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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2022

Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple (Malus sylvestris (L.) Mill.), a wild relative of the cultivated apple

O_LICharacterizing the phenotypic and genetic variation among populations of crop wild relatives help understanding the ecological and evolutionary processes involved in population divergence, and better harness their diversity to mitigate the impact of climate change on crops. We assessed genetic and phenotypic diversity of the European crabapple, Malus sylvestris, a main contributor to the cultivated apple genome (Malus domestica), and investigated for ecological divergence. C_LIO_LIWe assessed variation in growth rate and traits related to carbon uptake between seedlings measured in a common garden, and related it to the genetic ancestry of the seedlings, assessed using 13 microsatellite loci and Bayesian clustering method. The occurrence of patterns of isolation-by-distance, -by-climate and -by-adaptation that might have caused genetic and phenotypic differentiation among M. sylvestris populations was also tested. C_LIO_LISeedlings belonged to seven M. sylvestris populations in Europe, with 11.6% of seedlings introgressed by M. domestica. Significant trait variation among M. sylvestris populations was observed, which for some was of moderate to high heritability. Lack of association between trait and genetic divergence suggests that this significant phenotypic variation is not adaptive, but strong association between genetic variation and the climate during the last glacial maximum suggests local adaptation of M. sylvestris to past climates. C_LIO_LIThis study provides an insight into the ecological and evolutionary drivers of phenotypic and genetic differentiation among populations of a wild apple species and relative of cultivated apples, which is a starting point for future breeding programs. C_LI Societal impact StatementApple is a major fruit crop worldwide and a model species for understanding the evolutionary processes underlying perennial crop domestication. Several wild species have contributed to the genetic make-up of the cultivated apple, yet phenotypic and genetic diversity data across their natural distribution is lacking. This study revealed phenotypic variation between populations of the European crabapple, and showed that both geography, and surprisingly, past but not current climate, shaped its genetic structure. We provide a starting point for harnessing wild apple diversity for apple breeding programs to mitigate the impact of climate change on this perennial crop.

ecology↗

bioRxiv2022

Landscape configurations determining the genetic structure of the Yellow-Spotted Amazon River Turtle (Podocnemis unifilis) in Brazilian Amazonia

ContextWaterfalls and rapids of Amazon basin have been suggested as causing the speciation and genetic structure of many freshwater species, including turtles. The species behavior affects the way waterfalls and rapids limit gene flow. The Yellow-spotted River Turtle (Podocnemis unifilis), a widely distributed and endangered Amazonian turtle, does not show the habit to migrate long distances for breeding or eating, but has a complex geographic pattern of genetic variation. ObjectivesHere, we investigate isolation by distance and by resistance of P. unifilis. We analyzed if the species ecological niche and waterfalls explain the genetic distance in Brazilian Amazonia. MethodsWe evaluated the P. unifilis spatial distribution of genetic variability and diversity using the control region of mitochondrial DNA. We tested the hypotheses of isolation either by distance and resistance through an integrative approach using genetic, geographic, and ecological data. We created a resistance matrix using species niche modeling. We compared the explanation power of geographical distance (both linear and in-water distance) and resistance distance on genetic distance ({Phi}ST fixation index) using multiple regressions and Mantel tests. ResultsWe found a high genetic diversity and pattern of genetic structure proved to be geographically complex. The population structure followed some watersheds but also showed structuring within different rivers. We found that landscape resistance better explains genetic distance than linear and in-water distance. ConclusionsThe resistance of the landscape influences the displacement of individuals by aquatic, vegetational, biological, and geomorphological variables, and efforts to species conservation need to be applied throughout its distribution considering landscape genetics.

molecular biology↗

bioRxiv2022

1 Natural Genetic Variation in a Dopamine Receptor is Associated With Variation in Female Fertility in Drosophila melanogaster

