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bioRxiv2025

Pathogenic and genetic diversity of Sclerotium rolfsii, the causal agent of Southern blight of common bean in Uganda

Sclerotium rolfsi Sacc. is a soil born fungus that causes southern blight to many crops in the tropical and subtropical regions. In 2018, Southern blight was reported to be the most prevalent bean root rot in Uganda. Earlier studies ascertained the morphological and pathogenic diversity of S. rolfsii, but limited understanding of its genetic diversity exists. Knowledge of S. rolfsii genetic diversity is a critical resource in the development of common bean varieties with durable resistance to the pathogen. A total of 188 S. rolfsii strains were collected from seven agro-ecological zones of Uganda in 2013, 2020 and 2021, and characterized for pathogenecity, growth rate, the number and colour of sclerotia produced and colony texture. The genetic diversity of the 188 strains was assessed using single nucleotide polymorphisms (SNPs) obtained from whole genome sequencing. The growth rate of the strains ranged between 1.1 to 3.6 cm/day while the number of sclerotia produced ranged between 0 to 543 per strain. The strains had fluffy, fibrous and compact colony texture. The sclerotia were either brown or dark brown. The analyzed strains were pathogenic on common bean and caused a disease severity indices between 10.1% and 93.3%. Average polymorphic information content across all chromosomes was 0.322 with a minimum of 0.145 and maximum of 0.525. Average observed heterozygosity across all the chromosomes was 0.782. Population structure analysis identified five genetically distinct groups. The results of analysis of molecular variance revealed that 0.39% of the variation was between population while 11.98% was between samples within population and 87.62% between samples across populations. The average genetic distances between the isolates from different agro-ecological zones was 0.038 while the average similarity coefficient was 0.968 There were significant differences in the morphological traits and pathogenicity across the different genetic clusters. This high levels of genetic diversity within strains needs to be taken into consideration while selecting strains for screening breeding lines. Key word: Pathogenicity, genetic diversity, Characterisation, Southern blight, common bean

microbiology↗

bioRxiv2025

Anthropocene genetic diversity loss in the marine tropics

Genetic diversity is a crucial component of biodiversity, and as such, its maintenance and preservation is of high conservation concern. Tropical environments are undergoing intense rates of environmental change, and these changes may be driving large declines in genetic diversity. However, data on genetic diversity are highly skewed towards temperate regions. The degree to which diversity loss has occurred in tropical species, particularly marine species, remains an open and important question. Here, we directly compare genomic data from modern and museum collections of two commercially-harvested nearshore marine fishes (Equulites laterofenestra and Gazza minuta) gathered from a single location in the Philippines, spanning a century of intense environmental change. These data reveal a marked loss in genetic diversity and evidence for multiple orders of magnitude reductions in effective population size (Ne) in both species, indicating substantial genomic erosion. Such a decline highlights the long-lasting genomic consequences of anthropogenic activity and sheds light on an, until-now, invisible loss of diversity from the most biodiverse ocean region. Significance StatementRecent reports have shown that genetic diversity in marine fishes has declined either slightly or not at all during the Anthropocene. However, almost all studies investigating marine genetic diversity loss have been from temperate latitudes, whereas tropical marine environments experience some of the most intense human impacts. Here, we directly compare genomic data from modern and historical specimens of two commercially-harvested fishes from the Philippines. We show that marine species in the tropics have already lost substantial genetic diversity and may have undergone severe bottlenecks over the past century. These results shine a light on the previously invisible loss of genetic diversity in the most biodiverse region of the ocean, and they emphasize the evolutionary consequences of the Anthropocene.

ecology↗

bioRxiv2025

Interplay between purging and admixture shapes genetic load in an invasive guppy population

