Biology subjects

Gakuhari, T.

Publications and source records attributed to Gakuhari, T..

8 recordsLinked to original sources

bioRxiv2026

Matched full-UDG and non-UDG ancient DNA libraries reveal trade-offs in post-mortem damage correction for imputation and kinship inference

Ancient DNA studies increasingly combine full uracil-DNA glycosylase-treated, full-UDG, and non-UDG libraries, but which computational damage correction to apply before imputation and kinship analysis remains unsettled. We compared terminal trimming, base-quality rescaling and known-SNP masking in matched full-UDG and non-UDG libraries from the same extracts of two medieval Mongolian individuals. All methods reduced or reversed the difference in mean alternative-allele fraction between damage-prone and transversion SNPs but retained different proportions of covered sites. In non-UDG libraries, masking and rescaling within five bases of each fragment end produced similar cross-library non-reference discordance, NRD, while retaining 92% and 99.3% of covered sites, respectively. In these 3'-biased libraries, ten-base 3'-only trimming retained more covered sites at lower observed discordance than five-base-per-end symmetric trimming. ancIBD inferred widespread sharing of one identity-by-descent chromosome copy, IBD1, across correction methods. Uncorrected non-UDG data shifted TKGWV2 toward second-degree estimates, whereas corrected mixed-library comparisons supported first-degree relatedness. READv2 and the low rate of opposite-homozygote sites, IBS0, supported a parent-offspring relationship. Mitochondrial data and genetic sex favoured ORT16 as mother and ORT15 as son. No method performed best across all measures, so the choice depends on whether residual damage, site retention or the downstream analysis matters most.

bioinformatics↗

bioRxiv2025

Towards On-Site Paleogenomics: Application and Perspective of Nanopore Sequencing with Ancient DNA

Ancient DNA (aDNA) research has greatly advanced understanding of past populations, yet progress in this field is still limited by two fundamental issues: dependence on fixed laboratory infrastructure and ethical considerations surrounding the cross-border transfer of archaeological biological specimens. In this study, we present the first successful application of Oxford Nanopore Technologies (ONT) sequencing to authentic aDNA from ancient human remains dating to the Early Jomon period. Our results demonstrate that nanopore platforms can recover characteristic postmortem damage signatures, generate genome-wide information with time-stamped sequencing data, and produce population genetic inferences consistent with Illumina short-read data. Crucially, the ONT sequencing has enabled the first demonstration of time-resolved aDNA analysis. This enables key genetic metrics, such as biological sex inference, to be determined within the first 60 minutes of sequencing. The portability and operational simplicity of ONT devices provide a practical basis for on-site paleogenomics, facilitating the generation of genomic data directly at archaeological sites, in museums, or at local research institutions. This capability is particularly significant in regions where the export of biological specimens entails administrative procedures, often spanning several months or even years. By enabling local archaeologists and anthropologists to independently generate and interpret genomic data, on-site nanopore sequencing can accelerate global research alliance, and promote equitable scientific authorship and continuing dialogue on sample sovereignty and collaborative research practices between geneticists and field researchers. Together, our findings establish nanopore sequencing as a socially sustainable and viable tool for paleogenomics, offering new pathways for the rapid, field-deployable and ethical process of archaeological remains.

genomics↗

bioRxiv2024

Ancient genomics reveals a genetic continuum with dual structure in the Classic Copan

Copan was a major capital at the southeasternmost of the Maya civilization, serving as a crossroads connecting Central and South America. In 426/427 CE, the city witnessed the establishment of a royal dynasty, which endured for approximately 400 years. Despite extensive historical and archaeological records, there remains limited information regarding the genetic origins of people who resided in Copan. Here, we present seven Classic Copan genomes including an enigmatic dynastic ruler and his sacrificed companion. Our analysis identifies a high genetic affinity of the Classic Copan with present-day Maya. Both groups exhibit an admixture of Mesoamerican and South American Farmer (SAF) ancestry, with a shift in a dominant component from SAF to Mesoamerican. At the individual level, commoners show a more prominent SAF ancestry, while the royal individual demonstrates nearly equal contributions from two ancestors. These results highlight a dual ancestral structure in this geographic extreme of the Classic Maya state, uncovering a cline of Mesoamerican ancestry across individuals.

evolutionary biology↗

bioRxiv2024

Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia

Previous genomic studies understanding the dispersal of Homo sapiens have suggested that present-day East Eurasians and Native Americans can trace their ancestry to migrations from Southeast Asia. However, ineluctable adaptations during the Last Glacial Maximum (LGM) remain unclear. By analyzing 42 genomes of up to 30-fold coverage from prehistoric hunter-gatherers, Jomon, we reveal their descent from Upper Paleolithic (UP) foragers who migrated to and isolated in the Japanese archipelago during Late Pleistocene. We provide compelling evidence suggesting that these UP people underwent positive selection for cold environments, aiding their survival through the LGM facilitated by non-shivering thermogenesis and detecting it polygenically across multiple loci in the Jomon lineage. Our study pioneers the close estimation of the physiological adaptation of ancient humans by the paleogenomic approach.

