Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Association for the Advancement of Science (AAAS)  

Denisovans are an extinct hominin group defined by ancient genomes of Middle to Late Pleistocene fossils from southern Siberia. Although genomic evidence suggests their widespread distribution throughout eastern Asia and possibly Oceania, so far only a few fossils from the Altai and Tibet are confidently identified molecularly as Denisovan. We identified a hominin mandible (Penghu 1) from Taiwan (10,000 to 70,000 years ago or 130,000 to 190,000 years ago) as belonging to a male Denisovan by applying ancient protein analysis. We retrieved 4241 amino acid residues and identified two Denisovan-specific variants. The increased fossil sample of Denisovans demonstrates their wider distribution, including warm and humid regions, as well as their shared distinct robust dentognathic traits that markedly contrast with their sister group, Neanderthals.

DOI： 10.1126/science.ads3888

Web of Science

Scopus

PubMed

Authorship：Lead author,　Corresponding author   Publisher：Cold Spring Harbor Laboratory  

Summary

Ancient human bones degrade and sometimes disappear, especially in regions with acidic soils, making it difficult to obtain genetic information from past populations. To explore alternative sources, we analyzed ancient DNA from sediment samples collected from a burial site and a settlement site in Japan, both dating to around 1000 years ago. We found that ancient human mitochondrial DNA was obtained from sediments surrounding bones, particularly close to rib bones, while human DNA was rarely detected in the settlement site sediments. Furthermore, the mitochondrial haplogroups identified in the sediments were identical to those from human bones, confirming the reliability of this approach. Our findings suggest that genetic information about past human populations can be directly obtained from archaeological sediments in open-air sites. This method also provides a non-destructive alternative to bones and teeth, expanding possibilities for ancient DNA research in regions where skeletal remains are poorly preserved.

DOI： 10.1101/2025.03.19.643861

Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5–6.0 ka before present [BP]). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here, we examine ancient sedimentary DNA (sedaDNA) preserved at the Velký Mamuťák rock shelter in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder have clear representation by the Late Neolithic, around 6.0 ka BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age (∼4.1–3.0 ka BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the “Anthropocene.”

DOI： 10.1016/j.cub.2024.08.047

Scopus

Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

East and Southeast Asia have served as significant habitats for diverse hominins for more than one million years. This has been demonstrated by numerous studies over the past decade that have reported new discoveries, ages, morphological evidence, and ancient biomolecules from fossils. This has revolutionized our understanding of their evolution and dispersal. However, the existing literature lacks a comprehensive overview that combines insights from different scientific disciplines that are needed to address the still-uncertain or contentious aspects of this field. Here, we provide a synthesis of the timing and distribution of the different hominins that lived in East and Southeast Asia. We then review two biomolecular methods, ancient proteomics and sedimentary ancient DNA, which hold great promise for revealing hominin history in this area.

DOI： 10.1016/j.quascirev.2024.108669

Scopus

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Scientific Reports  

Detailed investigation of extremely severe pathological conditions in ancient human skeletons is important as it could shed light on the breadth of potential interactions between humans and disease etiologies in the past. Here, we applied palaeoproteomics to investigate an ancient human skeletal individual with severe oral pathology, focusing our research on bacterial pathogenic factors and host defense response. This female skeleton, from the Okhotsk period (i.e., fifth to thirteenth century) of Northern Japan, poses relevant amounts of abnormal dental calculus deposition and exhibits oral dysfunction due to severe periodontal disease. A shotgun mass-spectrometry analysis identified 81 human proteins and 15 bacterial proteins from the calculus of the subject. We identified two pathogenic or bioinvasive proteins originating from two of the three "red complex" bacteria, the core species associated with severe periodontal disease in modern humans, as well as two additional bioinvasive proteins of periodontal-associated bacteria. Moreover, we discovered defense response system-associated human proteins, although their proportion was mostly similar to those reported in ancient and modern human individuals with lower calculus deposition. These results suggest that the bacterial etiology was similar and the host defense response was not necessarily more intense in ancient individuals with significant amounts of abnormal dental calculus deposition.

DOI： 10.1038/s41598-024-55779-y

Scopus

PubMed

Language：Japanese   Book type：Textbook, survey, introduction

Presentation type：Public lecture, seminar, tutorial, course, or other speech  

Venue：オンライン  

Presentation type：Symposium, workshop panel (nominated)  

Language：Japanese   Presentation type：Poster presentation  

Venue：大阪府大阪市  

Presentation type：Oral presentation (general)  

Venue：Prague   Country：Czech Republic  

Presentation type：Oral presentation (general)  

Venue：Chiang Mai   Country：Thailand  

Language：Japanese   Publisher：岡山大学文明動態学研究所  

DOI： 10.18926/64203

CiNii Research

Language：Japanese   Publisher：一般社団法人 日本霊長類学会  

DOI： 10.2354/psj.39.012

CiNii Research

Language：Japanese   Publisher：Primate Society of Japan  

DOI： 10.2354/psj.38.022

CiNii Research

Publisher：Frontiers in Cellular and Infection Microbiology  

ERROR IN FIGURE/TABLE Error in Figures In the original article, there were mistakes in Figures 2 and 4 as published. The DRA number for modern samples without periodontitis in Figures 2 and 4 was incorrect. The correct number is DRA008582. The corrected Figures 2 and 4 appear below. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. TEXT CORRECTION In the original article, there was an error. The original article stated that “DRA012487” in the section of Data Availability Statement. This has been corrected to “DRA011882”. The corrected Data Availability Statement appears below. The datasets generated for this study can be found in the DNA Data Bank of Japan (http://www.ddbj.nig.ac.jp/) with the following accession number: DRA011882. The authors apologize for the error and state that it does not change the scientific conclusions of the article in any way. The original article has been updated.

DOI： 10.3389/fcimb.2022.871340

Scopus

Type：Peer review 

Number of peer-reviewed articles in foreign language journals：2

https://www.kyushu-u.ac.jp/ja/researches/view/1236/

https://www.soken.ac.jp/news/7118/

https://www.soken.ac.jp/news/6964/

https://www.u-ryukyu.ac.jp/news/11420/

Author：Other 

Author：Other