Demographic history can shape the genetic load of populations by influencing the efficacy of selection, levels of heterozygosity, and the incorporation of new variants via gene flow. Understanding these dynamics is crucial for identifying threats to population viability and predicting evolutionary trajectories of invasive populations translocated by humans into non-native environments. We investigate these processes in Trinidadian guppies (Poecilia reticulata) by estimating genetic loads across multiple populations, with a particular focus on a single expanding population in which translocated individuals have rapidly spread and replaced native individuals. Overall, we observe the expected negative relationship between neutral genetic diversity and relative genetic load. In the translocated population, patterns differ between strongly and weakly deleterious mutations. Strongly deleterious alleles are purged at the isolated translocation site but tend to accumulate along the expansion front. In contrast, the genetic load estimated based on weakly deleterious variants declines along the expansion gradient. These differing patterns can be explained by admixture with native populations (which carried fewer weakly deleterious mutations) reducing the overall genetic load of the population at the expansion front. However, admixture has also increased genetic diversity and introduced new strongly deleterious alleles, thereby reversing the purging effect. Together, our findings illustrate the complex interactions determining genetic load in subdivided populations, offering important insights into the evolutionary aspects of biological invasions.

evolutionary biology↗

bioRxiv2025

The genetic architecture of trabecular bone score and association with fracture: a genome-wide association and meta-analysis

BackgroundTrabecular bone score (TBS) is a texture-based measurement derived from DXA scans, which describes the distribution of mineral across the vertebral bodies. Identifying its genetic determinants is crucial for enhancing understanding of its biological basis and clarifying its relationship with fracture risk. MethodsWe conducted a large-scale genome-wide association study (GWAS) of TBS from 44,767 participants (95.08% European ancestry). Sex heterogeneity was assessed through sex-stratified GWAS. Post-GWAS analyses included functional annotation, gene-set enrichment analysis, and cis-expression quantitative trait locus (cis-eQTL) colocalization. Two-sample and multivariable Mendelian randomization (MR) were employed to investigate the causal effect of TBS on fractures. FindingsWe identified 33 independent variants associated with TBS, which explained 4.06% of TBS phenotypic variance. All the discovered signals map to previously identified BMD-associated loci. Additionally, we identified genetic variants in the RAB11FIP3 locus that exhibited a sex-heterogeneous effect, being associated with TBS exclusively in males. Functional annotation and colocalization identified functional genes related to TBS. The two-sample and multivariable MR analyses indicated that TBS potentially has an independent causal effect on fracture risk. InterpretationOur study unveiled 33 independent loci associated with TBS, all in BMD-associated loci. One locus was further identified as associated with TBS only in males. MR results suggested that genetically derived TBS may be causally associated with fracture risk at different sites, potentially beyond BMD. This study provides insights into the TBS genetic architecture and uncovers its potential clinical applications in fracture risk prediction. FundingAll funding information can be found in the Acknowledgements section. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSOsteoporosis is a common disease prevalent in older adults, mainly diagnosed by low bone mineral density and disruption of bone architecture. While the genetic determinants of bone mass have been well studied, the genetic architecture of bone features beyond BMD remains largely unknown. Added value of this studyThis study presents a large genome-wide association meta-analysis of the trabecular bone score (TBS), a measurement of trabecular distribution of bone mineralization across vertebral bodies. Our study identified 33 independent variants associated with TBS and one association signal only in males. Functional annotation highlighted crucial genes related to TBS. The two-sample and multivariable Mendelian randomization (MR) analyses suggested that TBS may be causally linked with fracture risk, potentially independent of BMD. Implications of all the available evidenceOur study represents an expansion of the traditional bone density phenotype used in most previous skeletal genetic studies. Based on the findings that all of the significant loci for TBS have been previously identified in GWAS of BMD, we conclude that TBS-associated variants have pleiotropic effects affecting not only mineral density but also the distribution patterns of minerals in the cancellous bone. Continuing to perform genetic studies of new skeletal phenotypes beyond BMD could ultimately impact the management and prediction of osteoporosis patients.