Fertility is a major component of fitness but its genetic architecture remains poorly understood. Using a full diallel cross of 50 Drosophila melanogaster Genetic Reference Panel inbred lines with full genome sequences, we found substantial genetic variation in fertility largely attributable to females. We mapped genes associated with variation in female fertility by genome-wide association analysis of common variants in the fly genome. Validation of candidate genes by RNAi knockdown confirmed the role of the dopamine 2-like receptor (Dop2R) in promoting egg laying. We replicated the Dop2R effect in an independently collected productivity dataset and showed that the effect of the Dop2R variant was mediated in part by regulatory gene expression variation. This study demonstrates the strong potential of genome-wide association analysis in this diverse panel of inbred strains and subsequent functional analyses for understanding the genetic architecture of fitness traits. Author SummaryIn evolutionary genetics, fitness is defined as the number of offspring an individual contributes to the next generation. This is determined by an individuals viability (its ability to survive past the reproductive age) and its fertility. Although understanding the genetic basis for natural variation in fitness is a major goal of evolutionary and population genetics, the genetic factors that contribute to variation in fertility in natural populations have remained largely unresolved. To address this issue, we took advantage of the Drosophila Genetic Reference Panel, a population of inbred, sequenced fly lines derived from a natural population. In this panel, there is minimal genetic variation among individuals within each line, whereas variation among the lines reflects the variation observed in the original population from which they were derived. We generated all possible pairwise crosses among 50 of these lines (2,500 distinct genotypes) and measured the productivity (number of offspring produced) for each genotype. We found considerable natural variation in productivity that was primarily determined by the female genotype. We performed a genome wide association as analysis and identified and functionally validated a dopamine receptor that plays a major role in determining variation in female fertility through an effect on egg-laying.

evolutionary biology↗

bioRxiv2022

Evidence for epigenetically influenced mutagenesis and genetic assimilation in nascent species complexes (Coregonus sp.)

Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental conditions for many generations, though there has been minimal empirical research on epigenetically induced mutagenesis in diversification and speciation. Whitefish, freshwater members of the salmonid family, are excellent systems to study phenotypic diversification and speciation due to the repeated divergence of benthic-limnetic species pairs serving as natural replicates. Here we investigate whole genome genetic and epigenetic differentiation between sympatric benthic-limnetic species pairs in lake and European whitefish (Coregonus clupeaformis and C. lavaretus) from four lakes (N=64). We found considerable, albeit variable, genetic and epigenetic differences between species pairs. All SNP types were enriched at CpG sites supporting the mutagenic nature of DNA methylation, though C>T SNPs were most common. We also found an enrichment of overlaps between outlier SNPs with the 5% highest FST between species and differentially methylated loci. This could possibly represent differentially methylated sites that have caused divergent genetic mutations between species, or divergent selection leading to both genetic and epigenetic variation at these sites. Our results support the hypothesis that DNA methylation contributes to phenotypic divergence and mutagenesis during whitefish speciation. Significance statementDNA methylation is an epigenetic mark known to change in response to the environment and induce genetic modifications such as point mutations, though its implications for evolution and speciation have not been thoroughly studied. We find considerable but variable genetic and epigenetic variation between whitefish benthic-limnetic species pairs, highlighting the potential for DNA methylation to contribute to mutagenesis and genetic evolution. Our study provides evidence that DNA methylation could have contributed to whitefish speciation, both through initially plastic methylation changes and by driving genetic divergence between species pairs.

evolutionary biology↗

bioRxiv2022

Heritable epigenetic variation facilitates long-term maintenance of epigenetic and genetic variation

