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. 2020 Apr 5;23(4):101032. doi: 10.1016/j.isci.2020.101032

A Matrilineal Genetic Perspective of Hanging Coffin Custom in Southern China and Northern Thailand

Xiaoming Zhang 1,13,14, Chunmei Li 1,13,14, Yanan Zhou 1,6,14, Jiahui Huang 1,6, Tengsong Yu 4, Xu Liu 2, Hong Shi 7,8, Hong Liu 9, Stephen Chia 10, Shenmin Huang 11, Yaozheng Guo 12, Rasmi Shoocongdej 5,∗, Xueping Ji 2,3,∗∗, Bing Su 1,13,15,∗∗∗
PMCID: PMC7163074  PMID: 32304863

Summary

Hanging Coffin is a unique and ancient burial custom that has been practiced in southern China, Southeast Asia, and near Oceania regions for more than 3,000 years. Here, we conducted mitochondrial whole-genome analyses of 41 human remains sampled from 13 Hanging Coffin sites in southern China and northern Thailand, which were dated between ∼2,500 and 660 years before present. We found that there were genetic connections between the Hanging Coffin people living in different geographic regions. Notably, the matrilineal genetic diversity of the Hanging Coffin people from southern China is much higher than those from northern Thailand, consistent with the hypothesized single origin of the Hanging Coffin custom in southern China about 3,600 years ago, followed by its dispersal in southern China through demic diffusion, whereas the major dispersal pattern in Southeast Asia is cultural assimilation in the past 2,000 years.

Subject Areas: Biological Sciences, Phylogenetics, Sequence Analysis, Paleogenetics

Graphical Abstract

graphic file with name fx1.jpg

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Highlights

  • •

    The historical Hanging Coffin populations share partial genetic affinity

  • •

    The mtDNA diversity of the Hanging Coffin people in southern China is high

  • •

    The aDNA data are consistent with a single origin of the Hanging Coffin custom

  • •

    Both cultural assimilation and demic diffusion occurred during the spread of the custom

Biological Sciences; Phylogenetics; Sequence Analysis; Paleogenetics

Introduction

Hanging Coffin (also known as Log Coffin in Thailand) is an ancient burial custom (Chen, 1996a), which has been practiced for ∼3,000 years over wide geographic regions covering southern China, mainland Southeast Asia (MSEA), island Southeast Asia (ISEA), and near Oceania regions (Chen, 1996b). The earliest site was radiocarbon dated as 3,620 ± 30 years before present (YBP), and it was proposed that the Hanging Coffin site located in Mount Wuyi of the coastal region in southeastern China was the origin area of the Hanging Coffin custom, followed by a massive population and cultural dispersal to other regions of southern China and further to the broad Southeast Asia (Chen, 1996c). Based on the radiocarbon dating series, distribution characteristics, and cultural connection pattern, it was hypothesized that the Hanging Coffin custom had an “East to West”and a “North to South” dispersion in southern China and Southeast Asia (Chen, 1996c), although the Log Coffin in northern Thailand has different shapes and sizes, carved elements, and wood materials, which was considered as a cultural adaptation to the local environment (Shoocongdej, 2018). However, the origin of the Hanging Coffin custom and its affiliated populations are still controversial. Craniological studies indicated the involvement of Daic (Tai-Kadai) people practicing the Hanging Coffin custom (Hu and Xiao, 1999a, Hu and Xiao, 1999b, Ji et al., 2005, Lin and Mei, 1982), whereas the evidence of sacrificial objects showed that the Mon-Khmer (MK) (Shoocongdej, 2018) and Hmong-Mien (HM) (Lin, 1981) people might play an important role, and even Han people were likely involved (Sichuan Provincial Museum Gcc, 1980; Lin, 1982).

To test these long-standing debates, we performed mitochondrial whole genome analysis of 41 individual human remains (31 samples were sequenced in this study) from 13 Hanging Coffin sites in southern China and northern Thailand, to delineate the general population histories, present-day population affiliation, and dispersal pattern of the Hanging Coffin custom.