genomics↗

bioRxiv2025

Tangled evolutionary history: genetically divergent taxa and hybrids characterise lantana invasions in Australia

Aimto investigate population genomics and phylogeography in invasive lantana, including its taxonomy, spatial distribution, and patterns of morphological and genetic variation across the Australian continent. Locationthe main area invaded by lantana on the Australian continent, i.e., coastal and subcoastal eastern Australia from northern Queensland to southern New South Wales up to approximately 100 km inland, across 22 degrees latitude. The native range of lantana in the Americas was also represented. Methodswe used DArTseq to generate genome-wide single nucleotide polymorphism (SNP) data for >600 individuals representing the native and Australian invaded ranges of lantana. We analysed data from >20,000 SNPs to identify distinct genetic clusters, and test the extent to which they corresponded with taxonomic descriptions and morphotype concepts used in lantana biological control. Genome sizes were estimated for a small representative subset of individuals using flow cytometry. We used MaxEnt to estimate habitat suitability for different lantana genetic clusters, and compared these predictions with observed patterns in biological control agent host-specificity. Resultsinvasive lantana in Australia consisted of several divergent genetic clusters of most likely tetraploid individuals. Gene flow between genetic clusters was limited, consistent with the notion that multiple species introductions and/or hybridisation events were part of the invasion history. Two widespread, homogeneous genetic clusters were found to be dominant in Australia; two other genetic clusters with more limited distributions were identified with potential for future spread. Biological control agent host preferences were consistent with identified genetic clusters. Main conclusionstreating invasive lantana as a single taxon may be counterproductive for effective management. Comprehensive taxonomic revision is needed to enable more precise identification of invasive taxa. Improved identification will support improved management, particularly if using biological control.

evolutionary biology↗

bioRxiv2025

Bursts of reproduction can create genetic structure in frequently recombining bacterial populations

In many bacterial species, strong genetic structure is present, where individuals are clustered into genetically distinct groupings within the species. However, high rates of homologous recombination have also been observed in many of these species, high enough that simple models of evolution predict that such genetic structure should be eliminated. One proposed resolution to this contradiction is the presence of recurrent bursts of reproduction caused by rapid adaptation or microepidemics. We investigate this hypothesis using coalescent simulations with recombination, focusing on the distribution of pairwise genetic distances. We show that bursty reproduction can indeed create genetic structure even when recombination is so frequent that all structure would be eliminated in the absence of bursts. We find that genetic structure is only possible when there is a burst of reproduction that is sufficiently large and recent in the populations history. In addition, we find that for other statistics beyond the distribution of pairwise distances, the simplest model of bursty reproduction does not produce distributions similar to those observed in nature. Interestingly, genetic structure from bursts of reproduction can appear among pairs of samples which do not share any genetic material by clonal descent, a feature which cannot be observed in populations whose structure is just a consequence of limited recombination.

evolutionary biology↗

bioRxiv2017

Incipient signs of genetic differentiation among African elephant populations in fragmenting miombo ecosystems in south-western Tanzania

Habitat fragmentation plays a major role in the reduction of genetic diversity among wildlife populations. The African savannah elephant population of the Ruaha-Rungwa and Katavi-Rukwa ecosystems in south-western Tanzania, comprises one of the worlds largest remaining elephant populations, but is increasingly threatened by loss of connectivity and poaching for ivory. We investigate whether there are incipient signs of genetic isolation (loss of heterozygosity) within the younger cohort as a result of habitat loss between the two ecosystems. To investigate the genetic structure of populations, we compared the genotypes for 11 microsatellite loci in the western (n = 81 individuals from Katavi-Rukwa), central (n = 36 individuals from Lukwati and Piti), and eastern populations (n = 193, individuals from Ruaha-Rungwa). We found evidence of significant genetic differentiation among the three populations, but the levels were low, suggesting recent divergence. Furthermore, we identified weak isolation by distance, suggesting higher gene flow among nearer individuals with samples within 50km of each other being more genetically similar to one another than beyond. Although sample sizes were small, a further analysis of genetic differences across populations and in separate age classes revealed evidence of increasing genetic structure among younger age classes across the landscape. In a long-lived species with overlapping generations, it takes a long time to develop genetic substructure even when there are substantial obstacles to migration. Thus, in these recently fragmented populations, inbreeding (and the loss of heterozygosity) may be less of an immediate concern than demography (the loss of adults due to illegal hunting).