evolutionary biology↗

bioRxiv2023

Genome analysis of the Jomon dogs reveals the oldest domestic dog lineage in Eastern Eurasia

Dog is the oldest domesticated animal that established close relationships with humans. Due to its ancient origin, when, where, and whether a single or dual domestication event occurred is still under debate. The dogs in the Jomon period (Jomon dogs) in the Japanese archipelago had little change in morphology from 10,000 to 3,000 years ago. Therefore, we expected that the ancient genome of the Jomon dogs would provide a clue to reveal the characteristics of the ancient East Asian dogs. Here, we have sequenced the genomes of three 6000-year-old Jomon dogs, one 3000-4000-year-old Jomon dog, and four late 8th century dogs excavated in Japan. Our analyses suggest that the Jomon dogs are a distinct lineage from the previously known ancient dogs and are one of the oldest among the dogs in East Eurasian lineages. In addition, the genome of the Jomon dogs contained 9.5% of the genome of Japanese wolf ancestry due to a single introgression event. We estimated the proportion of the Jomon dog lineage genome in the genomes of dogs, which indicates that the genomic composition derived from the Jomon dog lineage is one of the major sources of modern dog genomes. Furthermore, we estimated the early admixture events of dogs in East Eurasia by analyzing the ancient genomes of the Jomon dogs. Due to the admixture events, the Jomon dog-derived genome has been one of the genomic sources of a wide range of modern dogs.

evolutionary biology↗

bioRxiv2019

Jomon genome sheds light on East Asian population history

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

genomics↗

bioRxiv2018

A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes

To analyze a specific genome region using next-generation sequencing technologies, the enrichment of DNA libraries with targeted capture methods has been standardized. For enrichment of mitochondrial genome, a previous study developed an original targeted capture method that use baits constructed from long-range polymerase chain reaction (PCR) amplicons, common laboratory reagents, and equipment. In this study, a new targeted capture method is presented, that of bacterial artificial chromosome (BAC) double capture (BDC), modifying the previous method, but using BAC libraries as baits for sequencing a relatively large gene. We applied the BDC approach for the 214 kb autosomal region, ring finger protein 213, which is the susceptibility gene of moyamoya disease (MMD). To evaluate the reliability of BDC, cost and data quality were compared with those of a commercial kit. While the ratio of duplicate reads was higher, the cost was less than that of the commercial kit. The data quality was sufficiently the same as that of the kit. Thus, BDC can be an easy, low-cost, and useful method for analyzing individual genome region with substantial length.

genomics↗

bioRxiv2017

Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the origins and expansions of the Late Neolithic-Chalcolithic Cututeni-Tripolye Culture

BackgroundThe Eneolithic (~ 5,500 yrBP) site of Verteba Cave in Western Ukraine contains the largest collection of human skeletal remains associated with the archaeological Cucuteni-Tripolye Culture. Their subsistence economy is based largely on agro-pastoralism and had some of the largest and most dense settlement sites during the Middle Neolithic in all of Europe. To help understand the evolutionary history of the Tripolye people, we performed mtDNA analyses on ancient human remains excavated from several chambers within the cave.\n\nResultsBurials at Verteba Cave are largely commingled and secondary in nature. A total of 68 individual bone specimens were analyzed. Most of these specimens were found in association with well-defined Tripolye artifacts. We determined 28 mtDNA D-Loop (368 bp) sequences and defined 8 sequence types, belonging to haplogroups H, HV, W, K, and T. These results do not suggest continuity with local pre-Eneolithic peoples, but rather complete population replacement. We constructed maximum parsimonious networks from the data and generated population genetic statistics. Nucleotide diversity ({pi}) is low among all sequence types and our network analysis indicates highly similar mtDNA sequence types for samples in chamber G3. Using different sample sizes due to the uncertainly in number of individuals (11, 28, or 15), we found Tajimas D statistic to vary. When all sequence types are included (11 or 28), we do not find a trend for demographic expansion (negative but not significantly different from zero); however, when only samples from Site 7 (peak occupation) are included, we find a significantly negative value, indicative of demographic expansion.\n\nConclusionsOur results suggest individuals buried at Verteba Cave had overall low mtDNA diversity, most likely due to increased conflict among sedentary farmers and nomadic pastoralists to the East and North. Early Farmers tend to show demographic expansion. We find different signatures of demographic expansion for the Tripolye people that may be caused by existing population structure or the spatiotemporal nature of ancient data. Regardless, peoples of the Tripolye Culture are more closely related to early European farmers and lack genetic continuity with Mesolithic hunter-gatherers or pre-Eneolithic groups in Ukraine.

evolutionary biology↗