Biology subjects

Satta, Y.

Publications and source records attributed to Satta, Y..

8 recordsLinked to original sources

bioRxiv2024

Global adaptive evolution involved in neuroticism and educational behaviors through the spread of anatomically modern humans

A cumulative process of cultural evolution occurred globally alongside the spread of anatomically modern humans (AMHs). This process of evolution was likely accompanied by global changes in mental and behavioral phenotypes, resulting in cultural differences between AMHs and Neanderthals. Globally, selective increases of frequencies were detected in alleles, which contributed to the suppression of neuroticism and advanced learning. This finding indicates that neuroticism was suppressed and learning behaviors developed through the global spread of AMHs. It suggests that global adaptation to psychosocial stress occurred, which contributed to cumulative cultural evolution by increasing cooperative learning. A comparison of phenotypic trends at the population level indicates that such globally occurring adaptive evolution, entailing neuroticism suppression and increased learning behaviors has been more significant in AMHs than in Neanderthals. However, adaptive evolution toward greater intelligence was more significant in Neanderthals than in AMHs. These findings suggest that mental traits involved in cultural development evolved differently in AMHs and Neanderthals, and that learning behaviors such as cooperative learning, rather than intelligence, played an important role in AMH evolution.

evolutionary biology↗

bioRxiv2023

Distinct haplogroups with star-like diversification in the APOBEC3 regulatory region indicate ancient viral pandemics before and during the Out-of-Africa migration of modern humans

Human anti-viral APOBEC3s are crucial components of the innate immune response, playing a key role in inhibiting viral replication and proliferation by inducing mutations in viral genomes. In this study, in a regulatory region of [~]16 kb in the APOBEC3 gene cluster on human chromosome 22, we identified three distinct haplogroups that are maintained at high frequencies in both African and non-African populations today. Despite the long persistence of these haplogroups, one of which is shared by archaic hominins, the nucleotide diversity within each haplogroup was unusually low in non-Africans. The simultaneous observations of low intra-haplogroup diversity and high inter-haplogroup divergence were incompatible with neutrality, as demonstrated by the genome-wide empirical distribution and coalescence-based simulation tests. In addition to the three shared haplogroups, an ancestral sequence group was identified exclusively in African populations. To explain these features and investigate the underlying evolutionary mechanisms, we performed forward simulations to model the joint effects of balancing selection and population bottlenecks. We demonstrated the operation of balancing selection over the past [~]1 million years, as well as a hitherto unexplored reduction in intra-haplogroup diversity. The only unexplainable observation was the low diversity within African haplogroup I, which is unaffected by the non-African-specific bottleneck. We hypothesized that an extra haplotype turnover within haplogroup I occurred prior to the Out-of-Africa dispersal of modern humans. Finally, we discussed the functional importance of the APOBEC3 regulatory region in terms of evolutionary conservation in Hominidae, a target of natural selection in modern humans, and its relevance in GTEx eQTL. Significance statementThis study provides new insights into the joint effects of population bottlenecks and balancing selection on genetic diversity within haplogroups. First, we reveal how balancing selection interacts with demographic history to shape intra-haplogroup diversity, a previously unexplored aspect. Second, our findings are generalizable, as illustrated by the ABO locus--an established example of balancing selection--where low within-haplogroup diversity and high between-haplogroup divergence are also observed in non-African populations. Third, the involvement of balancing selection in a highly conserved regulatory region suggests functional significance in modulating the expression of all seven APOBEC3 genes. While further validation is needed, our findings underscore the evolutionary and functional importance of this region in human innate immunity.

evolutionary biology↗

bioRxiv2022

Identification of variation in Fibromelanosis region on chromosome 20 for determining the purity of Indonesian Cemani chicken

Ayam Cemani is a local Indonesian chicken with heavy pigmentation in plumage colour, skin, eyes, and inner body organs. This trait with dermal hyperpigmentation is identical to Fibromelanosis (Fm) mutation in a Silkie chicken. The causal mutation of the Fm trait is due to an inverted duplication and junction of two genomic regions involving the Endothelin3 (EDN3) gene on chromosome 20. There are two duplication boundaries; one is specific to the Fm allele, the other is common for both Fm and fm+ allele. Determining birds that are homozygous or heterozygous at this locus is useful for unifying the Fm trait of Cemani populations. This study develops a method for determining the presence or absence of Fm mutation by PCR amplification using the inverted sequences specific to the Fm allele. Further, it develops the restriction fragment length polymorphism (RFLP) method in regions common to the Fm and wild-type fm+ allele. We aim to establish a simple method for detecting homozygous (Fm/Fm) and heterozygous (Fm/fm+) individuals with Fm mutation and to clarify the degree of fixation of the Fm trait in the Ayam Cemani populations and the association between the phenotype and genotype. The result showed that mostly, the phenotype for Cemani with Fm/ fm+ genotype is reddish black in their comb; meanwhile, the Cemani with (Fm/Fm) genotype showed heavy black pigmentation. Our study concluded that using the PCR-RFLP method. We can discriminate between Fm homozygous and heterozygous birds in the Cemani population. Thus, this briefly genotyping method effectively maintains and protects the pure line of Cemani chicken.

genetics↗

bioRxiv2022

Spatial and temporal diversity of positive selection on shared haplotypes at the PSCA locus among worldwide human populations

