From bones to sediments: ancient human DNA from open-air archaeological sites

PRJEB87497 Original Paper / DOI2026-03-024 samples (study)

AI interpretationAI-generated

Can ancient human mtDNA be recovered from open-air sediments? A new test from Okinawa and Hokkaido.

This study tested whether human mitochondrial DNA (mtDNA) can be obtained from sediments at open-air archaeological sites, not just from bones. Researchers sampled sediments from two sites: Katsuren castle in Okinawa (12th-13th century) and Oshima 2 in Hokkaido (11th-12th century). They used both shotgun sequencing and targeted capture to enrich human mtDNA. The goal was to see if sediment DNA could reveal mtDNA haplogroups, offering a new way to study past people when bones are scarce.

Human mtDNA can be recovered from open-air archaeological sediments, as shown by successful haplogroup identification.
The study combined shotgun sequencing and targeted mtDNA capture to analyze sediment samples from two Japanese sites.
Sediment samples from different contexts (e.g., inside skulls, around bones) were compared with rib bone DNA from the same individuals.

Sample interpretation

The dataset includes 4 ancient samples with mtDNA haplogroups resolved. The most common haplogroup is M7a1b1 (2 samples), followed by D4j (1) and D4a1 (1). No Y-chromosome haplogroups were resolved. These mtDNA lineages are typical of East Asian populations, consistent with the Japanese archaeological context. The small sample size means these results are preliminary and should be interpreted with caution.

For genealogy enthusiasts

For ancestry enthusiasts, this study suggests that sediments at open-air sites can preserve ancient human mtDNA, potentially expanding where we can find genetic data. It highlights mtDNA as a tool for tracing maternal lineages even without well-preserved bones, but Y-DNA and autosomal data may be harder to obtain from such contexts.

Abstract

Five sediment samples were collected at a burial site, Katsuren castle, located in Okinawa, which dates to the mid-12th to early 13th century during the Gusuku period (Figure 1). Here, two burials with skeletal remains were found beneath the castle’s wall. One sediment sample from inside the skull was collected from Pit 138. From Pit 178, four sediment samples were obtained: one from inside the skull, one from sediment around the hip bones, one from sediment around the rib bones, and one from an area outside the pit (Figure 1, Table S1). Additionally, one rib bone was collected from each individual to compare with the results obtained from the sediments. The second site is a dwelling site known as Oshima 2, which dates to the 11th to 12th century during the Satsumon period and is located in Hokkaido (Figure 1). We collected eleven sediment samples from different contexts within the site (Figure S1, Table S2). DNA was extracted from all samples and sequenced using Illumina NovaSeq and iSeq platforms (see Methods). We performed a combination of shotgun sequencing (between 12447839 and 85971229 number of reads) and targeted capture enrichment for human mtDNA (between 70064 and 2174014 number of reads) to investigate the feasibility of determining human mtDNA haplogroups from sediment samples in open-air archaeological sites.

Samples & Data on TheYtree

4samples on site

0Y haplogroup resolved

Maternal (mtDNA) Haplogroups

M7a1b1 · 2 D4j · 1 D4a1 · 1