Abstract Sexual selection arises from individual differences in reproductive success, which can drive the maintenance of genetic polymorphisms in genes subject to balancing selection by the pleiotropic effects that trade-off between survival and reproduction. However, the extent to which sexual selection maintains genetic polymorphisms in wild populations remains unclear. Here, we explored on genomic signatures of balancing selection and selective sweep in the northern medaka, Oryzias sakaizumii in Japan by performing whole-genome resequencing of wild individuals. In addition, we re-evaluated the population genetic structure and admixture of Oryzias latipes and O. sakaizumii across the Japanese archipelago and detected genomic regions affected by introgression. Regions with signatures of selection from multiple statistics were located on eleven chromosomes. In particular, a region spanning 4.25 to 6.80 Mb on chromosome 18 showed high genetic diversity that could not be explained by sex differentiation or introgression from O. latipes in Eastern Japan. This pattern suggests that balancing selection maintains genetic polymorphisms in O. sakaizumii . Specifically, because a previously reported quantitative trait locus associated with female mating behavior overlaps with this region, we infer that sexual selection contributes to the maintenance of genetic polymorphism at this locus.

Abstract Characterized by the earliest use of pottery, the Jomon culture was a unique Neolithic culture that spread throughout the Japanese Archipelago. Previous archaeological evidence suggests that Jomon hunter-gatherers colonized the southernmost islands, the Ryukyu Archipelago, by approximately 7,000 years before present (YBP). However, genetic characteristics of the Ryukyu Jomon population and its contribution to the modern population have not been elucidated yet. In this study, we newly sequenced 273 modern and 25 ancient (6,700–900 YBP) whole genomes collected across the Ryukyu Archipelago. Our analysis demonstrated a genetic differentiation between the Hondo (Japanese mainland) and Ryukyu Jomon, dating back to ∼6,900 YBP. After the divergence from the Hondo Jomon, the Ryukyu Jomon experienced severe bottlenecks, with an effective population size of ∼2,000. Admixture between the Ryukyu Jomon and migrants from the historic Hondo population occurred ∼1,000 YBP, which corresponds to the widespread adoption of iron tools and agriculture in the Central Ryukyus. Different demographic histories between modern Hondo and Ryukyu populations resulted in different rates of Jomon ancestry in these populations. By providing a new perspective on the peopling of the Ryukyu Archipelago, this study significantly enhances our understanding of cultural transitions in the region.

Paired box gene 3 (PAX3) plays an important role in craniofacial development. Mutations in this gene are associated with Waardenburg syndrome, which is a condition characterized by facial anomalies such as widely spaced inner corners of the eyes. PAX3 gene polymorphisms are associated with the relative position of the nasal root (nasion), even among healthy individuals. Facial morphology has primarily been examined using three-dimensional (3D) facial scans of soft tissues, whereas studies focusing on hard tissues remain limited. Therefore, the present study aimed to analyze 3D craniofacial morphology in hard tissues using computed tomography imaging and investigate the influence of PAX3 polymorphisms on the 3D morphology of the nasal root. The analysis was conducted on three populations: 201 healthy Japanese, 74 healthy Korean, and 142 healthy Egyptian individuals. DNA was extracted from saliva samples, and the genotypes of two PAX3 single-nucleotide polymorphisms (SNPs; rs9288572 and rs7559271) were analyzed. A multiple regression analysis of the association between these SNPs and measurements related to nasal root morphology revealed a significant association between rs7559271 and the protrusion angle of the nasion. These findings suggest that PAX3 gene polymorphisms influence the morphological development of the nasal root within the normal range of hard tissues.