ecology↗

bioRxiv2018

Genetic and environmental influence on the human functional connectome

Detailed mapping of genetic and environmental influences on the functional connectome is a crucial step toward developing intermediate phenotypes between genes and clinical diagnoses or cognitive abilities. We analyze resting-state data from two, adult twin samples - 390 twins from the Colorado Longitudinal Twin Sample and 422 twins from the Human Connectome Project - to examine genetic and environmental influence on all pairwise functional connections between 264 brain regions (~35,000 functional connections). Non-shared environmental influence was high, genetic influence was moderate, and shared environmental influence was weak-to-moderate across the connectome. The brains genetic organization is diverse and not as one would expect based solely on structure evident in non-genetically informative data or lower-resolution data. As follow-up, we make novel classifications of functional connections and examine highly-localized connections with particularly strong genetic influence. This high-resolution genetic taxonomy of brain connectivity will be useful in understanding genetic influences on brain disorders.

neuroscience↗

bioRxiv2018

Flow regulation associated with decreased genetic health of a river-breeding frog species

River regulation or flow modification--the hydrological alteration of flow by dams and diversions--has been implicated as a cause of fundamental change to downstream aquatic ecosystems. Flow modification changes the patterns and functionality of the natural flow regime, and has the potential to restrict population connectivity and gene flow in river-dependent organisms. Since population connectivity and the maintenance of genetic diversity are fundamental drivers of long-term persistence, understanding the extent flow modification impacts these critical attributes of genetic health is an important goal for long-term conservation. Foothill yellow-legged frogs (Rana boylii) were historically abundant throughout many western rivers but have declined since the onset of regulation. However, the extent to which R. boylii populations in rivers with altered flow regimes are maintaining connectivity and genetic diversity is unknown. Here we use genetic methods to investigate the impacts of flow alteration on R. boylii to explore their potential for long-term persistence under continued flow modification. We found R. boylii in rivers with flow modification showed striking patterns of isolation and trajectories of genetic diversity loss relative to unregulated rivers. For example, flow modification explained the greatest amount of variance in population genetic differentiation compared with other covariates including geographic distance. Importantly, patterns of connectivity and genetic diversity loss were observed regardless of flow alteration level but were most prominent in locations with the greatest flow modification intensity. Although our results do not bode well for long-term persistence of R. boylii populations under current flow regulation regimes, they do highlight the power of genetic monitoring for assessing population health in aquatic organisms.

ecology↗

bioRxiv2018

Genetic heterogeneity in Anopheles darlingi related to biting behavior in western Amazon