The maintenance of genetic and phenotypic variation has long been one of the fundamental questions in population and quantitative genetics. A variety of factors have been implicated to explain the maintenance of genetic variation in some contexts (e.g. balancing selection), but the potential role of epigenetic regulation to influence population dynamics has been understudied. It is well recognized that epigenetic regulation, including histone methylation, small RNA expression, and DNA methylation, helps to define differences between cell types and facilitate phenotypic plasticity. In recent years, empirical studies have shown the potential for epigenetic regulation to also be heritable for at least a few generations without selection, raising the possibility that differences in epigenetic regulation can act alongside genetic variation to shape evolutionary trajectories. Like genetic mutation, heritable differences in epigenetic regulation can arise spontaneously; these are termed epimutations. Epimutations differ from genetic mutations in two key ways - they occur at a higher rate and the loci at which they occur often revert back to their original state within a few generations. Here, we present an extension of the standard population-genetic model with selection to incorporate epigenetic variation arising via epimutation. Our model assumes a diploid, sexually reproducing population with random mating. In addition to spontaneous genetic mutation, we included parameters for spontaneous epimutation and back-epimutation, allowing for four potential epialleles at a single locus (two genetic alleles, each with two epigenetic states), each of which affect fitness. We then analyzed the conditions under which stable epialleles were maintained. Our results show that highly reversible epialleles can be maintained in long-term equilibrium under neutral conditions in a manner that depends on the epimutation and back-epimutation rates, which we term epimutation-back-epimutation equilibrium. On the other hand, epialleles that compensate for deleterious mutations cause deviations from the expectations of mutation-selection balance by a simple factor that depends on the epimutation and back-epimutation rate. We also numerically analyze several sets of fitness parameters for which large deviations from mutation-selection balance occur. Together, these results demonstrate that transient epigenetic regulation may be an important factor in the maintenance of both epigenetic and genetic variation in populations.

evolutionary biology↗

bioRxiv2023

Low genetic differentiation across an entire continent: the Scots pine paradox

O_LIScots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. C_LIO_LITo understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2,321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species, and examined signals of genetic adaptation. C_LIO_LIWe found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expending populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of SNPs significantly linked to environmental gradients. C_LIO_LIThe results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment. C_LI

evolutionary biology↗

bioRxiv2023

The quantitative genetics of gene expression in Mimulus guttatus

Gene expression can be influenced by genetic variants that are closely linked to the expressed gene (cis eQTLs) and variants in other parts of the genome (trans eQTLs). We created a multiparental mapping population by sampling genotypes from a single natural population of Mimulus guttatus and scored gene expression in the leaves of 1,588 plants. We find that nearly every measured gene exhibits cis regulatory variation (91% have FDR < 0.05) and that cis eQTLs are usually allelic series with three or more functionally distinct alleles. The cis locus explains about two thirds of the standing genetic variance (on average) but varies among genes and tends to be greatest when there is high indel variation in the upstream regulatory region and high nucleotide diversity in the coding sequence. Despite mapping over 10,000 trans eQTL / affected gene pairs, most of the genetic variance generated by trans acting loci remains unexplained. This implies a large reservoir of trans acting genes with subtle or diffuse effects. Mapped trans eQTLs show lower allelic diversity but much higher genetic dominance than cis eQTLs. Several analyses also indicate that trans eQTL make a substantial contribution to the genetic correlations in expression among different genes. They may thus be essential determinants of "gene expression modules", which has important implications for the evolution of gene expression and also how it is studied by geneticists. Author summaryMimulus guttatus (yellow monkeyflower) is a model for the study of quantitative trait evolution in natural populations. Research has focused mainly on whole organism traits like flower size or herbivore resistance, but the level of expression of a gene is also a quantitative trait. In this study, we dissect leaf transcriptome variation using a breeding design that estimates the contribution of individual loci to expression variation (eQTLs). We find at least rough agreement to the "oligogenic model" where a major locus (the cis regulatory region) generates much of the genetic variation in the population. While associations studies routinely characterize genetic effects as binary (the two alternatives at a single nucleotide polymorphism or "SNP"), this description proves insufficient for Mimulus. Most loci exhibit multiple, and in some cases, a continuum of alleles. We find that trans eQTLs have different features than cis eQTLs, both in terms of the diversity and genetic dominance of alleles. These genetic features of eQTLs are critical determinants of the "G matrix", the genetic variances and covariances among all genes. The G matrix determines how gene expression will evolve under selection in response to changing environmental conditions. Our finding of large effect sizes and high allelic diversity suggests that the G matrix may be surprisingly malleable, even on ecological timescales.

