Early Austronesians Cultivated Rice and Millet Together: Tracing Taiwan's First Neolithic Crops

Millets, dogs, pigs and permanent settlement: productivity transitions in Neolithic northern China

The transition to sedentary agricultural societies in northern China fuelled considerable demographic growth from 5000 to 2000 BC. In this article, we draw together archaeobotanical, zooarchaeological and bioarchaeological data and explore the relationship between several aspects of this transition, with an emphasis on the millet-farming productivity during the Yangshao period and how it facilitated changes in animal husbandry and consolidation of sedentism. We place the period of domestication (the evolution of non-shattering, initial grain size increase and panicle development) between 8300 and 4300 BC. The domestication and post-domestication of foxtail (Setaria italica) and broomcorn (Panicum miliaceum) millet increased their productivity substantially, with much greater rate of change than for rice (Oryza sativa). However, millets are significantly less productive per hectare than wet rice farming, a point reflected in the greater geographical expanse of northern Neolithic millet cultures (5000-3000 BC) in comparison with their Yangtze rice-growing counterparts. The domestication of pigs in the Yellow River region is evidenced by changes in their morphology after 6000 BC, and a transition to a millet-based diet c. 4500-3500 BC. Genetic data and isotopic data from dogs indicate a similar dietary transition from 6000 to 4000 BC, leading to new starch-consuming dog breeds. Significant population increase associated with agricultural transitions arose predominately from the improvement of these crops and animals following domestication, leading to the formation of the first proto-urban centres and the demic-diffusion of millet agriculture beyond central northern China between 4300-2000 BC.

Population genetic admixture and evolutionary history in the Shandong Peninsula inferred from integrative modern and ancient genomic resources

BACKGROUND

Ancient northern East Asians (ANEA) from the Yellow River region, who pioneered millet cultivation, play a crucial role in understanding the origins of ethnolinguistically diverse populations in modern China and the entire landscape of deep genetic structure and variation discovery in modern East Asians. However, the direct links between ANEA and geographically proximate modern populations, as well as the biological adaptive processes involved, remain poorly understood.

RESULTS

Here, we generated genome-wide SNP data for 264 individuals from geographically different Han populations in Shandong. An integrated genomic resource encompassing both modern and ancient East Asians was compiled to examine fine-scale population admixture scenarios and adaptive traits. The reconstruction of demographic history and hierarchical clustering patterns revealed that individuals from the Shandong Peninsula share a close genetic affinity with ANEA, indicating long-term genetic continuity and mobility in the lower Yellow River basin since the early Neolithic period. Biological adaptive signatures, including those related to immune and metabolic pathways, were identified through analyses of haplotype homozygosity and allele frequency spectra. These signatures are linked to complex traits such as height and body mass index, which may be associated with adaptations to cold environments, dietary practices, and pathogen exposure. Additionally, allele frequency trajectories over time and a haplotype network of two highly differentiated genes, ABCC11 and SLC10A1, were delineated. These genes, which are associated with axillary odor and bilirubin metabolism, respectively, illustrate how local adaptations can influence the diversification of traits in East Asians.

CONCLUSIONS

Our findings provide a comprehensive genomic dataset that elucidates the fine-scale genetic history and evolutionary trajectory of natural selection signals and disease susceptibility in Han Chinese populations. This study serves as a paradigm for integrating spatiotemporally diverse ancient genomes in the era of population genomic medicine.

Delineating the dispersal of Y-chromosome sub-haplogroup O2a2b-P164 among Austronesian-speaking populations

This article reports on an exploration of the Y-chromosome sub-haplogroup O2a2b-P164 in Austronesian-speaking populations. Moderate to high abundance of the P 164 mutation is seen in the West Pacific including the Amis of Formosa (36%) and the Filipinos of Mindanao (50%) as well as in the Kiritimati of Micronesia (70%), and Tonga and Samoa of West Polynesia (54% and 33%, respectively), and it drops to low frequencies in populations of East Polynesia. The communities of Polynesia and Micronesia exhibit considerable inter- and intra-population haplotype sharing suggesting extensive population affinity. The observed affinities, as well as the ages and diversity values within the P 164 sub-haplogroup among Austronesian-speaking populations signal an ancestral migration route and relationships that link the Amis of Taiwan with distant communities in West and East Polynesia, Micronesia, and the Maori of New Zealand. High resolution sequencing of the Austronesian Y chromosome indicate that the P 164 lineage originated about 19,000 ya and then split into three branches separating the Ami aborigines, Southeast Asian and Polynesian/Micronesian populations about 4700 ya, roughly coinciding with the initiation of the Austronesian diaspora. The Y-chromosomes of all the Polynesian and Micronesian population examined belong to the new FT 257096 haplogroup.