The Ryukyu archipelago is located southwest of the Japanese islands, and people originally from this region, the Ryukyu population, have a unique genetic background distinct from that of other populations, including people from mainland Japan. However, few genetic studies have focused on the Ryukyu population. In this study, we performed genome-wide association studies (GWAS) on the serum levels of alanine aminotransferase (ALT, n = 15,224), aspartate aminotransferase (AST, n = 15,203), and gamma-glutamyl transferase (GGT, n = 14,496) in the Ryukyu population. We found 13 loci with a genome-wide significant association (P < 5 × 10−8), three for ALT, four for AST, and six for GGT, including one novel locus associated with ALT: rs117595134-A in HMMR/HMMR-AS1, ß = − 0.131, standard error = 0.024, P = 4.90 × 10−8. Rs117595134-A is common in the Japanese population but is not observed in other ethnic populations in the 1000 genomes database. Additionally, 77 of 80 loci derived from Korean GWAS and 541 of 716 loci from European GWAS showed the same directions of effect (P = 1.41 × 10−19, P = 2.50 × 10−44, binomial test), indicating that most of susceptibility loci are shared between the Ryukyu population and other ethnic populations.

The prehistoric Okhotsk culture was distributed along the southern coastal regions of the Sea of Okhotsk during the late first millennium AD. A previous study that performed whole-genome sequencing of a late Okhotsk individual suggested two migration waves from the Russian Far East to northern Japan. The first wave is estimated to have originated from the Kamchatka Peninsula around 2000 years before present (BP), and the second from the Amur Basin around 1600 BP. These findings suggest the past existence of an admixed hypothetical population between the Kamchatka and indigenous Jomon lineages in northern Japan between 2000 and 1600 BP, although direct genetic evidence has not yet been obtained. Here, we present the genome data of an early Okhotsk individual (NAT004) excavated from northern Japan. Admixture modelling reveals that the genome can be explained as a mixture of Kamchatka and Jomon ancestries, providing direct support for the existence of the previously hypothesized hypothetical population. This result offers new insights into the prehistoric population dynamics of northern Japan and contributes to the broader understanding of its archaeological and anthropological history.

The ‘thrifty’ variant hypothesis, which posits that certain genetic adaptations promoting efficient energy storage during periods of food scarcity, has been invoked to explain the high prevalence of obesity in modern human populations. Although several candidate variants have been proposed, the timing and effects of these variants on body mass index (BMI) in specific populations remain poorly understood. In this study, we performed whole-genome sequencing of 22 Tongan individuals. A previous study identified the rs373863828-A variant in the CREBRF gene as a target of positive selection in Samoans based on iHS analysis. Here, we replicated this signal in Tongans, confirming that this variant has been subject to adaptive pressures more broadly across Polynesian populations. Using the CLUES program, we inferred the allele frequency trajectory of rs373863828-A in Tongans, revealing a marked increase over the past ~100 generations that temporally aligns with the period of Polynesian maritime expansion. The trajectory of the Polygenic Score (PS) showed an increase in the PS for BMI in ancestors of Tongans between 150 and 50 generations ago, followed by a recent decline. Analysis of polarized trait integrated haplotype scores detected significant polygenic selection favoring lower BMI in recent generations. Our findings suggest that the CREBRF variant underwent strong positive selection during oceanic dispersal, while numerous modest-effect variants collectively contributed to adaptation to food-limited environments during long sea voyages. More recently, however, selection pressures may have shifted toward lower BMI, indicating a potential evolutionary mismatch between past adaptations and modern environments.

Facial features vary among ethnic groups, and the analysis of facial shape is important in examining the similarity of these features. Within the domain of genetic research, the relationship between face shape and genetic factors has been particularly emphasized. This study aims to identify genetic factors that influence facial shape by leveraging 3D facial data. With the recent development of point cloud deep learning networks, the possibility of applying them to ethnic identification using 3D data has emerged. In particular, PointNet++ is effective because it can capture important local regions in face shape classification due to its characteristics. However, while PointNet++ excels at local feature aggregation, it lacks the ability to consider relationships among local regions from a holistic perspective. To address this limitation, we propose the integration of a novel feature named Local Area Attention, enabling comprehensive learning by encompassing both overarching facial features and subtle local nuances. Additionally, the visual representation of the resultant attention map offers promise in genetic research applications, enabling the visualization of pivotal local regions crucial for 3D facial identification.