In the Amazon Basin, Anopheles (Nyssorhynchus) darlingi is the most aggressive and effective malaria vector. In endemic areas, behavioral aspects of anopheline species such as host preference, biting time and resting location after a blood meal have a key impact on malaria transmission dynamics and transmission control strategies. An. darlingi present a variety in behavior throughout its broad distribution including blood feeding related. To investigate the genetic basis of its biting behaviors, host-seeking An. darlingi were collected in two settlements (Granada and Remansinho) in Acre, Brazil. Mosquitoes were classified by captured location (indoors or outdoors) and time (dusk or dawn). Genome-wide SNPs were used to assess the degree of genetic diversity and structure in these groups. There was evidence of genetic component of biting behavior regarding both location and time in this species. This study supports that An. darlingi blood-feeding behavior has a genetic component. Additional ecological and genomic studies may help to understand the genetic basis of mosquito behavior and address appropriate surveillance and vector control.\n\nAuthor SummaryMalaria is a disease caused by parasite of the genus Plasmodium and is transmitted by mosquitoes of the genus Anopheles. In the Amazon Basin, the main malaria vector is Anopheles darlingi, which is present in high densities in this region. Egg development requires that females of this mosquito seek hosts for blood meals. Anopheles females blood feeding may occur indoor or outdoor the houses and typically from the sunset to dawn. Anopheles darlingi in particular present great variability regarding its behaviour, presenting variety of peak biting times and patterns. This work shows that there is a genetic component that partially explains these two behaviors: location of the blood meal (inside or outside the houses) and time of feeding. Single nucleotide polymorphisms (SNPs) scattered throughout the genome of Anopheles darlingi showed genetic diversity and structure in these groups. A comprehensive understanding of the genetic basis for mosquito behaviour may support innovative vector surveillance and control strategies.

epidemiology↗

bioRxiv2018

Patterns of speciation and parallel genetic evolution under adaptation from standing variation

Adaptation often proceeds via the sorting of standing variation, and natural selection acting on pairs of populations is a quantitative continuum ranging from parallel to divergent. Yet, it is unclear how the extent of parallel genetic evolution during adaptation from standing variation is affected by the difference in the direction of selection between populations. Nor is it clear whether the availability of standing variation for adaptation affects progress toward speciation in a manner that depends on the difference in the direction of selection. We conducted a theoretical study investigating these questions and have two primary findings. First, the extent of parallel genetic evolution between two populations is expected to rapidly decline as the difference in their directions of selection increases from fully parallel toward divergent, and this decline occurs more rapidly in organisms with greater trait dimensionality. This rapid decline results because seemingly small differences in the direction of selection cause steep reductions in the fraction of alleles that are beneficial in both populations. For example, populations adapting to optima separated by an angle of 33{degrees} have only 50% of potentially beneficial alleles in common (for a case of five trait dimensions). Second, we find that adaptation from standing variation leads to higher ecologically-dependent hybrid fitness under parallel selection, relative to when adaptation is from new mutation only. This occurs because genetic parallelism based on standing variation reduces the phenotypic segregation variance in hybrids when parents adapt to similar environments. In contrast, under divergent selection, the pleiotropic effects of alternative alleles fixed from standing variation change the major axes of phenotypic variation in hybrids and reduce their fitness in parental habitats. We conclude that adaptation from standing genetic variation is expected to slow progress toward speciation via parallel natural selection and can facilitate progress toward speciation via divergent natural selection.\n\nImpact summaryIt is increasingly clear that much of adaptation, especially that which occurs rapidly, proceeds from the sorting of ancestral standing variation rather than complete reliance on de novo mutation. In addition, evolutionary biologists are increasingly embracing the fact that the difference in the direction of natural selection on pairs of populations is a quantitative continuum ranging from completely parallel to completely divergent. In this article, we ask two questions. First, how does the degree of genetic parallelism--here, adaptation using the same alleles in allopatric populations--depend on the differences in the direction of natural selection acting on two populations, from parallel (0{degrees}) to divergent (180{degrees})? And second, how does adaptation from standing variation affect progress toward speciation, and does its effect depend on the direction of natural selection? We develop theory to address these questions. We first find that very small differences in the direction of selection (angle) can largely preclude genetic parallelism. Second, we find that adaptation from standing variation has implications for speciation that change along the continuum from parallel to divergent selection. Under parallel selection, high genetic parallelism causes inter-population hybrids to have high mean fitness when their parents adapt from standing variation. As selection tends toward divergent, adaptation from standing variation is less beneficial for hybrid fitness and under completely divergent selection causes inter-population hybrids to have lower mean fitness than when adaptation was from new mutation alone. In sum, our results provide general insight into patterns of genetic parallelism and speciation along the continuum of parallel to divergent natural selection when adaptation is from standing variation.

