancient sequence; hollow circle, modern mitogenome. Node colours represent the haplogroup, grey, A; red, A2b2, green, A2b3; yellow, A4’5; blue, B.

Conclusion:

The dispersal of dogs across the Pacific is inseparably linked to the relationships between dogs and people. Unlike movement across continental landmasses, Pacific dogs must have been transported by people across the waters that separate islands. The ancient mitogenomes sequenced from archaeological dog specimens presented here offer a novel series of individual insights into the history of dog translocation from Southeast Asia as it occurred prior to the influence of modern European dog breeds. We generated seven mitogenomes and five partial sequences from ancient MSEA, ISEA and Pacific dogs, and four modern dingoes. Despite the small sample size, our results reveal levels of complexity and discontinuity in the introduction and movement of dogs, which are mirrored in the archaeological and linguistic evidence, suggesting at least three introductions of dogs to the wider Pacific region, in addition to the earlier appearance of the dingo in Australia. Further mtDNA studies of ancient dogs and modern village populations throughout the region may contribute additional data that can be used to evaluate these hypothesised dispersals. Autosomal and Y-chromosome analyses also have the potential to generate additional information about dog dispersal, which could reveal different dispersal signatures based on sex, or phenotypic characteristics, though the environmental conditions in the region are not particularly conducive to aDNA preservation.

Our molecular genetic analyses reveal one of the earliest dogs present in ISEA around 3,000 years ago from Timor-Leste possesses a mtDNA lineage not found elsewhere in the region. We also found similarities between mtDNA of modern dingoes and NGSDs and an ancient Taiwanese sequence, which supports previous observations about possible links between Y-chromosome markers of modern dingoes and a modern Taiwanese sample. More work is required to address whether these connections reflect the genetic diversity of a shared ancestral population in mainland China, or attest to a currently unknown dispersal event linking the two populations. Archaeological evidence for the introduction of dogs to Oceania as part of the LCC is extremely limited. Nonetheless, we demonstrate that mitogenomes from dogs in terminal Lapita and post-Lapita levels of archaeological sites along the south coast of mainland New Guinea also show affinities with an Iron Age dog specimen from Taiwan, raising the possibility of at least one introduction of dogs during Austronesian expansions ultimately from the north. Finally, we have identified a major late introduction of dogs across the islands of Oceania beginning around 2,000 years ago, which appears to have originated in MSEA, not Taiwan, and culminated in the establishment of dog populations in initial colonisation-era sites throughout East Polynesia.

phylogenetic-dingo
Molecular phylogenetic analysis by maximum likelihood method, implemented in MEGA71. The evolutionary history shown inferred by using the maximum likelihood method based on the Hasegawa-Kishino-Yano model. The tree with the highest log likelihood (-25257.5243) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.0500)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 0.0010% sites). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 45 nucleotide sequences. There were a total of 16774 positions in the final dataset.

Also related, open access Elucidating biogeographical patterns in Australian native canids using genome wide SNPs, by Cairns et al., PLOS One (2018).

Abstract:

Dingoes play a strong role in Australia’s ecological framework as the apex predator but are under threat from hybridization and agricultural control programs. Government legislation lists the conservation of the dingo as an important aim, yet little is known about the biogeography of this enigmatic canine, making conservation difficult. Mitochondrial and Y chromosome DNA studies show evidence of population structure within the dingo. Here, we present the data from Illumina HD canine chip genotyping for 23 dingoes from five regional populations, and five New Guinea Singing Dogs to further explore patterns of biogeography using genome-wide data. Whole genome single nucleotide polymorphism (SNP) data supported the presence of three distinct dingo populations (or ESUs) subject to geographical subdivision: southeastern (SE), Fraser Island (FI) and northwestern (NW). These ESUs should be managed discretely. The FI dingoes are a known reservoir of pure, genetically distinct dingoes. Elevated inbreeding coefficients identified here suggest this population may be genetically compromised and in need of rescue; current lethal management strategies that do not consider genetic information should be suspended until further data can be gathered. D statistics identify evidence of historical admixture or ancestry sharing between southeastern dingoes and South East Asian village dogs. Conservation efforts on mainland Australia should focus on the SE dingo population that is under pressure from domestic dog hybridization and high levels of lethal control. Further data concerning the genetic health, demographics and prevalence of hybridization in the SE and FI dingo populations is urgently needed to develop evidence based conservation and management strategies.

