Biology subjects

Nakagome, S.

Publications and source records attributed to Nakagome, S..

5 recordsLinked to original sources

bioRxiv2026

PIGSTI: a modular, reproducible pipeline for detecting species identity, pathogens, and microbes from animal palaeogenomic data

Ancient genomics has enabled discovery of diverse pathogens across various time periods, host species, and material types. However, existing palaeogenomic pipelines predominantly focus on screening data from human hosts, or do not incorporate microbial screening methodologies. We present PIGSTI (Pathogen anImal Genome Sequence ToolkIt), a bioinformatic pipeline specifically designed for both the initial screening and subsequent detection of pathogens in shotgun sequencing data from ancient animal remains. PIGSTI's integrated Snakemake workflow performs both host detection, genome mapping and pathogen identification, generating outputs suitable for population genetics and phylogenetic analyses. Testing on 952 newly sequenced and publicly available animal palaeogenomic datasets, we identified ~15 ancient zoonotic and animal pathogens with high confidence, including the first documented case of Rickettsia felis and Leptospira borgpetersenii in an ancient animal. Our results demonstrate PIGSTI's utility for screening pathogen diversity in ancient animal hosts and reconstructing historical host-pathogen relationships.

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↗

bioRxiv2020

A statistical modelling reveals bi-directional chromatin scanning by RAG in the human TCR-α locus

Rearrangements of germline variable (V), diversity (D), and joining (J) coding gene segments generate a diverse T cell receptor (TCR) repertoire. Two different molecular mechanisms govern a stochastic nature of gene choices by the recombination activating gene (RAG) protein complex. One is diffusion access in which a chromatin loop containing a coding gene bounces back and forth until the loop encounters a distant gene. The other is a linear chromatin scan, which extrudes chromatin loops to assemble a gene pair in a distance-dependent manner. However, the extent to which those two mechanisms underlie V(D)J recombination in human TCRs still remains unclear. Applying statistical modelling to TCR sequence data, we infer the stochastic process of gene choices during this recombination. The inferred usage of V and J gene segments vary from gene to gene. This pattern of gene usage is consistent across individuals, suggesting a fundamental bias in the gene choice. Our modelling shows the dependency of VJ pairing on their linear distance in the TCR- locus; proximal-proximal and distal-distal VJ pairs are more preferred than proximal-distal or distal-proximal gene pairs. These results support bi-directional RAG scanning into proximal and distal sides of the TCR- V gene locus.

genomics↗

bioRxiv2019

Sex-specific phenotypic effects and evolutionary history of an ancient deletion polymorphism of the human growth hormone receptor

The deletion of the third exon of the growth hormone receptor (GHR) is one of the most common genomic structural variants in the human genome. This deletion (GHRd3) has been linked to response to growth hormone, placenta size, birth weight, growth after birth, time of puberty, adult height, and longevity. However, its evolutionary history and the molecular mechanisms through which it affects phenotypes remain unresolved. Here, we analyzed thousands of genomes and provide evidence that this deletion was nearly fixed in the ancestral population of anatomically modern humans and Neanderthals. However, it underwent a paradoxical adaptive reduction in frequency approximately 30 thousand years ago in East Asia that roughly corresponds with the emergence of archaeological evidence for multiple modern human behaviors, dramatic changes in climate, and a concurrent population expansion. Further, we provide evidence that GHRd3 is associated with protection from edematous severe acute malnutrition primarily in males. Using a mouse line engineered to contain the deletion, we found Ghrd3s effect on the liver transcriptome of male mice grown without any calorie restriction mimics response to calorie restriction through regulation of circadian pathways. In contrast, under calorie restriction, Ghrd3 leads to the female-like gene expression in male livers. As a likely consequence, the dramatic weight difference between male and female mice disappears among GHRd3 mice under calorie restriction. Our data provide evidence for sex- and environment-dependent effects of GHRd3 and are consistent with a model in which the allele frequency of GHRd3 varies throughout human evolution as a response to fluctuations in resource availability.

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↗