Results

Authenticity of Ancient DNAs for the Hanging Coffin Samples

We collected 31 individual human remains from 3, 1, and 9 Hanging Coffin archaeological sites located in Yunnan and Guangxi provinces of China and northern Thailand, respectively. According to the published culture relics, the Yunnan sites were dated as 1,246 ± 65 to 660 ± 30 YBP (uncalibrated) (radiocarbon-dated in Peking University, China) (Ji et al., 2005) and the northern Thailand sites were dated as 2,209 ± 97 to 1,240 ± 90 YBP (uncalibrated) (Figure 1) (McColl et al., 2018, Shoocongdej, 2018). For the Guangxi site, we performed radiocarbon dating using wood chips sampled from the coffins (Beta Analytic testing laboratory, USA), and the uncalibrated date is 2,490 ± 30 YBP (Figure S3C) and the calibrated date is 2,730–2,460 YBP.

Figure 1.

Figure 1

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Geographic Distribution and Panorama View of the Unearthed Hanging Coffin Sites

The red labels indicate the sampling sites with uncalibrated dating. The blue labels indicate the reported Hanging Coffin sites, and very few of them contained human remains. We conducted a medicolegal cranial reconstruction using an almost complete skull from the Washi Hanging Coffin site (the bottom left panel). The two panels on the right show the unearthed human remains from the Hanging Coffin sites. The distribution map of the reported Hanging Coffin sites was redrawn based on the map in the book entitled “Cliff-Burial in China” (Chen, 1996). See also in Figure S3.

We extracted ancient DNAs (aDNAs) from these human remains using the published method (Allentoft et al., 2015, Dabney et al., 2013, Rohland and Hofreiter, 2007). With the use of the human mtDNA probes (Enk et al., 2014), we enriched the aDNA extracts for the mitochondrial genome (see details in Supplemental Information). We then sequenced the constructed aDNA libraries using the Illumina Hiseq X Ten platform. We first assessed the authenticity of the obtained mtDNA genome data by evaluating several key indexes, including terminal damage rate (Figure S1A), average fragmental length, mapping rate, as well as mtDNA contamination rate. All samples showed damage patterns typical of aDNA with minimal amounts of contamination (Table S1). The sequencing depth is high (>10×) for most of the samples, from which we obtained complete mtDNA genome sequences (>95%), and only three samples had relatively low coverages (66.55%–88.88%) and were excluded from the following analyses. In addition, we included the published mtDNA genome data of 10 Log Coffin samples from the Long Long Rak archaeological site, northern Thailand (McColl et al., 2018).

Maternal Affinity of the Hanging Coffin Samples Revealed by the mtDNA Haplotype

Considering the same burial custom, similar relic culture, and close geographic locations, we grouped the Hanging Coffin samples into two populations from Yunnan and Thailand, respectively. In view of mtDNA haplotype, the Hanging Coffin samples from Yunnan were highly diversified, and among the nine individuals, we detected eight different mtDNA lineages, including B4c2c, B4a1c4, B6a, C7a, F3a1, G3a1, N9a3, and R9. In contrast, the haplotype diversity of the samples from northern Thailand is relatively low, and only 7 lineages (B5a1d, F1a1a1, F1f, F1c1a2, G2b1a, G3a1, and N8) were detected in 28 individuals. The two Guangxi samples both belong to the G3a1 lineage, which is also present in both Yunnan and northern Thailand.

To relate these Hanging Coffin samples to current human populations, we collected the mtDNA genome data of 280 Asia-Pacific populations (28,618 sequences) from the previous publications (Table S2). We first constructed a phylogenetic tree by integrating our data with the published 433 complete mtDNA genome sequences (Brandao et al., 2016, Cavadas et al., 2015, Delfin et al., 2014, Genomes Project et al., 2015, Jiang et al., 2014, Jinam et al., 2012; Ko et al., 2014; Kong et al., 2003, Kutanan et al., 2017, Kutanan et al., 2018, Lippold et al., 2014, Liu et al., 2012, Ma et al., 2016, Macaulay et al., 2005, Peng et al., 2018, Tanaka et al., 2004, Zhang et al., 2008, Zhang et al., 2013) (Figures 2A, 2B, and S2). The results show that the Hanging Coffin individuals are closely related with several present-day populations in southern China and MSEA, including the Daic populations from southern China (such as the Dai, Shui, and Zhuang ethnic groups) and northern Thailand (the Tai ethnic group), the MK populations from northern Thailand, as well as the HM populations from southern China (such as Yao in Guangxi) and northern Vietnam. In particular, we observed several cases of identical mtDNA mutation motifs between the Hanging Coffin samples and the current populations. For example, in the B6a lineage, the Yunnan Hanging Coffin sample (WXWS2) shares the same mutation motif with six present-day MK individuals from northern Thailand and one Han individual from southern China. In the B4c2c lineage, the Yunnan Hanging Coffin sample (DSG-4) shares the same mutation motif with one Thai individual from northern Thailand and one Dai individual from southwestern China. In addition, in the C7a lineage, the mtDNA haplotype of the Hanging Coffin sample from Yunnan (WXWS-1) is ancestral to many present-day individuals including Thai, MK, and Karen populations from northern Thailand, consistent with the proposed “North to South” dispersal route (Chen, 1996b) (Figures 2A, 2B, and S2). Importantly, the Hanging Coffin populations from southern China (Yunnan and Guangxi) and northern Thailand share the G3a1 lineage, an indication of a close genetic affinity, suggesting that the custom dispersed to different regions in a relatively short period of time. The genetic affinity of the Hanging Coffin samples is further supported by network analysis with more global populations using the hypervariable segment-I and the mitochondrial genome sequence data (Figure 2C).