evolutionary biology↗

bioRxiv2018

Genetic differentiation is determined by geographic distance in Clarkia pulchella

Both environmental differences and geographic distances may contribute to the genetic differentiation of populations on the landscape. Understanding the relative importance of these drivers is of particular interest in the context of geographic range limits, as both swamping gene flow and lack of genetic diversity are hypothesized causes of range limits. We investigated the landscape genetic structure of 32 populations of the annual wildflower Clarkia pulchella from across the species geographic range in the interior Pacific North-west. We tested whether climatic differences between populations influenced the magnitude of their genetic differentiation. We also investigated patterns of population structure and geographic gradients in genetic diversity. Contrary to our expectations, we found an increase in genetic diversity near the species northern range edge. We found no notable contribution of climatic differences to genetic differentiation, indicating that any processes that might operate to differentiate populations based on temperature or precipitation are not affecting the putatively neutral loci in these analyses. Rather, these results support seed and pollen movement at limited distances relative to the species range and that this movement and the subsequent incorporation of immigrants into the local gene pool are not influenced by temperature or precipitation similarities among populations. We found that populations in the northern and southern parts of the range tended to belong to distinct genetic groups and that central and eastern populations were admixed between these two groups. This pattern could be the result of a past or current geographic barrier associated with the Columbia Plateau, or it could be the result of spread from separate sets of refugia after the last glacial maximum.

evolutionary biology↗

bioRxiv2018

Shared genetic aetiology between cognitive performance and brain activations in language and math tasks

Cognitive performance is highly heritable. However, little is known about common genetic influences on cognitive ability and brain activation when engaged in a cognitive task. The Human Connectome Project (HCP) offers a unique opportunity to study this shared genetic etiology with an extended pedigree of 785 individuals. To investigate this common genetic origin, we took advantage of the HCP dataset, which includes both language and mathematics activation tasks. Using the HCP multimodal parcellation, we identified areals in which inter-individual functional MRI (fMRI) activation variance was significantly explained by genetics. Then, we performed bivariate genetic analyses between the neural activations and behavioral scores, corresponding to the fMRI task accuracies, fluid intelligence, working memory and language performance. We observed that several parts of the language network along the superior temporal sulcus, as well as the angular gyrus belonging to the math processing network, are significantly genetically correlated with these indicators of cognitive performance. This shared genetic etiology provides insights into the brain areas where the human-specific genetic repertoire is expressed. Studying the association of polygenic risk scores, using variants associated with human cognitive ability and brain activation, would provide an opportunity to better understand where these variants are influential.

neuroscience↗

bioRxiv2018

Genetic hubs: a phylogeographer’s widget for pinpointing of ancestral populations

Statistical phylogeography benefits from the development of increasingly realistic models of spatially structured genetic variation. Their fitting, however, is computationally demanding and requires population and/or genomic sampling that is not available for many species of interest. Genetic hubs is a method that can be used for exploratory analyses of various kinds of genetic data, including those as typical in mitochondrial phylogeography, i.e. many small samples of single locus genotypes scattered throughout the species distributional range. Genetic hubs allows to quantify and visualize gradients of genetic variation with the aim to pinpoint possible origin of expansion. It estimates local genetic variability as an accessibility of all genetic variation from the site in question and it allows to take dissimilarity of genotypes into account. The method represents fast and versatile tool that can be used whenever history of range expansion is assumed to shape the observed distribution of genetic variation and it is useful especially for preliminary analyses whose purpose is to provide sound basis for formulation of testable hypotheses and design of follow-up studies.

