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PubMed2025

From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.

Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.

Humans↗
PubMed2026

The Jumonji C domain-containing proteins GmJMJ19 and GmJMJ20 link florigen signaling with epigenetic regulation of photoperiodic flowering and post-flowering plant height in soybean.

Soybean (Glycine max) is a photoperiod-sensitive legume whose latitudinal adaptation depends on the precise control of flowering time and plant height. Histone demethylases of the JmjC domain-containing (JMJ) protein family have been implicated in these processes across plant species, but their specific roles in soybean remain largely unexplored. Here, we identify soybean GmJMJ19 and GmJMJ20, two closely related JMJD5/KDM8 orthologs, as master epigenetic regulators that coordinately control both photoperiodic flowering and post-flowering plant height. Both genes exhibit intrinsic, rhythmic expression peaking at ZT12, and their encoded proteins physically interact with the florigen proteins FT2a and FT5a. Loss-of-function mutants display delayed flowering under long days (LDs) and increased plant height under both LDs and short days (SDs), whereas overexpression phenocopies the mutant flowering phenotype, indicating revealing a critical dosage requirement for proper function. Mechanistically, GmJMJ19 and GmJMJ20 are recruited by the FT/FD transcriptional complex to directly activate AP1a and AP1c expression through chromatin modulation. Population genomic analyses reveal distinct selection signatures: GmJMJ19 underwent sustained directional selection during cultivation, whereas GmJMJ20 experienced an early domestication sweep with limited subsequent change. Haplotype analysis identifies coordinated latitudinal clines, with the JMJ19H1/JMJ20H1 combination predominating at high latitudes to promote early flowering and limit height, while JMJ19H2/JMJ20H2 and wild JMJ19H3/JMJ20H3 alleles prevail at low latitudes, conferring later flowering and increased height. Collectively, our findings establish GmJMJ19 and GmJMJ20 as central chromatin regulators linking florigen signaling to downstream target expression and provide valuable allelic resources for breeding regionally adapted soybean varieties across a wide range of latitudinal environments.

Histone modulation↗
PubMed1979

Analysis of multiple birth rates in Japan. 1. Secular trend, maternal age effect, and geographical variation in twinning rates.

Mean twin, triplet, and quadruplet birth rates in Japan from 1951 to 1968 were 6.41, 0.056, and 0.00094 per 1,000, respectively. In 1974 the corresponding figures were 5.83, 0.059, and 0.00329. No quintuplets were born in the former period, but a set was born in the latter year, the rate being 0.47 per million. From 1955 to 1966 the MZ twinning rate increased slightly, but decreased thereafter. This increase was limited to live-born MZ twins, particularly in the higher maternal age groups. The DZ twinning rate declined in the entire period, particularly in higher maternal age groups. This decline appeared to be essentially limited to fetal deaths. Among live births the MZ twinning rate underwent a nearly linear increase with maternal age, whereas the DZ twinning rate attained a mode in the maternal age group 35--39 years. The MZ and the DZ twinning rates among fetal deaths by maternal age had unimodal distributions with modes in maternal age groups 25--29 and 30--34 years, respectively. As to the DZ twinning rate, a geographical cline was noted, with a high rate in the northeast of Japan; the rate was positively correlated with latitude, which also positively correlated with the presence of multiple births among relatives. A negative but nonsignificant correlation was seen between the DZ twinning rate and the proportion of mothers treated with ovulation-inducing hormone. The proportion was higher in mothers of unlike-sexed twins than in those of like-sexed twins and in mothers of triplets than in those of twins. An association between DZ twinning rate and age-specific fertility per married woman is suggested to exist among higher maternal age groups in the northeast part of Japan in earlier years.

Adult↗
PubMed2026

Dissecting contributions of directional and balancing selection to trajectories of mitochondrial haplotype evolution in Drosophila melanogaster.