dingo-australia-pca
Principal components analysis (PCA) based upon filtered whole genome SNP genotypes (58,512 sites) for 23 dingoes, 5 NGSD, 8 Borneo village dogs, 9 Vietnam village dogs, 10 Portugal village dogs and 8 Australian cattle dogs (‘Dataset B’). Colours represent population clusters: red for SE dingoes, purple for FI dingoes, blue for NW dingoes, dark green for NGSD, light green for Borneo village dogs, orange for Vietnam village dogs, yellow for Portugal village dogs and grey for Australian cattle dogs. (A) PC 1 versus PC 2. (B) PC 1 versus PC 3.

As I said in a previous post, the study of dogs may be useful to trace population migrations and to assess strong cultural contacts. Especially, as in this case, when crossbreeding among cultures is not easy…

Related:

Oldest bubonic plague genome decoded in Srubna ca. 3800 YBP

New open access paper from the Max Planck Institute: Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague, by Spyrou et al., Nature Communications (2018) 9:2234.

Interesting excerpts from the paper and supplementary materials (emphasis mine):

Here, we analyse material from the Mikhailovsky II burial site, which was excavated in 2015 and is one of numerous kurgan cemeteries identified in the Samara Oblast. It consists of seven kurgan burials, and is chronologically associated to the ‘Pokrovka’ phase (3,900-3,750 BP) of the ‘Srubnaya’ culture (3,850-3,150 BP) (radiocarbon dates produced in this study provided in Supplementary Table 6), also referred to as the ‘proto-Srubnaya’ that is considered the earliest phase of the LBA in the Samara Oblast. All sex and age groups were represented in this cemetery. We analysed nine individuals buried in three kurgans and identified two individuals buried in the same kurgan (see Supplementary Figure 1) to be positive for Y. pestis. According to anthropological analysis these were a 30-40 year-old male (RT5) and 35- 45 year-old female (RT6).

After its divergence from Y. pseudotuberculosis, Y. pestis acquired its high pathogenicity and distinct niche mainly by chromosomal gene loss16 as well as the acquisition of two virulence-associated plasmids, pMT1 and pPCP11,17,18. Throughout this process, one of the most crucial evolutionary adaptations related to its pathogenicity was its ability to colonise arthropods, a phenotypic/functional gain mediated by a combination of chromosomal and plasmid loci19,20. These genetic changes are central to the most common “bubonic” form of the disease, where bacteria enter the body via the bite of an infected flea, travel via the lymph to the closest lymph node and replicate while evading host defences. Recent ancient genomic investigations of Y. pestis have identified its earliest known variants in Eurasia during the Late Neolithic/Bronze Age period (LNBA) that show genetic characteristics incompatible with arthropod adaptation. These strains, therefore, have been considered incapable of an efficient flea-based transmission2; however, the alternative early-phase transmission could have provided an independent means of arthropod dissemination2,3,21. To date, the earliest evidence of a Y. pestis strain with signatures associated with flea adaptation has been reported during the Iron Age through shotgun sequencing of an ~2900-year-old genome from Armenia (strain RISE397), though at a coverage too low (0.25-fold) to permit confident phylogenetic positioning2. Although the mechanism by which the LNBA lineage caused human disease is unclear, its frequency in Eurasia during the Bronze Age2,3 and its phylogeographic pattern that mimics contemporaneous human migrations are noteworthy3.

population-srubna-pca
Population genetic analysis to infer the ancestry of RT5. b Principal component analysis (PCA) of modern-day western Eurasian populations (not shown) and projected ancient populations (n = 82, see population labels), including the newly sequenced RT5 individual from Samara and c estimation of ancestral admixture components using ADMIXTURE analysis (K= 12) (see Supplementary Methods)

The central steppe region seems to have played a significant role as a migration corridor during the entire Bronze Age, and as such, it likely facilitated the spread of human-associated pathogens, such as Y. pestis, across Eurasia. Here, we explore additional Y. pestis diversity in that region by isolating strains from LBA Samara, in Russia. We identify a Y. pestis lineage contemporaneous to the LNBA strains with genomic variants consistent with flea adaptation. This reveals the co-circulation of two Y. pestis lineages during the Bronze Age with different properties in terms of their transmission and disease potentials.