evolutionary biology↗

bioRxiv2024

Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations

In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these two fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we derive a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., Genome-Wide Association Studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur using analytical theory and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate this by showing how a standard GWAS technique--including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model--can mitigate spurious correlations in phylogenetic analyses. As a case study of this, we re-examine an analysis testing for co-evolution of expression levels between genes across a fungal phylogeny, and show that including covariance matrix eigenvectors as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.

genomics↗

bioRxiv2024

A multivariate approach to joint testing of main genetic and gene-environment interaction effects

Gene-environment (GxE) interactions crucially contribute to complex phenotypes. The statistical power of a GxE interaction study is limited mainly due to weak GxE interaction effect sizes. To utilize the individually weak GxE effects to improve the discovery of associated genetic loci, Kraft et al. [1] proposed a joint test of the main genetic and GxE effects for a univariate phenotype. We develop a testing procedure to evaluate combined genetic and GxE effects on a multivariate phenotype to enhance the power by merging pleiotropy in the main genetic and GxE effects. We base the approach on a general linear hypothesis testing framework for a multivariate regression for continuous phenotypes. We implement the generalized estimating equations (GEE) technique under the seemingly unrelated regressions (SUR) setup for binary or mixed phenotypes. We use extensive simulations to show that the test for joint multivariate genetic and GxE effects outperforms the univariate joint test of genetic and GxE effects and the test for multivariate GxE effect concerning power when there is pleiotropy. The test produces a higher power than the test for multivariate main genetic effect for a weak genetic and substantial GxE effect. For more prominent genetic effects, the latter performs better with a limited increase in power. Overall, the multivariate joint approach offers high power across diverse simulation scenarios. We apply the methods to lipid phenotypes with sleep duration as an environmental factor in the UK Biobank. The proposed approach identified six independent associated genetic loci missed by other competing methods.

genomics↗

bioRxiv2024

Genetic diversity of Toscana virus glycoproteins affects the kinetics of virus entry and the infectivity of newly produced virions

Toscana virus (TOSV) is a pathogenic and transmissible Phlebovirus of the Bunyavirales order. Although TOSV is considered one of the leading causes of meningitis and encephalitis in humans during summer in the Mediterranean basin, its biology remains poorly characterized and neglected due to lack of tools to study the virus. To date, two principal genetic lineages (A and B) have been identified among TOSV-isolated strains based on phylogenetic analysis. The impact of TOSV genetic diversity on its biology is still unknown but highly relevant because it may influence the severity of the disease, viral tropism, and vaccine design. To address these questions, a reverse genetic approach based on two TOSV strains belonging to lineage A or B (i.e., TOSV-A and TOSV-B) and displaying different in vitro replicative fitness was used. Our results demonstrate that TOSV-A and TOSV-B have different Gn and Gc glycoproteins sequences which are responsible for the observed differences in terms of replicative fitness. Moreover, our data show that TOSV-A and TOSV-B display different entry kinetics and that newly-produced virions have different infectivity. This comparative approach allowed us to demonstrate that the genetic diversity of TOSV can significantly impact viral properties. This study highlights the need for a better molecular characterisation of the genome of circulating TOSV strains and, more specifically, of the viral Gn and Gc glycoproteins. Indeed, these proteins may strongly modulate viral pathogenicity and disease. Further work in this direction will provide important data to develop preventive strategies against this emerging pathogen taking into account TOSV glycoproteins genetic diversity. Authors SummaryToscana virus (TOSV) is a leading cause of aseptic brain infection in the Mediterranean basin during the summer. Despite the significant burden that TOSV represents to human health, the biology of this pathogen remains poorly understood and neglected. While distinct TOSV genetic lineages have been identified, the relationship between their genetic diversity and pathogenicity is still unclear. This point, however, is critical to understand the disease and design preventive strategies such as vaccines targeting circulating TOSV strains. Here, a reverse genetic approach was used to produce reassortant and chimeric viruses between two TOSV strains (referred to as TOSV-A and TOSV-B) belonging to the two main genetic lineages and displaying differential in vitro replication capacities. Our results show that the viral glycoproteins are key determinants in modulating TOSV replication. In addition, they demonstrate that viral entry and infectious viral particles production differ between TOSV-A and TOSV-B. This study provides the first evidence of differences in replication capacity between two genetically distinct TOSV viruses, and highlights the need for better molecular characterisation of circulating TOSV strains.