Emerging evidence suggests mtDNA haplotypes contribute to fitness variation and local adaptation, with directional thermal selection and negative frequency-dependent selection shaping haplotype diversity. However, their interplay remains unexplored. We conducted experimental evolution using Drosophila melanogaster populations from opposite ends of an Australian latitudinal cline (Melbourne and Townsville), exposing them to contrasting temperatures (17°C versus 27°C) and varying starting frequencies of two mtDNA haplotypes (A1 and B1) that occur at appreciable frequencies in these populations. We paired this with population genetic simulations to estimate selection and its influence on haplotype trajectories. Haplotype frequencies were influenced by interactions involving temperature, starting frequency, and nuclear genomic background (Melbourne, Townsville, or admixed). Although prior work predicted A1 should be favoured at the warmer temperature and B1 at the cooler temperature, A1 was generally favoured across both temperatures. Simulations supported directional selection in populations evolving at 17°C in the Melbourne background; otherwise dynamics were best explained by balancing selection shaped by negative frequency-dependent fitness effects. Patterns also varied across nuclear backgrounds, suggestive of mito-nuclear epistasis. These findings challenge a simple thermal adaptation model of mtDNA dynamics, suggesting that mtDNA evolution is shaped by interacting effects of temperature, frequency-dependence, nuclear background and experimental environment.

adaptation↗
PubMed1979

Immunogenetic studies on wild pigs in Japan.

The variations of blood groups in the two subspecies of wild pigs in Japan (Sus scrofa leucomystax and S.s. riukiuanus) were investigated by serological techniques. S.s. leucomystax showed polymorphism in the A and F systems. S.s. riukiuanus showed a little polymorphism in the F system only. As a whole, there was a great similarity in erythrocyte antigen structures of both S.s. leucomystax and S.s. riukiuanus. In comparison with the erythrocyte antigen frequenties of wild pigs in the Eurasian Continent reported by other workers. East-West geographical clines in the frequencies of Ea, Fa, Ga, Ka, Kb and Lh antigens were clearly observed. From the results of investigation on genetic similarities among seven wild pig populations, it was made clear that the two Japanese strains were very close and were closer to Far Eastern TS.s. ussuricus) than Middle Asian (S.s. nigripes), Transcausian (S.s. attila) and European pigs (S.s. ferus).

Animals↗
PubMed1978

HLA polymorphism in Israel. 9. An overall comparative analysis.

HLA gene frequencies in 11 Israeli populations and nine other relevant populations were used to calculate genetic distances in a quantitative assessment of their similarities and differences. The shortest distance found is between Polish and Rumanian Jews, while the largest is between Russian Jews and Black Africans. Estimates of "average" distances within major population groups suggest that the Ashkenazi Jews (Poles, Russians, Rumanians and Germans) are a more homogeneous population than East European non-Jews or than Middle-Eastern populations (Arabs, Armenians, Lebanese and Turks). A cline of distances between Ashkenazi Jews and other Jewish communities parallels their geographic distribution; however, the relatively large distance between the two North African communities (Libyans and Moroccans) demonstrates that geographic proximity is not necessarily correlated with genetic similarity. The Jewish populations, especially the Ashkenazi, show a clear divergence from their neighboring non-Jewish populations, among whom they have lived for many centuries. There are indications in the HLA data of a common origin for the diverse Jewish populations.

Gene Frequency↗
PubMed2025

Experimental Validation of Genome-Environment Associations in Arabidopsis.

Identifying the genetic basis of local adaptation is a key goal in evolutionary biology. Allele frequency clines along environmental gradients, known as genotype-environment associations (GEA), are often used to detect potential loci causing local adaptation but are rarely followed by experimental validation. Here, we tested loci identified in three moisture-related GEA studies on Arabidopsis. We studied 42 GEA-identified genes using t-DNA knockout lines under drought and tested effects on flowering time, an adaptive trait, and genotype-by-environment (GxE) interactions for performance and fitness. In total, 16/42 genes had significant effects on traits involved in local adaptation or performance responses to the environment. We found that wrky38 mutants had significant GxE effects for fitness; lsd1 plants had a significant GxE effect for flowering time, and 11 genes showed flowering time effects with no drought interaction. However, most GEA candidates did not exhibit GxE. In the follow-up experiments, wrky38 caused decreased stomatal conductance and specific leaf area under drought, indicating potentially adaptive drought avoidance. Additionally, GEA identified natural putative LoF variants of WRKY38 associated with dry environments, as well as alleles associated with variation in LSD1 expression. While only a few GEA-identified genes were validated for GxE interactions for fitness, we likely overlooked some genes because experiments might not well represent natural environments and t-DNA insertions might not well represent natural alleles. Nevertheless, GEAs apparently identified some genes contributing to local adaptation. GEA and follow-up experiments are straightforward to implement in model systems and demonstrate prospects for GEA discovery of new local adaptations.