A recent study has suggested that flea-adapted Y. pestis, along with its potential to cause bubonic plague in humans, likely originated around 3000y BP2. Contrary to such conclusions, the lineage giving rise to our Y. pestis isolates (RT5 and RT6) likely arose ~4000 years ago (Supplementary Tables 6 and 9), and possessed all vital genetic characteristics required for flea-borne transmission of plague in rodents, humans and other mammals. (…)

Moreover, our analysis of the previously published Iron Age RISE397 strain from modern-day Armenia2 revealed its close relationship to RT5 and RT6 (Supplementary Fig. 4). Note that the modern 0.PE2 and 0.PE7 lineages, which are known to possess all genomic characteristics that confer adaptation to fleas19, fall ancestral to RT5 (Fig. 2b) and RISE397 (Supplementary Fig. 4), but are more derived than the LNBA lineage. Our phylogenetic and dating results thus suggest that 0.PE2 and 0.PE7 also originated during the Bronze Age, with their mean divergence here estimated to 4474 (HPD 95%: 3936–5158) and 5237 (HPD 95%: 4248–6346) years BP, respectively, based on the Bayesian skyline model (Supplementary Table 9). While these lineages may have been confined to sylvatic rodent reservoirs during the EBA, the possibility that they co circulated among human populations contemporaneously with the LNBA lineage should be considered. Although the places of origin of 0.PE2 and 0.PE7 are not known, today, their strains are isolated from modern-day China and the Caucasus region. In terms of their disease potential, both 0.PE2 and 0.PE7 possess pMT1 plasmids with fully functional ymt genes, but 0.PE2 strains lack pPCP144, and though frequently recovered from sylvatic rodent reservoirs, their virulence in humans is not known. On the other hand, the more basal 0.PE7 contains pPCP12 and has previously been associated with human bubonic plague12. It is, therefore, tempting to hypothesise that efficient flea adaptation in Y. pestis, as well as the potential for bubonic disease, might have evolved earlier than 5000 years ago.

plague-clade-tree
Maximum Clade Credibility tree. The MCC tree was produced using TreeAnnotator of BEAST v1.88 and is a product of demographic analysis based on the Coalescent Skyline model, summarizing 27,001 trees. The tree was visualized in FigTree v1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). It is presented in a temporal scale between 6,000 and 0 yBP, and the mean divergence dates of major Y. pestis lineages are indicated on each corresponding node.

It seems possible that already in the Bronze Age, with the establishment of transport and trade networks, the interconnectivity between Europe and Asia that is also reflected in the ancient human genomes, likely contributed to the spread of infectious disease. Similarly, the abundant trade routes of the medieval period are considered the main conduit for plague’s movement between Asia and Europe8,12. Our current data suggest a more complex model, where at least two human-associated lineages (LNBA and RT5) with different transmission potentials were established in Eurasia during the Bronze Age (Fig. 2b, c).

The haplogroup of RT5 is R1a1a1b-Z645 (most likely Z93, only with coverage of 1-fold), mtDNA U2e2a.

See also materials from the Max Plank Institute.

Related:

Ancient Di-Qiang people show early links with Han Chinese

china-genetics-peoples

Bernard Sécher reports on a recent article, Ancient DNA reveals genetic connections between early Di-Qiang and Han Chinese, by Li et al., BMC Evolutionary Biology (2017).

Abstract:

Background
Ancient Di-Qiang people once resided in the Ganqing region of China, adjacent to the Central Plain area from where Han Chinese originated. While gene flow between the Di-Qiang and Han Chinese has been proposed, there is no evidence to support this view. Here we analyzed the human remains from an early Di-Qiang site (Mogou site dated ~4000 years old) and compared them to other ancient DNA across China, including an early Han-related site (Hengbei site dated ~3000 years old) to establish the underlying genetic relationship between the Di-Qiang and ancestors of Han Chinese.