microbiology↗

bioRxiv2024

Unraveling genetic load dynamics during biological invasion: insights from two invasive insect species

Many invasive species undergo a significant reduction in genetic diversity, i.e. a genetic bottleneck, in the early stages of invasion. However, this reduction does not necessarily prevent them from achieving considerable ecological success and becoming highly efficient colonizers. Here we investigated the purge hypothesis, which suggests that demographic bottlenecks may facilitate conditions (e.g., increased homozygosity and inbreeding) under which natural selection can purge deleterious mutations, thereby reducing genetic load. We used a transcriptome-based exome capture protocol to identify thousands of SNPs in coding regions of native and invasive populations of two highly successful invasive insect species, the western corn rootworm (Chrysomelidae: Diabrotica virgifera virgifera) and the harlequin ladybird (Coccinelidae: Harmonia axyridis). We categorized and polarized SNPs to investigate changes in genetic load between invasive populations and their sources. Our results differed between species. In D. virgifera virgifera, although there was a general reduction in genetic diversity in invasive populations, including that associated with genetic load, we found no clear evidence for purging of genetic load, except marginally for highly deleterious mutations in one European population. Conversely, in H. axyridis, the reduction in genetic diversity was minimal, and we detected signs of genetic load fixation in invasive populations. These findings provide new insights into the evolution of genetic load during invasions, but do not offer a definitive answer to the purge hypothesis. Future research should include larger genomic datasets and a broader range of invasive species to further elucidate these dynamics.

evolutionary biology↗

bioRxiv2024

The genetic architecture of cortical similarity networks

The genetic architecture of human brain networks is central to understanding the organization and evolution of the cortex, the causal relationships between brain structure and function, and the pathogenesis of heritable neuropsychiatric disorders. However, the current understanding of the genetics of brain networks remains fragmented. Here, we investigated common genetic effects on Morphometric INverse Divergence (MIND), a biologically-validated, heritable, and multimodal MRI metric of inter-areal similarity and connectivity. Using a discovery dataset (N>30,000 adults), we estimated subject-specific MIND networks from the multivariate distributions of four MRI features at each of 23 cortical areas and performed genome-wide association studies (GWAS) at each of the 276 inter-areal edges. These edge-level genetic effects were highly replicated by parallel GWAS of an independent validation dataset (N>18,000 adults). We found that strong genetic correlations between multiple edges were largely reducible to two gradients of genetically-determined cortical similarity, each of which was aligned with geodesic distance from one of the two phylogenetically primitive areas (paleocortex and archicortex) predicted by the dual origin theory of cortical evolution. Genetic MIND gradients were more heritable than comparable gradients derived from GWAS of functional MRI connectivity networks; and the paleocortical trend was genetically correlated with, and causally predictive of, functional connectivity. Finally, we identified multiple global and local genetic correlations between both MIND gradients and nine clinical diagnoses or biomedical traits, indicating that the normative genetic architecture of human brain networks is pleiotropically associated with inherited risk of neuropsychiatric disorders and systemic metabolic and immune traits. These results provide fresh insight into the dual origins of the human cortex and their implications for brain function and health.

neuroscience↗

bioRxiv2025

Caudata macrogenetics: Species range size predicts intraspecific genetic variation in global salamanders