The role of hybridization in morphological diversification is a fundamental topic in evolutionary biology. However, despite the accumulated knowledge on adult hybrid variation, how hybridization affects ontogenetic allometry is less well understood. Here, we investigated the effects of hybridization on postnatal ontogenetic allometry in the skulls of a putative hybrid population of introduced Taiwanese macaques (Macaca cyclopis) and native Japanese macaques (Macaca fuscata). Genomic analyses indicated that the population consisted of individuals with varying degrees of admixture, formed by male migration from Japanese to Taiwanese macaques. For overall skull shape, ontogenetic trajectories were shifted by hybridization in a nearly additive manner, with moderate transgressive variation observed throughout development. In contrast, for the maxillary sinus (hollow space in the face), hybrids grew as fast as Taiwanese macaques, diverging from Japanese macaques, which showed slow growth. Consequently, adult hybrids showed a mosaic pattern, that is, the maxillary sinus is as large as that of Taiwanese macaques, while the overall skull shape is intermediate. Our findings suggest that the transgressive variation can be caused by prenatal shape modification and nonadditive inheritance on regional growth rates, highlighting the complex genetic and ontogenetic bases underlying hybridization-induced morphological diversification.

Facial features vary among ethnic groups, and the analysis of facial shape is important in examining the similarity of these features. 3D facial point cloud data possesses diverse feature sets and has garnered significant attention for its applications in face recognition and face shape analysis. Within the domain of genetic research, the relationship between face shape and genetic factors has been particularly emphasized. Analyzing 3D facial data allows for the identification of specific genetic information that influences facial morphology. However, 3D facial data analysis via conventional image processing methods based on deep learning has proven to be challenging; thus, effective methods have not yet been established. Therefore, we propose a framework for face shape analysis by point cloud deep learning for genetic research based on PointNet and PointNet++, which allows direct input of 3D facial data, for advanced facial point cloud analysis. Furthermore, we propose a data augmentation method based on farthest point sampling that enables stable learning even with a small data set.

Natural selection signatures across Japanese subpopulations are under-explored. Here we conducted genome-wide selection scans with 622,926 single nucleotide polymorphisms for 20,366 Japanese individuals, who were recruited from the main-islands of Japanese Archipelago (Hondo) and the Ryukyu Archipelago (Ryukyu), representing two major Japanese subpopulations. The integrated haplotype score (iHS) analysis identified several signals in one or both subpopulations. We found a novel candidate locus at IKZF2, especially in Ryukyu. Significant signals were observed in the major histocompatibility complex region in both subpopulations. The lead variants differed and demonstrated substantial allele frequency differences between Hondo and Ryukyu. The lead variant in Hondo tags HLA-A*33:03-C*14:03-B*44:03-DRB1*13:02-DQB1*06:04-DPB1*04:01, a haplotype specific to Japanese and Korean. While in Ryukyu, the lead variant tags DRB1*15:01-DQB1*06:02, which had been recognized as a genetic risk factor for narcolepsy. In contrast, it is reported to confer protective effects against type 1 diabetes and human T lymphotropic virus type 1-associated myelopathy/tropical spastic paraparesis. The FastSMC analysis identified 8 loci potentially affected by selection within the past 20-150 generations, including 2 novel candidate loci. The analysis also showed differences in selection patterns of ALDH2 between Hondo and Ryukyu, a gene recognized to be specifically targeted by selection in East Asian. In summary, our study provided insights into the selection signatures within the Japanese and nominated potential sources of selection pressure.