Results
We found Mogou mtDNA haplogroups were highly diverse, comprising 14 haplogroups: A, B, C, D (D*, D4, D5), F, G, M7, M8, M10, M13, M25, N*, N9a, and Z. In contrast, Mogou males were all Y-DNA haplogroup O3a2/P201; specifically one male was further assigned to O3a2c1a/M117 using targeted unique regions on the non-recombining region of the Y-chromosome. We compared Mogou to 7 other ancient and 38 modern Chinese groups, in a total of 1793 individuals, and found that Mogou shared close genetic distances with Taojiazhai (a more recent Di-Qiang population), Hengbei, and Northern Han. We modeled their interactions using Approximate Bayesian Computation, and support was given to a potential admixture of ~13-18% between the Mogou and Northern Han around 3300–3800 years ago.

Conclusions
Mogou harbors the earliest genetically identifiable Di-Qiang, ancestral to the Taojiazhai, and up to ~33% paternal and ~70% of its maternal haplogroups could be found in present-day Northern Han Chinese.

chinese-ancient-modern-genetics-pca
MDS plot of genetic distance Fst between 3 ancient and 38 modern Chinese groups

Interesting times now for the investigation of potential migrations associated with the expansion of Sino-Tibetan and Altaic languages

Related:

Two more studies on the genetic history of East Asia: Han Chinese and Thailand

chinese-eurasian-drift

A comprehensive map of genetic variation in the world’s largest ethnic group – Han Chinese, by Charleston et al. (2017).

It is believed – based on uniparental markers from modern and ancient DNA samples and array-based genome-wide data – that Han Chinese originated in the Central Plain region of China during prehistoric times, expanding with agriculture and technology northward and southward, to become the largest Chinese ethnic group.

Abstract:

As are most non-European populations around the globe, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our dataset. Individuals from our study come from 19 out of 22 provinces across China, allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identify previously unrecognized population structure along the East-West axis of China and report unique signals of admixture across geographical space, such as European influences among the Northwestern provinces of China. Finally, we identified a number of highly differentiated loci, indicative of local adaptation in the Han Chinese. In particular, we detected extreme differentiation among the Han Chinese at MTHFR, ADH7, and FADS loci, suggesting that these loci may not be specifically selected in Tibetan and Inuit populations as previously suggested. On the other hand, we find that Neandertal ancestry does not vary significantly across the provinces, consistent with admixture prior to the dispersal of modern Han Chinese. Furthermore, contrary to a previous report, Neandertal ancestry does not explain a significant amount of heritability in depression. Our findings provide the largest genetic data set so far made available for Han Chinese and provide insights into the history and population structure of the world’s largest ethnic group.

Using Shanghai individuals as representatives, shared drift between Chinese and ancient humans are computed by calculating the outgroup f3 statistics of the form f3(Mbuty;X, Y), with ancient individuals separated into approximately Palaeolithic, Mesolithic, Neolithic , and Chalcolithic-Medieval times. it is found that modern Chinese individuals show greater shared drift with pre-Neolithic hunter-gatherers rather than Neolithic farmers (Featured image from the article).

EDIT (17/7/2017): Davidski at Eurogenes shares an interesting view on this kind of results:

These sorts of estimates always look way off. And I doubt that it’s largely the result of the Silk Road, which linked China to the Near East and Mediterranean rather than to Northern Europe. More likely it reflects gene flow from the Pontic-Caspian steppe in Eastern Europe during the Bronze and Iron ages, via the Afanasievo, Andronovo, and other closely related steppe peoples


New insights from Thailand into the maternal genetic history of Mainland Southeast Asia, by Kutanan et al. (2017)

Abstract:

Tai-Kadai (TK) is one of the major language families in Mainland Southeast Asia (MSEA), with a concentration in the area of Thailand and Laos. Our previous study of 1,234 mtDNA genome sequences supported a demic diffusion scenario in the spread of TK languages from southern China to Laos as well as northern and northeastern Thailand. Here we add an additional 560 mtDNA sequences from 22 groups, with a focus on the TK-speaking central Thai people and the Sino-Tibetan speaking Karen. We find extensive diversity, including 62 haplogroups not reported previously from this region. Demic diffusion is still a preferable scenario for central Thais, emphasizing the extension and expansion of TK people through MSEA, although there is also some support for an admixture model. We also tested competing models concerning the genetic relationships of groups from the major MSEA languages, and found support for an ancestral relationship of TK and Austronesian-speaking groups.