AimGenetic diversity contains valuable information about ecological and evolutionary aspects of species. Intraspecific genetic variation is shaped by species natural history traits and by characteristics of geography and climate within their ranges. Amphibians are of ecological and conservation interest because of their global distribution, deep history, trait diversity, and roles within ecological communities. Here, we studied genetic variation within salamanders to investigate predictors of nucleotide diversity and spatial patterns of genetic differentiation. LocationGlobal. Time PeriodPresent. Major Taxa StudiedSalamanders. MethodsWe repurposed mitochondrial DNA sequences and ecological data from open-access databases for 220 salamander species. We calculated nucleotide diversity ({pi}) and tested for isolation by distance (IBD) and isolation by environment (IBE). We analyzed these three variables with random forest and phylogenetic comparative methods using 28 predictors expected to be associated with genetic variation. ResultsWe recovered 8,108 Cytb sequences with their associated geographic coordinates, of which 7,007 sequences were manually curated by us. Range size, lineage age, and sample size were important predictors of genetic variation. We found higher diversity in regions including the Neotropics and central-eastern Europe. The absence of phylogenetic signal in {pi}, IBD, and IBE suggests that genetic variation is shaped by local ecological and geographical factors rather than by shared ancestry. Main ConclusionsOur finding of range size as an important predictor aligns with theoretical expectations that species with larger ranges tend to harbor more genetic diversity. Furthermore, lineage age being an important predictor is in line with the clade-age hypothesis, in which species with longer divergence times have higher genetic diversity because they have had more time to accumulate genetic variation. Our results underscore the importance of integrating spatial data into macrogenetic studies, providing valuable information for future studies and conservation strategies targeting regions with high or low genetic diversity.

evolutionary biology↗

bioRxiv2025

The Effects of Intraspecies and Interspecies Competition on Genetic Device Construction and Performance

Future genetic devices expressed in microbes need to be tested in complex environments containing multiple organisms to expand their usability. We sought to determine if genetic parts designed for monoculture are predictable when used in co-culture by testing constitutive Anderson promoters driving expression of chromoproteins from a plasmid. In Escherichia coli monoculture a high copy number origin of replication causes stochastic expression regardless of promoter strength, and high Anderson promoter strength leads to selection for inactivating mutations, resulting in inconsistent chromoprotein expression. Medium and low strength Anderson promoters function more predictably in E. coli monoculture but experience an increase in inactivating mutations when grown in co-culture over many generations with Pseudomonas aeruginosa. Expression from native promoters instead of Anderson promoters can lead to stable expression in a complex wastewater culture. Overall, we show intraspecies selection for inactivating mutations due to a competitive growth advantage for E. coli that do not express the genetic device compared to their peers that retain the functional device. We show additional interspecies selection against the functional device when E. coli is co-cultured with another organism. Together, these two selection pressures create a significant barrier to genetic device function in microbial communities that we overcome by utilize a native E. coli promoter. Future strategies for genetic device design in microorganisms that need to function in a complex microbial environment should focus on native promoters and/or strategies that give the microorganism carrying the device a selective or growth advantage. ImportanceFirst generation biotechnology focused on genetic devices designed for use in monoculture conditions. Next generation biotechnology devices will need to function in complex ecosystems with other organisms, so we sought to create conditions where the genetic device retained function when the organism carrying it is in co-culture with other organisms. We discovered that when the genetic device is a significant resource burden on the organism carrying the device mutations will be selected for due to intraspecies and interspecies selection pressures and the device will be rendered non-functional. Therefore, genetic device design for complex ecosystems in next generation biotechnology needs to balance functionality of the genetic device with the need to reduce resource burden on the organism carrying it.

synthetic biology↗

bioRxiv2025

Rapid genetic diversification of Bacteroides thetaiotaomicron in mono-associated mice revealed through deep population-level sequencing

