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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2025

Genetic Diversity, Taxonomic Insights and Geographic Distribution of Bubo bubo Subspecies in Iran

The Eurasian Eagle Owl (Bubo bubo) exhibits a complex taxonomic structure with multiple subspecies across its broad geographic range, including southwestern Asia. While much is known about the species distribution in Europe and Asia, the taxonomic status and distribution of B. bubo subspecies in Iran remain poorly understood. This study aims to explore the genetic diversity and taxonomic relationships of B. bubo subspecies in Iran through mitochondrial gene analysis, focusing on nucleotide sequences of the cytochrome b (cytb) gene. A total of 36 samples collected from diverse localities across Iran, representing different ecological regions. Phylogenetic analysis revealed two distinct clades: one comprising western Iranian samples clustering with European (mostly from Germany) samples, and the other consisting of eastern and southern Iranian samples that shared haplotypes with populations from China. Notably, the western Iranian clade exhibited a minimal genetic distance from European populations, while the eastern Iranian clade was genetically similar to Chinese B. bubo subspecies, including B. bubo turkomanus. The genetic diversity indices for the Iranian population were relatively low, with three identified haplotypes and low nucleotide and haplotype diversity. Demographic analyses indicated a potential population expansion for the species, supported by a unimodal mismatch distribution and negative neutrality indices, although these results were not statistically significant for the Iranian population. The findings suggest that two subspecies, B. bubo nikolskii and B. bubo interpositus, are likely present in Iran, aligning with recent taxonomic assessments, but further investigation with additional genetic markers is needed to clarify the deeper evolutionary relationships among these populations. This study contributes new insights into the genetic landscape of B. bubo in Iran and the broader Palearctic region, with implications for conservation and future taxonomic revisions. Simple SummaryThis study examines the genetic diversity, taxonomic relationships, and geographic distribution of Bubo bubo subspecies in Iran, utilizing mitochondrial gene analysis, with a particular focus on the cytochrome b (cytb) gene. The research, based on 36 samples from various regions in Iran, reveals two distinct clades: one aligning with European populations and the other sharing haplotypes with Chinese subspecies. While genetic diversity in Iranian populations was relatively low, the findings highlight the presence of B. bubo nikolskii and B. bubo interpositus subspecies in Iran, emphasizing the importance of further genetic investigations for conservation and taxonomic revisions in the Palearctic region.

zoology↗

bioRxiv2025

Unique genetic bases of repeated life-history divergence associated with high altitude adaptation in Mimulus perennials

Understanding evolutionary repeatability is a central question in biology, as it informs how predictably organisms respond to similar selection pressures. However, the extent to which phenotypic repeatability is recapitulated at the genetic level remains unclear, particularly for quantitative traits. The recurrent evolution of similar phenotypes in high altitude plant populations relative to their low altitude counterparts offers an ideal model for testing genetic repeatability, as these habitats are associated with shifts in complex suites of phenotypes. Here, we investigate the modularity and genetic architecture of life-history trait divergence across four independent transitions to high altitude habitats among closely related perennial taxa in the Mimulus guttatus species complex. High altitude taxa exhibit largely repeated phenotypic evolution in 40 univariate traits and suites of traits form correlated modules that are highly similar across taxa. Nonetheless, the genetic architecture underlying each trait was largely non-repeatable, a pattern consistent for both quantitative and genetically simple traits. Despite a general lack of overall repeatability, individual QTLs with larger effects and those that were associated with multiple traits were more likely to be repeatable than smaller-effect or single-trait associated loci. These findings suggest that evolution may follow distinct genetic pathways while repeatedly converging on functionally integrated trait modules. Additionally, although there may be several genetic routes to the same phenotypic outcomes, aspects of genetic architecture can influence the most likely genetic routes taken. Overall, our results provide insights into adaptation to high altitude environments and also advance our understanding of evolutionary repeatability of complex traits.

evolutionary biology↗

bioRxiv2025

Large scale, low coverage population genomics approach to assess genetic variation and structure across vulnerable Swedish sand lizard populations

Genomics has emerged as a powerful tool in conservation biology, offering valuable insights into the genetic diversity, population connectivity and adaptive potential of threatened species. Here, we apply a large-scale, low-coverage whole genome sequencing approach to the conservation genomics of the Swedish sand lizard (Lacerta agilis). Sand lizards occur in fragmented populations across Sweden, with varying population sizes and degrees of isolation, and face significant threats from habitat degradation and land use change. In this study, we sequenced 139 individuals to investigate genetic diversity, population structure and genetic load. We reveal strong population structure among Swedish sand lizards and identify populations with low genetic diversity and realised high genetic load. Genetic diversity in populations declined with increasing latitude, likely reflecting the historical northward expansion process and the subsequent population fragmentation and isolation. We observe strong population structure and reveal genetic distinctiveness of populations; findings with significant conservation implications. For example, the Sormon population, a relict population in central Sweden, appears genetically distinct from all other populations. Further, the northern-most populations in Dalarna appear relatively small, with high genetic load, and thus may require intensive management via e.g., restored open successional habitat to aid population recovery. Our study adds to the growing field of conservation genomics and demonstrates the value of high-resolution whole genome approaches to the conservation efforts for threatened populations. Finally, our research contributes crucial insights for the conservation management of this vulnerable species in Sweden.

genomics↗

bioRxiv2017

Widespread southern forests during the Last Glacial Maximum, not refugia, explain genetic structure of two eastern North American hickory species