Arabidopsis↗
PubMed1978

Synthetic maps of human gene frequencies in Europeans.

Multivarate techniques can be used to condense the information for a large number of loci and alleles into one or a few synthetic variables. The geographic distribution of synthetic variables can be plotted by the same technique used in mapping the gene frequency of a single allele. Synthetic maps were constructed for Europe and the Near East, with the use of principal components to condense the information of 38 independent alleles from ten loci. The first principal component summarizes close to 30% of the total information and shows gradients. Maps thus constructed show clines in remarkable agreement with those expected on the basis of the spread of early farming in Europe, thus supporting the hypothesis that this spread was a demic spread rather than a cultural diffusion of farming technology.

Agriculture↗
PubMed1978

Immunoglobulin Gm and Km genetic markers in Vietnamese.

The distribution of the G1m (1,2,3,17), G2m(23), G3m(5,10,11,13,14,15,21,28) and Km (1,2) allotypic markers has been examined in 122 unrelated Vietnamese subjects originating from all regions of Vietnam. The 13 observed phenotypes have been explained by means of 8 haplotypes: 5 'major' ones (which are also known to be usual in all other reported Mongoloid populations) and 3 'minor' ones. Consideration of gene frequencies allows easy integration of Vietnamese within the south-north cline of Gm haplotype distribution in East Asia, where they insert between Southern Chinese, on one hand, and Singapore as well as South Central Chinese on the other hand. The observed Km10.290 frequency value revealed to be of the same order of magnitude as the values reported for most other non-Thai Mongoloids.

Gene Frequency↗
PubMed1979

Polymorphism of red cell glutamic-pyruvic transaminase in Japanese: gene frequencies in samples from Northern Japan.

The genetic polymorphism of red cell GPT was investigated by starch-gel electrophoresis in four samples from northern Japan including a sample of the Ainu of Hokkaido. The distribution of the Gpt1 gene frequencies among 10 samples excluding the Ainu so far examined showed heterogeneity. The geographical cline of Gpt1 gene frequency reported in southern Japan was not observed in northern Japan.

Adult↗
PubMed1976

Basicranial morphology of the early tertiary tarsiiform Rooneyia from Texas.

The newly prepared middle ear cavity of Rooneyia viejaensis revealed the enlarged lateral branch of the internal carotid, an ancestral tarsiiform but advanced primate character. The ectotympanic is well inside the bulla proper and it appears that the annulus membrane and the tissues of the external auditory tube became ossified to form the tarsiiform ectotympanic. The polarity of several character clines of tarsiiform basicrania are discussed. Evidence is lacking from basicranial morphology to corroborate the hypothesized special relationship of microchoerine omomyids and Tarsius.

Animals↗
PubMed1979

Systematic relationships of gorillas from Kahuzi Tshiaberimu and Kayonza.

Previous classifications of gorillas from Mt. Kahuzi, Mt. Tshiaberimu and the Kayonza Forest, placing them in Gorilla gorilla graueri or G.g. beringei, somewhat over-simplify a complex situation. Both Kahuzi and Tshiaberimu gorillas are close to graueri and should be placed in that subspecies, but each (in different ways) shows some approach to beringei, either through independent adaptation to extreme montane conditions, or because they may be points along a (now disrupted) cline from one race to the other. A hypothesis for the dispersal of beringei is presented, making use of geophysical data on the movement of the African plate over the Virunga 'hot-spot'.

Adaptation, Biological↗
PubMed1978

Skin color, ethnicity, and blood pressure II: Detroit whites.