Figure 2.

Figure 2

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The mtDNA Genome Diversity of the Hanging Coffin Populations

(A) The schematic phylogeographic tree of the Hanging Coffin related mtDNA lineages, which was constructed based on the complete mtDNA sequences in Figure S2. The Hanging Coffin samples are those triangles highlighted with broken circles.

(B) The geographic distribution of the included present-day populations.

(C and D) (C) The network of mtDNA lineages based on hypervariable segment-1 and complete mtDNA sequences. The short lines on the branches indicate mutation steps, and those branches without short lines have only one mutation step. (D) The Bayesian skyline plot showing historic changes of female effective population size of the F1a1a1 lineage in samples from Southeast Asia. HC, Hanging Coffin; AA, Austro-Asiatic; HM, Hmong-Mien; AU, Austronesian; TB, Tibeto-Burman; AJK, Altaic + Japanese + Korean.

See also in Figure S2.

Although there is genetic affinity among the Hanging Coffin populations from different geographic regions, we saw a clear divergence between the Yunnan and the northern Thailand populations as only one haplotype (G3a1) out of the 14 detected haplotypes is shared between them. For the northern Thailand population, according to the Bayes Skyline Plot simulation, the prevalent mtDNA lineages (B5a1d, F1a1a1, and F1f) all show a rapid population expansion starting about 7,500 YBP (∼8,200 YBP for the F1a1a1 lineage and ∼7,000 YBP for the F1f lineage) (Figures 2A, 2C and 2D). This date not only precedes the known massive migration of Thai people from southern China into Thailand between the 8th and 10th centuries (He, 2015, Pittayaporn and Pittayawat, 2014) but also is earlier than the earliest radiocarbon date (∼2,200 YBP) of the Log Coffin in northern Thailand. Given that these mtDNA lineages are also prevalent in the present-day MK populations from northern Thailand, we speculate that these mtDNA lineages likely originated locally. In other words, the Log Coffin human remains from northern Thailand were probably due to cultural assimilation rather than demic diffusion of the Hanging Coffin custom.

Maternal Affinity of the Hanging Coffin Samples with Current Asia-Pacific Populations

We analyzed the relationships among the Hanging Coffin populations and the present-day Asia-Pacific populations. First, we constructed a PCA (principal-component analysis) map of 280 populations based on their mtDNA haplotype frequencies (Table S2). The Guangxi Hanging Coffin site has only two samples and was therefore excluded. The two Hanging Coffin populations cluster closely with each other, and they both belong to the “Southern Population” group (Figure S1B). Further analysis including only those “Southern Populations” indicates that the Hanging Coffin populations from Yunnan and northern Thailand cluster together with one Thai, two MK, and one Tibeto-Burman (Karen people) populations from northern Thailand and one MK, one Austronesian, and one HM populations from Vietnam (Figure 3A). The PCA pattern is further supported by the calculated average number of pairwise differences (measured by ΦST) of the 31 representative Asia-Pacific populations and the two Hanging Coffin populations (Figure 3B).

Figure 3.

Figure 3

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Genetic Affinity of the Hanging Coffin Populations with Current Asia-Pacific Populations

(A) The PCA plot indicates a relatively close relationship of the Hanging Coffin populations with the “Southern” populations. The present-day populations showing close relationship to the two Hanging Coffin population are labeled with numbers, including 1, MK_Central Thailand; 2, AA_North Vietnam; 3, HM_North Vietnam; 4, AU_South Vietnam; 5, TB_North Thailand; 6, Thai_North; 7, AA_Northeast Thailand; 8, Han_CHS_China; 9, Han_Shanghai_China; and 10, Han_CHB_China.