The Ryukyu Islands are located in the southernmost part of the Japanese Archipelago and consist of several island groups. Each island group has its own history and culture, which differ from those of mainland Japan. People of the Ryukyu Islands are genetically subdivided; however, their detailed demographic history remains unclear. We report the results of a whole-genome sequencing analysis of a total of 50 Ryukyu islanders, focusing on genetic differentiation between Miyako and Okinawa islanders. We confirmed that Miyako and Okinawa islanders cluster differently in principal component analysis and ADMIXTURE analysis and that there is a population structure among Miyako islanders. The present study supports the hypothesis that population differentiation is primarily caused by genetic drift rather than by differences in the rate of migration from surrounding regions, such as the Japanese main islands or Taiwan. In addition, the genetic cline observed among Miyako and Okinawa islanders can be explained by recurrent migration beyond the bounds of these islands. Our analysis also suggested that the presence of multiple subpopulations during the Neolithic Ryukyu Jomon period is not crucial to explain the modern Ryukyu populations. However, the assumption of multiple subpopulations during the time of admixture with mainland Japanese is necessary to explain the modern Ryukyu populations. Our findings add insights that could help clarify the complex history of populations in the Ryukyu Islands.

Cortical bone thickness is important for the mechanical function of bone. Ontogeny, aging, sex, body size, hormone levels, diet, behavior, and genetics potentially cause variations in postcranial cortical robusticity. However, the factors associated with cranial cortical robusticity remain poorly understood. Few studies have examined cortical robusticity in both cranial and postcranial bones jointly. In the present study, we used computed tomography (CT) images to measure cortical bone thicknesses in the cranial vault and humeral diaphysis. This study clearly showed that females have a greater cranial vault thickness and greater age-related increase in cranial vault thickness than males. We found an age-related increase in the full thickness of the temporal cranial vault and the width of the humeral diaphysis, as well as an age-related decrease in the cortical thickness of the frontal cranial vault and the cortical thickness of the humeral diaphysis, suggesting that the mechanisms of bone modeling in cranial and long bones are similar. A positive correlation between cortical indices in the cranial vault and humeral diaphysis also suggested that common factors affect cortical robusticity. We also examined the association of polymorphisms in the WNT16 and TNFSF11 genes with bone thickness. However, no significant associations were observed. The present study provides fundamental knowledge about similarities and differences in the mechanisms of bone modeling between cranial and postcranial bones.

Single nucleotide variations (SNVs) in the nuclear genome have been used widely to analyze phylogenetic and population genomic structure. Cost-effective genotyping can be achieved by sequencing PCR amplicons using short 3-10 base sequences as primers to arbitrarily amplify thousands of sites in the genome using only a few primers. While previous methods have produced an insufficient number of SNVs to perform population genomic analyses, we designed a new primer set to improve the sequencing efficiency. To demonstrate the effectiveness of our method, we examined the population genetic structure of the small freshwater fish, medaka (Oryzias latipes). Specifically, we attempted to reconstruct the genetic admixture of the orange mutant strain, Himedaka. Although the strain is widely kept as an ornamental fish and for experimental purposes, the genetic background of the nuclear genome of commercial stock is less clear. We obtained 2987 informative SNVs with no missing genotype calls for 67 individuals from 15 wild populations and three artificial strains using the HiSeq X platform. The estimated phylogenic and population genetic structures of the wild populations were consistent with previous studies, corroborating the accuracy of our genotyping method. Admixture analysis focusing on Himedaka showed that at least two wild populations contributed SNVs to the nuclear genome of this mutant strain. Population genomics analyses based on nuclear SNVs data are indispensable to identify admixture events, including natural hybridization and anthropogenic introductions. The method developed in this study will be useful for future population genomics studies on medaka and on other organisms.

Sexual selection may have played a role in the formation and maintenance of phenotypic diversity among human populations. A theoretical study has shown that phenotypic diversification between neighboring populations connected by gene flow can occur if individuals have a mating preference for typical characteristics of their population (i.e., own-group preference), or if preferences are culturally transmitted only between the members of the same population (i.e., model-dependent mate-choice copying). To date, however, empirical investigation is lacking on the presence or absence of own-group preference and model-dependent mate-choice copying in neighboring populations exhibiting phenotypic differentiation. Here we report the results of an experiment on preference for faces in Okinawa Islanders and Mainland Japanese as an example of such populations. It was suggested that female Okinawa Islanders tend to prefer male faces of their own population to those of Mainland Japanese, and male Okinawa Islanders’ evaluation of faces is affected more by members of their own population than those of the other. These findings support the argument that the phenotypic difference between Okinawa Islanders and Mainland Japanese may be partially explicable by sexual selection.