The genomic diversity of Taiwanese Austronesian groups: Implications for the "Into- and Out-of-Taiwan" models

The origin and dispersal of the Austronesian language family, one of the largest and most widespread in the world, have long attracted the attention of linguists, archaeologists, and geneticists. Even though there is a growing consensus that Taiwan is the source of the spread of Austronesian languages, little is known about the migration patterns of the early Austronesians who settled in and left Taiwan, i.e. the "Into-Taiwan" and "out-of-Taiwan" events. In particular, the genetic diversity and structure within Taiwan and how this relates to the into-/out-of-Taiwan events are largely unexplored, primarily because most genomic studies have largely utilized data from just two of the 16 recognized Highland Austronesian groups in Taiwan. In this study, we generated the largest genome-wide data set of Taiwanese Austronesians to date, including six Highland groups and one Lowland group from across the island and two Taiwanese Han groups. We identified fine-scale genomic structure in Taiwan, inferred the ancestry profile of the ancestors of Austronesians, and found that the southern Taiwanese Austronesians show excess genetic affinities with the Austronesians outside of Taiwan. Our findings thus shed new light on the Into- and Out-of-Taiwan dispersals.

Rice and millet cultivated in Ha Long Bay of Northern Vietnam 4000 years ago

Research has generally outlined that the Neolithic East Asian farmers expanded into Southeast Asia, leading to substantial social and cultural transformations. However, the associated archaeobotanical evidence until now has been insufficient to clarify the exact timing, dispersal route, and farming package of the emergence of agriculture in Mainland Southeast Asia. To clarify these issues, the micro-plant remains of phytolith and starch from three Neolithic sites in Ha Long Bay were extracted and analyzed. This study validates the earliest evidence of co-cropping in northern Vietnam, involving the cultivation of rice together with foxtail millet at 4000 years BP or slightly earlier. Moreover, the results indicate that at least two patterns of subsistence strategy were practiced simultaneously during the initial farming phase in the region. The Trang Kenh people, a regional variant of the Phung Nguyen cultural group often have been seen as the first farmers in northern Vietnam, and they mainly practiced a cereal-based subsistence strategy with more vital cultural characteristics of southern China origin. Meanwhile, the Ha Long people, mainly composed of indigenous hunter-gatherer descendants, continued to utilize a wide range of their preferred plant resources such as taros, yams, and acorns, while they absorbed and incorporated new elements such as millet and rice into their food system. This study provides solid information to understand the diverse economic systems among different cultural groups in Vietnam.

Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop—Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan

‘Breadfruit’ is a common tree species in Taiwan. In the indigenous Austronesian Amis culture of eastern Taiwan, ‘breadfruit’ is known as Pacilo, and its fruits are consumed as food. On Lanyu (Botel Tobago) where the indigenous Yami people live, ‘breadfruit’ is called Cipoho and used for constructing houses and plank-boats. Elsewhere in Taiwan, ‘breadfruit’ is also a common ornamental tree. As an essential component of traditional Yami culture, Cipoho has long been assumed to have been transported from the Batanes Island of the Philippines to Lanyu. As such, it represents a commensal species that potentially can be used to test the hypothesis of the northward Austronesian migration ‘into’ Taiwan. However, recent phylogenomic studies using target enrichment show that Taiwanese ‘breadfruit’ might not be the same as the Pacific breadfruit (Artocarpus altilis), which was domesticated in Oceania and widely cultivated throughout the tropics. To resolve persistent misidentification of this culturally and economically important tree species of Taiwan, we sampled 36 trees of Taiwanese Artocarpus and used the Moraceae probe set to enrich 529 nuclear genes. Along with 28 archived Artocarpus sequence datasets (representing a dozen taxa from all subgenera), phylogenomic analyses showed that all Taiwanese ‘breadfruit’ samples, together with a cultivated ornamental tree from Hawaii, form a fully supported clade within the A. treculianus complex, which is composed only of endemic Philippine species. Morphologically, the Taiwanese ‘breadfruit’ matches the characters of A. treculianus. Within the Taiwanese samples of A. treculianus, Amis samples form a fully supported clade derived from within the paraphyletic grade composed of Yami samples, suggesting a Lanyu origin. Results of our target enrichment phylogenomics are consistent with the scenario that Cipoho was transported northward from the Philippines to Lanyu by Yami ancestors, though the possibility that A. treculianus is native to Lanyu cannot be ruled out completely.