Bacteria often feature short generation times and large populations, thereby allowing them to quickly evolve and adapt to new environments. Although it is known that gut bacteria can evolve on relatively short time scales, the extent of genetic diversification of bacteria in the gut environment remains underexplored. Here, we characterize the genetic diversification of the gut commensal Bacteroides thetaiotaomicron during 28 days of colonization of germ-free mice using deep shotgun sequencing as well as genome analysis of evolved isolates. We detect thousands of genetic polymorphisms as early as three days post inoculation and observe highly dynamic genetic diversity in the distal gut. We identify multiple haplotypes of a phase-variable polysaccharide utilization locus (BT2260 - BT2268) and propose that phase variation may be an important mechanism for diversification and adaptation in the gut. In addition, we find evidence that hybrid two-component system (HTCS) regulators are mutational hotspots. We identify multiple persistent and parallelly evolved genetic polymorphisms in genes, including the TonB-dependent transporter BT0867 - a homolog of BF3581 from the commensal colonization factor (ccf) in B. fragilis. Lastly, we find that the small intestine accumulated approximately 20 times more polymorphisms compared to the large intestine, highlighting overall the importance of studying spatiotemporal distribution of genetic variants. These results underscore the prevalence of rapid genetic diversification of gut bacteria, which may have important implications for adaptation as well as interactions in the microbiome and with the host. ImportanceStudying the within-host evolution of gut commensals is an essential step for understanding the role of microbiome in health and disease. It can provide insights into the mechanisms underlying the development of various gastrointestinal disorders, metabolic conditions, autoimmune diseases, and other health disorders. Additionally, this kind of research can further drive the development of personalized therapies, such as strain-level or gene specific interventions for improving health outcomes. Here, we report extensive genetic variation within days upon colonization of mice with B. thetaiotaomicron and identify genes that accumulate persistent and highly prevalent genetic polymorphisms across a mouse population. We also detect several haplotypes in phase-variable loci. Altogether, our findings underscore the rapid pace of genetic diversification and phase variation upon colonization of the gut environment.

microbiology↗

bioRxiv2025

Predator induced phenotypes are inherited over four generations in genetically identical Daphnia lumholtzi

Teaser TextCan the ghosts of environments past shape organismal phenotypes of future generations? In an experiment with clonal Daphnia lumholtzi, we reveal that predator-induced changes in body shape in one generation can persist across several unexposed generations, even when the predator signal is long gone. Exposing only the first generation to predator cues, we tracked morphological shifts through five generations of genetically identical individuals. We found that these induced plastic phenotypes persisted to the F4 generation before fading in F5. This discovery supports the importance of non-genetic inheritance and underscores the powerful interplay between ancestral and current environments in shaping organismal form and function. Environmental variation can induce phenotypic changes through adaptation of populations and acclimation of individuals. While genetic adaptation creates persistent change within a population via allele frequency shifts, reversible plastic phenotypes can be inherited through non-genetic mechanisms. However, most transgenerational plasticity studies examine generations where direct embryonic or germline exposure to environmental cues cannot be excluded. Empirical evidence for persistence definitively beyond the critical threshold for distinguishing true transgenerational plasticity from in utero exposure remains scarce, particularly for vertebrate predator-induced defenses. We measured phenotypic effects of vertebrate predator exposure in the clonally reproducing water flea, Daphnia lumholtzi, isolating environmental effects from genetic variation. We exposed the F0 generation to fish conditioned media, then measured morphological defenses in definitively unexposed F3, F4, and F5 generations characterizing the temporal dynamics of non-genetic inheritance. Predator-induced morphologies persisted through F4 before receding in F5, demonstrating that non-genetic effects extend well beyond the embryonically exposed F1 and germ cell exposed F2 generations. This provides rare empirical evidence for transgenerational plasticity lasting through F4, without confounding genetic variation. We also examined ontogenetic patterns of somatic and defensive trait development, revealing trait-specific temporal dynamics in transgenerational effect expression and decay. These results highlight how current and ancestral environments interact to determine phenotypic variation across generations and underscores the ecological significance of non-genetic inheritance in natural populations, particularly for understanding population responses to environmental change and predator reintroduction. Characterizing molecular mechanisms underlying transgenerational phenotypic plasticity remains critical for predicting persistence and ecological consequences of non-genetic inheritance.