Various applications have been developed in facial research to aid the recognition of personal attributes, analysis of race, and personal authentication for the security industry and other research fields. Because of the wealth of information contained in 3D facial images, 3D face recognition has recently become an active research field. Nevertheless, because of its high dimension, 3D face recognition remains a difficult task. We propose a 3D facial ethnicity identification method on the basis of cylindrical projection and deep learning in this paper. In the proposed method, we first use cylindrical projection to convert a 3D facial image (scanned 3D data) to a 2D grayscale image. The depth information is represented by the grayscale. The transformed 2D image is then fed into a convolutional neural network for ethnicity recognition. The proposed method is alignment-free, and any existing convolutional neural networks developed for 2D image recognition can be used to identify ethnicity. The effectiveness of the proposed method was validated on our private 3D dataset and demonstrated that the proposed method can give promising identification performances between the Mainland Japanese and the Ryukyuan.

Although temperament has been regarded as an innate aspect of human personality, its association with proteins involved in embryonic development is unclear. Reelin, encoded by RELN, plays an important role in brain development. Herein, we investigated the association between the RELN rs7341475 (G/A) single nucleotide polymorphism, detected as a female-specific risk factor for schizophrenia, brain structure, and temperament to elucidate the role of RELN in the development of human personality. In this study, 1580 healthy young Japanese adults were genotyped for RELN rs7341475 and completed the Temperament and Character Inventory. Whole-brain analysis of covariance was conducted to investigate differences between genotypes in regional gray matter volume (rGMV) and cortical morphology. Additionally, multiple regression analysis was performed to examine the association of four temperaments with rGMV. Those statistical analyses were performed separately for males and females. Individuals with G/G homozygosity showed significantly greater rGMV in several areas of the brain, particularly the bilateral cingulate and temporal gyrus, as well as a larger value of fractal dimension in the left lateral occipital cortex. Furthermore, of the four temperaments, the novelty seeking was significantly and positively associated with rGMV in the right superior temporal gyrus, partially overlapping with areas where differences between the rs7341475 genotypes were detected. The above findings were detected only in females, but not in males. This is the first study to demonstrate the contribution of RELN rs7341475 to differences in brain structure in Japanese females, which may indicate vulnerability to schizophrenia and variations in human personality.

In our previous study, we created a glucagon-like peptide-2 (GLP-2) derivative with the functional sequence PAS-CPP to achieve efficient uptake by the respiratory epithelium and trigeminal nerve. By using octaarginine for cell penetrating peptides (CPP) and FFLIPKG, a reverse sequence of a part of the cathepsin D sequence for the penetration accelerating sequence (PAS), we found that the derivative was taken up by the cells through macropinocytosis and efficiently escaped from the endosomes and exited the cells. Moreover, it showed drug effects by intranasal (in.) administration at the same dose as intracerebroventricular (icv.) administration, which is direct drug administration into the brain. The purpose of this study was to elucidate the cause of the drug effect of in. administered PAS-CPP-GLP-2 at the same dose as that by icv. administration. The present results suggested that although icv. administered PAS-CPP-GLP-2 entered the cerebrospinal fluid, it barely penetrated the perivascular space of the brain, and therefore, only a small amount of the administered dose may have reached the site of action in the brain. In contrast, it was qualitatively suggested that in. administered PAS-CPP-GLP-2 migrates from the trigeminal nerve to the central nervous system via the principal sensory trigeminal nucleus and then through the trigeminal lemniscus. The present results show that nose-to-brain delivery by trigeminal axons, which is assumed to be a transcellular pathway, may be possible. As the drug can be delivered into the nerve, it is expected to be applied not only as a central delivery route but also for the treatment of neurological diseases.