evolutionary biology↗

bioRxiv2018

Unlimited genetic switches for cell-type specific manipulation

Gaining independent genetic access to discrete cell types is critical to interrogate their biological functions, as well as to deliver precise gene therapy. Transcriptome analyses have allowed us to profile cell populations with extraordinary precision, revealing that cell types are typically defined by a unique combination of genetic markers. Given the lack of adequate tools to target cell types based on multiple markers, most cell types have remained inaccessible to genetic manipulation. Here, we present CaSSA, a platform to create unlimited genetic switches based on CRISPR/Cas9 (Ca) and the DNA repair mechanism known as single-strand annealing (SSA). CaSSA allows engineering of independent genetic switches that each respond to a specific gRNA. Expressing multiple gRNAs in specific patterns enables multiplex cell type-specific manipulations and combinatorial genetic targeting. CaSSA is thus a new genetic tool that conceptually works as an unlimited number of recombinases and will facilitate genetic access to cell types in diverse organisms.

developmental biology↗

bioRxiv2019

Habitat loss does not always entail negative genetic consequences

Although habitat loss has large, consistently negative effects on biodiversity, its genetic consequences are not yet fully understood. In this paper, we assess the genetic consequences of extreme habitat loss driven by mining in two endemic plants from Amazonian Savannas. Our analyses are the first to overcome major methodological limitations like the confounding effect of habitat fragmentation, historical processes underpinning genetic differentiation, time-lags between the onset of disturbances and genetic outcomes, and the need for large numbers of samples, genetic markers and replicated landscapes to ensure sufficient statistical power. We found that both species are remarkably resilient, as genetic diversity and gene flow patterns were unaffected by habitat loss. Our study unambiguously demonstrates that it is not possible to generalize about the genetic consequences of habitat loss, and imply that future conservation efforts need to consider species-specific genetic information.

ecology↗

bioRxiv2019

The determinants of genetic diversity in butterflies - Lewontin's paradox revisited

Under the neutral theory genetic diversity is expected to be a simple function of population size. However, comparative studies have consistently failed to find any strong correlation between measures of census population size and genetic diversity. Instead, a recent comparative study across several animal phyla identified propagule size as the strongest predictor of genetic diversity, suggesting that r-strategists that produce many offspring but invest little in each, have greater long-term effective population sizes. We present a comparison of genome-wide levels of genetic diversity across 38 species of European butterflies (Papilionoidea). We show that across butterflies, genetic diversity varies over an order of magnitude and that this variation cannot be explained by differences in abundance, fecundity, host plant use or geographic range. Instead, we find that genetic diversity is negatively correlated with body size and positively with the length of the genetic map. This suggests that variation in genetic diversity is determined both by fluctuation in Ne and the effect of selection on linked neutral sites.

evolutionary biology↗

bioRxiv2019

A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals

BackgroundThe gut microbiome is an important determinant of human health. Its composition has been shown to be influenced by multiple environmental factors and likely by host genetic variation. In the framework of the Milieu Interieur Consortium, a total of 1,000 healthy individuals of western European ancestry, with a 1:1 sex ratio and evenly stratified across five decades of life (age 20 - 69), were recruited. We generated 16S ribosomal RNA profiles from stool samples for 858 participants. We investigated genetic and non-genetic factors that contribute to individual differences in fecal microbiome composition. ResultsAmong 110 demographic, clinical and environmental factors, 11 were identified as significantly correlated with -diversity, {beta}-diversity or abundance of specific microbial communities in multivariable models. Age and blood alanine aminotransferase levels showed the strongest associations with microbiome diversity. In total, all non-genetic factors explained 16.4% of the variance. We then searched for associations between >5 million single nucleotide polymorphisms and the same indicators of fecal microbiome diversity, including the significant non-genetic factors as covariates. No genome-wide significant associations were identified after correction for multiple testing. A small fraction of previously reported associations between human genetic variants and specific taxa could be replicated in our cohort, while no replication was observed for any of the diversity metrics. ConclusionIn a well-characterized cohort of healthy individuals, we identified several non-genetic variables associated with fecal microbiome diversity. In contrast, host genetics only had a negligible influence. Demographic and environmental factors are thus the main contributors to fecal microbiome composition in healthy individuals.

genomics↗