(B) The average pairwise differences are calculated based on the ΦST index using the Arlequin (version 3.5.0) software, which confirms the genetic affinity of the Hanging Coffin populations with the “Southern” populations as shown in the PCA map. The red boxes indicate those populations showing the smallest genetic distance to the two Hanging Coffin populations in the heatmap.

(C) The spectrum of mtDNA lineages of the Yunnan Hanging Coffin population when compared with those of the present-day “Southern” populations.

(D) The spectrum of mtDNA lineages of the Hanging Coffin population from northern Thailand when compared with those of the present-day “Southern” populations. The present-day “Southern” populations are grouped in large (left panel) and small (right panel) geographic regions. The number in the bracket refers to the sample size of each population. HC, Hanging Coffin; AA, Austro-Asiatic; HM, Hmong-Mien; AU, Austronesian; TB, Tibeto-Burman.

See also in Figure S1.

The comparison of mtDNA lineage component frequency spectrum confirmed the close relationship of the southern populations with the Hanging Coffin populations (Figures 3C and 3D). The Hanging Coffin populations show the closest affinity with present-day Daic populations in southern China and northern Thailand, and some of the other surrounding populations in Southeastern Asia also share maternal lineages with the Hanging Coffin populations, an implication of gene flow among populations belonging to different language families. Of the eight lineages that appeared in the Hanging Coffin population from Yunnan, four are present in two present-day Thai populations from northern Thailand and Vietnam (Figure 3C). In contrast, the present-day Thai population from northern Thailand harbors six of the seven Hanging Coffin lineages in Thailand, a clear indication of genetic affinity with the historic Log Coffin population (Figure 3D, left panel). Furthermore, within the present-day Thai populations from northern Thailand, we found two Thai sub-branches (Khon Mueang and Thai Yuan) that showed the closest affinity to the Log Coffin population by harboring four of the seven lineages with similar lineage frequency spectrum (Figure 3D, right panel).

Discussion

The Hanging Coffin burial custom is a unique cultural relic once widely distributed in the Yangtze River and the Pearl River basins of southern China, Southeast Asia, and near Oceania regions. This custom had vanished in mainland China and MSEA a couple of hundred years ago, but is still practiced in some remote ISEA regions, e.g., the Yami ethnic group in Lanyu region of Taiwan, China, and the Toraja people in Sulawesi of Indonesia (Chen, 1996d). In regard to the chronological order of the Hanging Coffin archaeological sites, the proposed route of dispersal was called “the more east, the more ancient, the more west, the more recent,” and the archaeological sites in southern China are in general older than those in Southeast Asia, consistent with an “East to West and North to South” dispersal pattern (Chen, 1996c).

The Hanging Coffin sites not only show continuity in terms of time and geographic regions but also have similar cultural connotation (choice of burial location, coffin shape, and funerary objects) (Chen, 1996e). In addition, the Hanging Coffin relics in southern China and Southeast Asia share many common cultural elements with the ancient “Baiyue” (means hundreds of “Yue” tribes, who were the ancestors of the present-day Daic speakers) tribe relics, such as the stepped adze (found in Guangxi, Guangdong, and Fujian of China, Borneo and Sulawesi of Indonesia and the Philippine archipelago), the shoulder stone artifacts (originated in the Pearl River Delta region and found in Guangxi and Hainan island of China, Vietnam, the Malay peninsula, and west to Assam of India and Bangladesh), and the geometric impression pottery (the most ancient unearthed cultural relics in the Hemudu and the Liangzhu sites of China, and found from southern mainland China to Taiwan, Indo-China, and the Kalumparp region of Sulawesi) (Chen, 1996f).

