Dataset Information

Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China.

ABSTRACT:

Background

The West Liao River valley in Northeast China is an ecologically diverse region, populated in prehistory by human populations with a wide range of cultures and modes of subsistence. To help understand the human evolutionary history of this region, we performed Y chromosome analyses on ancient human remains from archaeological sites ranging in age from 6500 to 2700 BP.

Results

47 of the 70 individuals provided reproducible results. They were assigned into five different Y sub-haplogroups using diagnostic single nucleotide polymorphisms, namely N1 (xN1a, N1c), N1c, C/C3e, O3a (O3a3) and O3a3c. We also used 17 Y short tandem repeat loci in the non-recombining portion of the Y chromosome. There appears to be significant genetic differences between populations of the West Liao River valley and adjacent cultural complexes in the prehistoric period, and these prehistoric populations were shown to carry similar haplotypes as present-day Northeast Asians, but at markedly different frequencies.

Conclusion

Our results suggest that the prehistoric cultural transitions were associated with immigration from the Yellow River valley and the northern steppe into the West Liao River valley. They reveal the temporal continuity of Y chromosome lineages in populations of the West Liao River valley over 5000 years, with a concurrent increase in lineage diversity caused by an influx of immigrants from other populations.

SUBMITTER: Cui Y

PROVIDER: S-EPMC3850526 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature

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Publications

Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China.

Cui Yinqiu Y Li Hongjie H Ning Chao C Zhang Ye Y Chen Lu L Zhao Xin X Hagelberg Erika E Zhou Hui H

BMC evolutionary biology 20130930

<h4>Background</h4>The West Liao River valley in Northeast China is an ecologically diverse region, populated in prehistory by human populations with a wide range of cultures and modes of subsistence. To help understand the human evolutionary history of this region, we performed Y chromosome analyses on ancient human remains from archaeological sites ranging in age from 6500 to 2700 BP.<h4>Results</h4>47 of the 70 individuals provided reproducible results. They were assigned into five different ...[more]

PMID: 24079706

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Project description:Haploid high quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudo-haploid data, i.e. they randomly sample only one sequencing read per site. We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Most genomic regions we investigated show little to no mapping bias but even a small proportion of sites with bias can impact analyses of those particular loci or slightly skew genome-wide estimates. Therefore, reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.

Project description:BackgroundBy comparing the differences in plant use between various cultures or regions, we can gain a better understanding of traditional knowledge of plant use among different groups, which may lead to a more objective understanding. Even though the Tibetan and Daman people live in the same ecosystem in Gyirong town, China, their cultural backgrounds and livelihoods differ. Therefore, the objective of this study is to document the traditional knowledge of plant use among the Daman people and compare it with the local Tibetan knowledge of plant use. By doing so, we aim to explore the relationship between plant selection and use and the cultural backgrounds of different groups.MethodsDuring fieldwork, ethnobotanical data were collected using various methods including free listings, key informant interviews, and semi-structured interviews. To quantify the importance of plant species in the Daman people's culture, the culture importance index, informant consensus factor index, and The Index of Agreement on Species consensus (IASc) were used. In addition, we cited previous ethnobotanical survey data from the Tibetan in Gyirong. To more comprehensively compare the differences in plant use between the Daman and Tibetan, this study constructed a knowledge network to compare the knowledge differences between the two groups.ResultsIn this study, traditional knowledge was collected from 32 Daman informants, resulting in a total of 68 species belonging to 39 families mentioned by Daman people and 111 species mentioned by Tibetans. Of these, 58 plants were used by both populations. The plants were classified into 3 categories and 28 subcategories, with 22 identical classes in both groups. The majority of use categories showed a high degree of sharing in both groups, and the Tibetan people had more plant use categories than the Daman people. Five plants with IASc value > 0.5 were identified in both groups: Rhododendron anthopogon D. Don, Artemisia japonica Thunb., Juniperus indica Bertol., Gastrodia elata Blume, and Rheum australe D. Don. The analysis of the knowledge network revealed a 66% overlap between the knowledge of the Daman and the knowledge of the Tibetans. Additionally, the plant knowledge of Tibetan people was found to be richer and more complex than that of the Daman people. However, the Daman people possess 30 unique knowledge items.ConclusionsFrom the perspective of plant use, the history of the Daman people's discrete migration on the border between China and Nepal allows them to retain their own knowledge of plant use. The status quo of joining Chinese nationality and settling in Gyirong town allows them to gradually integrate into the local Tibetan society. In summary, despite living in the same ecosystem and biodiversity background, the plant utilization of the Daman people and Tibetans still shows significant differences, which are due to their different cultural backgrounds and social status.

Dataset Information

Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China.

Background

Results

Conclusion

Publications

Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China.

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