evolutionary biology↗

bioRxiv2025

Distinct, asynchronous processes underlie cultural and genetic variation in a bird species with a complex song repertoire

Dialects in birdsongs represent population clusters and cultural diversity. Cultural and genetic variation in animals, however, do not always evolve along the same trajectory. Few studies have tested this in a wild songbird with a continuous learning strategy. Songbirds (oscine Passeriformes) with a continual learning window exhibit great song diversity and may show cultural differentiation that outpaces genetic divergence. We investigate cultural and genetic variation in a tropical endemic songbird in a topographically and climatically complex sky-island landscape of the Western Ghats of India. We combine fine-scale acoustic, behavioural, and genetic data: from 90 individuals (10,816 songs), analysed using frequency-temporal parameters and a linguistic method for syntax; a playback experiment with 136 trials to compare behavioural responses to local and non-local songs; and blood samples from 242 individuals (10,638 SNPs) to infer genetic population structure. We find no difference in songs across locations and individuals in the time-frequency domain, but only in syntax. One-third of notes, the smallest vocal units, are widely shared across all individuals in their distribution. Longer note combinations result in greater individual differences within populations, but only form small differences between populations. Geographic distance strongly predicts genetic but not song syntactic differences, and playback experiments show equal responses to local and non-local songs. Thus, strong individual signatures but weak local-level dialects are generated by a shared note repertoire and associated combinatorial syntax. We highlight that cultural transmission may operate at fine social scales, decoupled from genetic structure, which is strongly driven by isolation-by-distance. Significance statementWhether learned behaviours exhibit patterns similar to those of inherited genes remains a long-standing question in evolutionary biology. Birdsong has a strong cultural component paralleling human language, yet most knowledge comes from birds with a narrow learning window. Open-ended learners, who acquire new songs throughout life like humans, are poorly documented in the wild. We studied such a songbird restricted to the tropical cloud montane forests of southern India. Songs appear acoustically similar across populations but differ in how basic units are ordered (syntax), while individuals are more distinct from each other in longer note combinations than populations are. Genetic similarity decreased with geographic distance. Culturally learned traits can thus evolve independently of genetic structure, showing how learning decouples behaviour from geography-driven genetic ancestry.

evolutionary biology↗

bioRxiv2017

Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks

Cauliflower (Brassica oleracea var. botrytis) is an important vegetable crop for human nutrition. We characterized 192 cauliflower accessions from the USDA and IPK genebanks with genotyping by sequencing (GBS). They originated from 26 different countries and represent about 44% of all cauliflower accessions in both genebanks. The analysis of genetic diversity revealed that accessions formed two major groups that represented the two genebanks and were not related to the country of origin. This differentiation was robust with respect to the analysis methods that included principal component analysis, ADMIXTURE and neighbor-joining trees. Genetic diversity was higher in the USDA collection and significant phenotypic differences between the two genebanks were found in three out of six traits investigated. GBS data have a high proportion of missing data, but we observed that the exclusion of single nucleotide polymorphisms (SNPs) with missing data or the imputation of missing SNP alleles produced very similar results. The results indicate that the composition and type of accessions have a strong effect on the structure of genetic diversity of ex situ collections, although regeneration procedures and local adaptation to regeneration conditions may also contribute to a divergence. Fst-based outlier tests of genetic differentiation identified only a small proportion (<1%) of SNPs that are highly differentiated between the two genebanks, which indicates that selection during seed regeneration is not a major cause of differentiation between genebanks. Seed regeneration procedures of both genebanks do not result in different levels of genetic drift and loss of genetic variation. We therefore conclude that the composition and type of accessions mainly influence the level of genetic diversity and explain the strong genetic differentiation between the two ex situ collections. In summary, GBS is a useful method for characterizing genetic diversity in cauliflower genebank material and our results suggest that it may be useful to incorporate routine genotyping into accession management and seed regeneration to monitor the diversity present in ex situ collections and to reduce the loss of genetic diversity during seed regeneration.

plant biology↗