The human culture and language spread patterns around the world are mainly explained by two alternative models: the demic diffusion model, which involves massive human migration to other places, and the cultural assimilation model, which refers to major cultural transmission between populations and involves limited genetic exchange between them (Cavalli-Sforza et al., 1994). Our genetic data reveal that the Hanging Coffin populations from southern China and northern Thailand are genetically linked with a “North to South” decline of mtDNA haplotype diversity, consistent with the hypothesized migratory route of the Hanging Coffin custom based on cultural relics (Chen, 1996a). In addition, they both show a close genetic affinity to the present-day Daic populations living in these regions, congruent with the “North to South” dispersal route (Chen, 1996b). However, these two Hanging Coffin populations share very few mtDNA lineages (1 of 14), an indication of limited genetic exchange, which fits the model of cultural assimilation rather than demic diffusion during the historic spread of this custom to Southeast Asia. Combining our genetic results with the archaeological evidence, we speculate that the Hanging Coffin culture originated from the southeastern coastal region (likely in the Mount Wuyi region of China) ∼ 3,600 YBP among the ancient “Baiyue” tribes, and this unique burial custom expanded to the wider southern China regions in the following millennia through demic diffusion. Then the Hanging Coffin custom spread southward to Southeast Asia mostly by cultural assimilation (Figure 4). It should be noted that due to the limited human remain samples from restricted geographic regions in this study, we cannot rule out other possible scenarios in view of direction and route of custom spread. Future studies with more samples covering more relic sites are needed to test the proposed dispersal pattern of the Hanging Coffin custom.

Figure 4.

Figure 4

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The Proposed Origin and Dispersal Pattern of the Hanging Coffin Custom

The approximate range of distribution of the ancient “Baiyue” tribes is highlighted in gray. The two different dispersal patterns of the Hanging Coffin custom are indicated by two arrows with different colors. The major historic tribes involved in the Hanging Coffin custom are labeled with different symbols. The Yangtze River and the Pearl River are indicated with blue lines. The pie shows the rough mtDNA lineage component in different Hanging Coffin tribes.

Limitations of the Study

In this study, we only explored the matrilineal genetic perspective due to the difficulty of acquiring genomic and Y-DNA data. Also, the sampled Hanging Coffin sites are limited.

Methods

All methods can be found in the accompanying Transparent Methods supplemental file.

Acknowledgments

This study was supported by the National Natural Science Foundation of China (NSFC, 31601018, 31871258, and 41620104007) and Yunnan provincial ‘"ten thousand people plan" youth top talent’ project (2019) to X.Z, Strategic Priority Research Program (XDB26000000) of Chinese Academy of Sciences (CAS) to X.J, Western Young Scholar (Y802551081) of CAS to C.L, 41962003 of NSFC to S.H, and Thailand Research Fund (TRF) (RTA6080001 and RDG55H0006) to R.S. Exploration Society of China in Hong Kong and Zhaotong Institute of Cultural Relics Protection and Archaeology organized and financially supported the field survey.

Author Contributions

B.S., X.J., and R.S. designed the study; X.J., R.S., X.L., Y.G., S.H., H.L., and T.Y. collected the samples; X.Z., Y.Z., and J.H. conducted the experiment; H.S. and C.L. provided technical assistance in the experiments; X.Z., C.L., Y.Z., and J.H. analyzed the data; X.Z., C.L., S.C., S.H., R.S., X.J., and B.S. wrote the manuscript.

Declaration of Interests

The authors declare no competing interests.

Published: April 24, 2020

Footnotes

Supplemental Information can be found online at https://doi.org/10.1016/j.isci.2020.101032.

Contributor Information

Rasmi Shoocongdej, Email: rasmi13@hotmail.com.

Xueping Ji, Email: jxpchina@foxmail.com.

Bing Su, Email: sub@mail.kiz.ac.cn.

Data and Code Availability

GenBank accession numbers for the mtDNA genome sequences of the 31 Hanging Coffin samples are MN006845–MN006875.

Supplemental Information

Document S1. Transparent Methods, Figures S1–S3, and Table S3
mmc1.pdf (2.7MB, pdf)
Table S1. The Metadata of the 41 Hanging Coffin Samples in This Study, Related to Figure 1 and Transparent Methods
mmc2.xlsx (22.3KB, xlsx)
Table S2. The mtDNA Haplogroup Frequencies (%) in Asia-Pacific Populations, Related to Figure 3A
mmc3.xlsx (862.1KB, xlsx)

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Document S1. Transparent Methods, Figures S1–S3, and Table S3
mmc1.pdf (2.7MB, pdf)
Table S1. The Metadata of the 41 Hanging Coffin Samples in This Study, Related to Figure 1 and Transparent Methods
mmc2.xlsx (22.3KB, xlsx)
Table S2. The mtDNA Haplogroup Frequencies (%) in Asia-Pacific Populations, Related to Figure 3A
mmc3.xlsx (862.1KB, xlsx)

Data Availability Statement

GenBank accession numbers for the mtDNA genome sequences of the 31 Hanging Coffin samples are MN006845–MN006875.

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