Modes of reproduction in animals are diverse, with different modes having evolved independently in multiple lineages across a variety of taxa. However, an understanding of the genomic change driving the transition between different modes of reproduction is limited. Several ricefishes (Adrianichthyidae) on the island of Sulawesi have a unique mode of reproduction called "pelvic-fin brooding," wherein females carry externally fertilized eggs until hatching using their pelvic fins. Phylogenomic analysis demonstrated pelvic-fin brooders to have evolved at least twice in two distant clades of the Adrianichthyidae. We investigated the genetic architecture of the evolution of this unique mode of reproduction. Morphological analyses and laboratory observations revealed that females of pelvic-fin brooders have longer pelvic fins and a deeper abdominal concavity, and that they can carry an egg clutch for longer than nonbrooding adrianichthyids, suggesting that these traits play important roles in this reproductive mode. Quantitative trait locus mapping using a cross between a pelvic-fin brooder Oryzias eversi and a nonbrooding O. dopingdopingensis reveals different traits involved in pelvic-fin brooding to be controlled by different loci on different chromosomes. Genomic analyses of admixture detected no signatures of introgression between two lineages with pelvic-fin brooders, indicating that introgression is unlikely to be responsible for repeated evolution of pelvic-fin brooding. These findings suggest that multiple independent mutations may have contributed to the convergent evolution of this novel mode of reproduction.

Cost-effective genotyping can be achieved by sequencing PCR amplicons. Short 3-10 base primers can arbitrarily amplify thousands of loci using only a few primers. To improve the sequencing efficiency of the multiple arbitrary amplicon sequencing (MAAS) approach, we designed new primers and examined their efficiency in sequencing and genotyping. To demonstrate the effectiveness of our method, we applied it to examining the population structure of the small freshwater fish, medaka (Oryzias latipes). We obtained 2987 informative SNVs with no missing genotype calls for 67 individuals from 15 wild populations and three artificial strains. The estimated phylogenic and population genetic structures of the wild populations were consistent with previous studies, corroborating the accuracy of our genotyping method. We also attempted to reconstruct the genetic backgrounds of a commercial orange mutant strain, Himedaka, which has caused a genetic disturbance in wild populations. Our admixture analysis focusing on Himedaka showed that at least two wild populations had genetically been contributed to the nuclear genome of this mutant strain. Our genotyping methods and results will be useful in quantitative assessments of genetic disturbance by this commercially available strain.

Background: The etiology of bipolar disorder (BD) is poorly understood. Considering the complexity of BD, pedigree-based sequencing studies focusing on haplotypes at specific loci may be practical to discover high impact risk variants. This study comprehensively examined the haplotype sequence at 1p36-35 BD and recurrent depressive disorder (RDD) susceptibility loci. Methods: We surveyed BD families in Okinawa, Japan. We performed linkage analysis and determined the phased sequence of the affected haplotype using whole genome sequencing. We filtered rare missense variants on the haplotype. For validation, we conducted a case-control genetic association study on approximately 3000 Japanese subjects. Results: We identified a three-generation multiplex pedigree with BD and RDD. Strikingly, we identified a significant linkage with mood disorders (logarithm of odds [LOD] = 3.61) at 1p36-35, supported in other ancestry studies. Finally, we determined the entire sequence of the 6.4-Mb haplotype shared by all affected subjects. Moreover, we found a rare triplet of missense variants in the SPOCD1 gene on the haplotype. Notably, despite the rare frequency, one heterozygote with multiple SPOCD1 variants was identified in an independent set of 88 BD type I genotyping samples. Limitations: The 1p36-35 sequence was obtained from only a single pedigree. The replicate sample was small. Short-read sequencing might miss structural variants. A polygenic risk score was not analyzed. Conclusion: The 1p36-35 haplotype sequence may be valuable for future BD variant studies. In particular, SPOCD1 is a promising candidate gene and should be validated.