Census areas in Detroit were ranked for their stress scores based on instability (e.g., crime, marital break up) and socioeconomic status. Four areas were selected for detailed study: 1) high stress, population predominantly black and 2) white, and 3) low stress, population predominantly black and 4) white. A sample was drawn from each area of persons of the predominant race, 25-60 years old, married and living with spouse, and having relatives in the Detroit Area. Nurses interviewed such persons; three blood pressure readings were taken during the first half-hour of medical history, and skin color was rated. While lighter skin color showed a negligible relation to higher blood pressure, a four-category division of European national background based on a skin color cline in Europe from Northern areas to the Mediterranean was significantly associated with a nurse-rating of skin color. The rank order of this four category variable, white ethnicity, was related linearly to both systolic and diastolic blood pressure means. Respondents with parents from Mediterranean countries had the lowest pressures and those from Northern Europe had the highest. The relationship is stronger for women than men. The relationship was independent of nine other control variables including age, overweight, smoking etc., and high and low stress areas, although of greater magnitude for the high than low stress groups. In this article, findings in whites are compared with prior results in blacks. Findings suggest that physiological and biological correlates exist that can be explored profitably by future research.

Adult↗
PubMedDate not supplied

[Qualitative study of a mathematical model of the open futile cycle fructose-6-P--fructose-1,6-P2].

A simple mathematical model of the open futile cycle fructose-6-P in equilibrium fructose-1,6-P2 in which the fructose bisphosphatase reaction is inhibited by excess of its substrate has been analysed. A detailed qualitative investigation of the model shows that it possesses all properties characteristic of any other dynamical system of the second order which has a hysteretic major null-cline, 1 to 3 steady states and is capable of generating self-oscillations.

Chemical Phenomena↗
PubMed1979

[Geographical pathology and genetic markers: detection of associations (author's transl)].

The study of potential associations between genetic markers and various diseases is an important approach in epidemiology. With such studies it is possible to reveal an hereditary component for multifactorial diseases. There are three kinds of analyses: --comparisons of the frequency of the marker in patients and in a control group; --investigations of genetic markers in families with high incidence of disease; --studies of geographical clines between the incidence of the disease and the marker frequency. The interpretation of such geographical associations is difficult. These associations can be the reflect of the migration of susceptibility genes with genetic markers. The HLA system is the better for this kind of approach.

Breast Neoplasms↗
PubMed1976

HLA antigens in Japanese populations.

HLA antigens in 841 healthy, unrelated Japanese from nine widely separated geographic localities were studied. The five most common antigens observed in order of decreasing frequency were for the HLA-A locus: HLA-A9, A2, A10, AW32 and A11; and for the HLA-B locus: HLA-'B5' (= HLA-B5+B17), BW40, B12, B14 and B8. The allelic frequency of undetected antigens of the HLA-A locus was .14-.37, and that of the HLA-B locus, .32-.67, indicating that there were serological difficulties in typing for Japanese antigens using antisera from Caucasians. Marked gene frequency clines were observed for HLA-A9 and HLA-A2 from south (Okinawa) to north (Nagoya). Two haplotypes, HLA-A9, B5 and HLA-A10, BW40 were shown to be in linkage disequilibrium in four of the nine subpopulations.

Alleles↗
PubMed1978

Acute hemorrhagic cystitis. Industrial exposure to the pesticide chlordimeform.

An outbreak of hematuria occurred from May 20 to May 23, 1975, among employees of a chemical packaging plant. Nine of 22 workers who packaged the insecticide chlordimeform in a separate shed became severely ill with abdominal pain, dysuria, urgency to void, or hematuria. None of 18 persons who worked in other areas of the plant were affected. Four additional workers who had packaged the chemical during the previous year had a history of similar symptoms. Bladder biopsy specimens from three affected persons showed severe hemorrhagic cystitis; chlordimeform and 2-methyl-4-chloroaniline, a metabolite of chlordimeform, were present in urine specimens collected three days after exposure. The illness lasted from one week to two months; the workers recovered completely. Chlordimeform that was injected subcutaneously into three cats produced similar, though less severe, changes in the bladders of two animals.

Acute Disease↗