Selection on standing genetic variation is important for rapid local genetic adaptation when the environment changes. We report that, for the prostate stem cell antigen (PSCA) gene, different populations have different target haplotypes, even though haplotypes are not unique to specific populations. The C-C-A haplotype, whereby the first C is located at rs2294008 of PSCA and is a low risk allele for gastric cancer, has become a target of positive selection mainly in Asian populations. Conversely, the C-A-G haplotype carrying the same C allele has become a selection target in African populations. However, Asian and African populations share both haplotypes, consistent with the haplotype divergence time (170 kya) prior to out-of-Africa. The frequency of C-C-A/C-A-G is 0.344/0.278 in Asia and 0.209/0.416 in Africa. 2D-SFS analysis revealed that the extent of intra-allelic variability of the target haplotype is extremely small in each local population, suggesting that C-C-A or C-A-G is under ongoing hard sweeps in local populations. From the TMRCA of selected haplotypes, the estimated onset times of positive selection were recent (3-55 kya), concurrently with population subdivision from a common ancestor. Additionally, estimated selection coefficients from ABC analysis were up to [~]3%, similar to those at other loci under recent positive selection on standing genetic variation. Phylogeny of local populations and TMRCA of selected haplotypes revealed that spatial and temporal switching of positive selection targets is a unique and novel feature of ongoing positive selection at PSCA. This switching may reflect potential of rapid adaptability to distinct environments.

evolutionary biology↗

bioRxiv2021

Lower promoter activity of the ST8SIA2 gene has been favored in evolving human collective brains

ST8SIA2 is the main factor regulating expression of the phenotype involved in schizophrenia. Lowered promoter activity of the ST8SIA2 gene is considered to be protective against schizophrenia by conferring tolerance to psychosocial stress. Here, we examined the promoter type composition of anatomically modern humans (AMHs) and archaic humans (AHs; Neanderthals and Denisovans), and compared the promoter activity at the population level (population promoter activity; PPA) between them. In AMHs, the TCT-type, showing the second lowest promoter activity, was most prevalent in the ancestral population of non-Africans. However, the detection of only the CGT-type from AH samples and recombination tracts in AH sequences showed that the CGT- and TGT-types, exhibiting the two highest promoter activities, were common in AH populations. Furthermore, interspecies gene flow occurred into AMHs from AHs and into Denisovans from Neanderthals, influencing promoter-type compositions independently in both AMHs and AHs. The difference of promoter-type composition makes PPA unique in each population. East and Southeast Asian populations show the lowest PPA. This results from the selective increase of the CGC-type, showing the lowest promoter activity, in these populations. Every non-African population shows significantly lower PPA than African populations, resulting from the TCT-type having the highest prevalence in the ancestral population of non-Africans. In addition, PPA reduction is also found among subpopulations within Africa via a slight increase of the TCT-type. These findings indicate a trend toward lower PPA in the spread of AMHs, interpreted as a continuous adaptation to psychosocial stress arising in migration. This trend is considered as genetic tuning for the evolution of collective brains. The inferred promoter-type composition of AHs differed markedly from that of AMHs, resulting in higher PPA in AHs than in AMHs. This suggests that the trend toward lower PPA is a unique feature in AMH spread.

evolutionary biology↗

bioRxiv2020

Population genomics on the origin of lactase persistence in Europe and South Asia

The C to T mutation at rs4988235 located upstream of the lactase (LCT) gene is the primary determinant for lactase persistence (LP) that is prevalent among Europeans and South Asians. Here, we review evolutionary studies of this mutation based on ancient and present-day human genomes with the following concluding remarks: the mutation arose in the Pontic Steppe somewhere between 23,000 and 5960 years ago, emigrated into Europe and South Asia in the Bronze Age via the expansion of the Steppe ancestry, and experienced local hard sweeps with their delayed onsets occurring between 5000 and 3280 years ago. We also argue that the G to A mutation at rs182549 arose earlier than 23,000 years ago, the intermediate CA haplotype ancestral to the LP-related TA haplotype is still represented by samples from Tuscans, admixed Americans and South Asians, and the great majority of G to A mutated descendants have hitchhiked since the C to T mutation was favored by local selection.

evolutionary biology↗

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↗

bioRxiv2018

Complex haplotypes of metabolizing GSTM1 gene deletion harbors signatures of a selective sweep in East Asian populations

The deletion of the metabolizing Glutathione S-transferase Mu 1 (GSTM1) gene was previously associated with multiple cancers, metabolic and autoimmune disorders, as well as drug response. It is unusually common, with allele frequency reaching up to 75% in some human populations. Such high allele frequency of a derived allele with apparent impact on an otherwise conserved gene is a rare phenomenon. To investigate the evolutionary history of this locus, we analyzed 310 genomes using population genetics tools. Our analysis revealed a surprising lack of linkage disequilibrium between the deletion and the flanking single nucleotide variants in this locus, indicating gene conversion events. Tests that measure extended homozygosity and rapid change in allele frequency identified signatures of an incomplete soft-sweep in the locus. Using empirical approaches, we identified the Tanuki haplogroup, which carries the GSTM1 deletion and is found in approximately 70% of East Asian chromosomes. This haplogroup has rapidly increased its frequency in East Asian populations, contributing to a high population differentiation among continental human populations. We showed that extended homozygosity and population differentiation for this haplogroup is incompatible with simulated neutral expectations in East Asian populations. In parallel, we revealed that the Tanuki haplogroup is significantly associated with the expression levels of other GSTM genes. Collectively, our results suggest that the Tanuki haplogroup has likely undergone a soft sweep in East Asia with multiple functional consequences. Our study provides the necessary framework for further studies to elucidate the evolutionary reasons that maintain disease-susceptibility variants in the GSTM1 locus.\n\nLay summaryHere, we describe the evolutionary forces that shape the variation in a genomic region, which has been associated with bladder cancer, metabolic and autoimmune disorders and response to different drugs. Our results reveal a new genetic type common in Asian populations that may have important evolutionary and biomedical implications.

genetics↗