Biology subjects

Shimmura, T.

Publications and source records attributed to Shimmura, T..

3 recordsLinked to original sources

bioRxiv2025

Prenatal valproic acid-exposed autism marmosets increase mutual gaze and reduce inter-individual distance during dyadic social interactions

Autism spectrum disorder (ASD) is associated with differences in social interaction, including alterations in gaze behavior and interpersonal distance. Although most assessments of ASD remain individual-centric, emerging human studies indicate that social difficulties may arise from atypical dyadic coordination rather than from reduced social interest alone. We examined dyadic coordination in a non-human primate model of ASD, focusing on gaze and inter-individual distance during minimally constrained first encounters between prenatal valproic acid-exposed marmosets (VPA) and unexposed conspecifics (UE). Markerless pose estimation quantified frame-by-frame gaze direction and spacing, comparing VPA-UE with UE-UE dyads. VPA-UE pairs exhibited a higher proportion of mutual-gaze events than UE-UE pairs. VPA individuals showed more rapid looks in response to the partners gaze, yet spent less time looking at the partner when unobserved. VPA-UE dyads maintained shorter inter-individual distances than UE-UE dyads, and closer spacing was associated with decreased stability of mutual gaze. These findings reveal a dyadic coordination pattern in VPA-UE pairs, with rapid responsiveness coupled with distance-dependent fragility, paralleling features reported in human ASD. Our dyad-centric, markerless framework yields ecologically grounded readouts and potential intervention targets that leverage intact social responsiveness while accommodating altered spatial coordination.

neuroscience↗

bioRxiv2023

Noncoding genetic variation in ISPD distinguishes gamecocks from nongame chickens

Chickens were domesticated >4,000 years ago, probably first for fighting them and only later as a source of food. Fighting chickens, commonly known as gamecocks, continue to be bred throughout the world, but the genetic relationships among geographically diverse gamecocks and with nongame chickens are not known. Here, we sequenced the genomes of 44 geographically diverse gamecocks and of 62 nongame chickens representing a variety of breeds. We combined these sequences with published genomes to generate the most diverse chicken genomes dataset yet assembled, at 307 samples. We found that gamecocks do not form a homogeneous group, yet they share genetic similarities that distinguish them from nongame chickens. Such similarities are likely the result of a common origin before their local diversification into, or mixing with, nongame chickens. Particularly noteworthy is a variant in an intron of ISPD, an extreme outlier present at a frequency of 90% in gamecocks but only 4% in nongame chickens. The ISPD locus has the strongest signal of selection in gamecocks, suggesting it is important for fighting performance. Because ISPD variants that are highly prevalent in gamecocks are still segregating in nongame chickens, selective breeding may help reduce its frequency in farm conditions in which aggression is not a desired trait. Altogether, our work provides genomic resources for agricultural genetics, uncovers a common origin for gamecocks from around the world and what distinguishes them genetically from chickens bred for purposes other than fighting, and points to ISPD as the most important locus related to fighting performance.

evolutionary biology↗

bioRxiv2019

The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response

The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organization, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated, and this may be key to the susceptibility of quail to H5N1. This genome will facilitate further research into diverse research questions using the quail as a model avian species.

genomics↗