AimPhylogeographic studies of temperate forest taxa often infer complex histories involving population subdivision into distinct refugia during the Last Glacial Maximum (LGM). However, temperate forests may have been broadly distributed in southeastern North America during the LGM. We investigate genome-wide genetic structure in two widespread eastern North America tree species to determine if range expansion from a contiguous area or from genetically isolated refugia better explains the postglacial history of trees and forests from this region.\n\nLocationEastern North America (ENA).\n\nTaxaBitternut hickory (Carya cordiformis (Wangenh.) K.Koch) and shagbark hickory (Carya ovata (Mill.) K.Koch).\n\nMethodsGenetic diversity and differentiation indices were calculated from >1,000 nuclear SNP loci genotyped in ca. 180 individuals per species sampled across ENA. Genetic structure was investigated using principle component analysis and genetic clustering algorithms. As an additional tool for inference, areas of suitable habitat during the LGM were predicted using species distribution models (SDMs).\n\nResultsPopulations across all latitudes showed similar levels of genetic diversity. Most genetic variation was weakly differentiated across ENA, with the exception of an outlier population of Carya ovata in Texas. Genetic structure in each species exhibited an isolation-by-distance pattern. SDMs predicted high LGM habitat suitability over much of the southeastern United States.\n\nMain conclusionsBoth hickory species likely survived the LGM in a large region of continuous habitat and recolonized northern areas in a single expanding front that encountered few migration barriers. More complex scenarios, such as forest refugia, need not be invoked to explain genetic structure. The genetically distinct Texas population of Carya ovata could represent a separate glacial refugium, but other explanations are possible. Relative to that of other temperate forest regions, the phylogeographic history of ENA may have been exceptionally simple, involving a northward range shift but without well defined refugia.

evolutionary biology↗

bioRxiv2018

A guide to using a multiple-matrix animal model to disentangle genetic and nongenetic causes of phenotypic variance

Non-genetic influences on phenotypic traits can affect our interpretation of genetic variance and the evolutionary potential of populations to respond to selection, with consequences for our ability to predict the outcomes of selection. Long-term population surveys and experiments have shown that quantitative genetic estimates are influenced by nongenetic effects, including shared environmental effects, epigenetic effects, and social interactions. Recent developments to the \"animal model\" of quantitative genetics can now allow us to calculate precise individual-based measures of non-genetic phenotypic variance. These models can be applied to a much broader range of contexts and data types than used previously, with the potential to greatly expand our understanding of nongenetic effects on evolutionary potential. Here, we provide the first practical guide for researchers interested in distinguishing between genetic and nongenetic causes of phenotypic variation in the animal model. The methods use matrices describing individual similarity in nongenetic effects, analogous to the additive genetic relatedness matrix. In a simulation of various phenotypic traits, accounting for environmental, epigenetic, or cultural resemblance between individuals reduced estimates of additive genetic variance, changing the interpretation of evolutionary potential. These variances were estimable for both direct and parental nongenetic variances. Our tutorial outlines an easy way to account for these effects in both wild and experimental populations. These models have the potential to add to our understanding of the effects of genetic and nongenetic effects on evolutionary potential. This should be of interest both to those studying heritability, and those who wish to understand nongenetic variance.

evolutionary biology↗

bioRxiv2018

Selection, linkage, and population structure interact to shape genetic variation among threespine stickleback genomes

The outcome of selection on genetic variation depends on the geographic organization of individuals and populations as well as the syntenic organization of loci within the genome. Spatially variable selection between marine and freshwater habitats has had a significant and heterogeneous impact on patterns of genetic variation across the genome of threespine stickleback fish. When marine stickleback invade freshwater habitats, more than a quarter of the genome can respond to divergent selection, even in as little as 50 years. This process largely uses standing genetic variation that can be found ubiquitously at low frequency in marine populations, can be millions of years old, and is likely maintained by significant bidirectional gene flow. Here, we combine population genomic data of marine and freshwater stickleback from Cook Inlet, Alaska, with genetic maps of stickleback fish derived from those same populations to examine how linkage to loci under selection affects genetic variation across the stickleback genome. Divergent selection has had opposing effects on linked genetic variation on chromosomes from marine and freshwater stickleback populations: near loci under selection, marine chromosomes are depauperate of variation while these same regions among freshwater genomes are the most genetically diverse. Forward genetic simulations recapitulate this pattern when different selective environments also differ in population structure. Lastly, dense genetic maps demonstrate that the interaction between selection and population structure may impact large stretches of the stickleback genome. These findings advance our understanding of how the structuring of populations across geography influences the outcomes of selection, and how the recombination landscape broadens the genomic reach of selection.

evolutionary biology↗

bioRxiv2018

Effect of riverscape and exotic introgression on the genetic structure and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

How environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization with O. mykiss and of riverscape and climatic variables on the genetic variation among O. chrysogaster populations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272 O. chrysogaster and O. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six for O. chrysogater and one for aquaculture O. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests that O. chrysogater may require conservation planning given i) exotic introgression from O. mykiss locally threatening O. chrysogater genetic integrity, and ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.

evolutionary biology↗

bioRxiv2018

Whole-Cortex Mapping of Common Genetic Influences on Depression and Social Deficits

BackgroundSocial processes are associated with depression, particularly understanding and responding to others, deficits in which can manifest as callousness/unemotionality (CU). Thus, CU may reflect some of the genetic risk to depression. Further, this vulnerability likely reflects the neurological substrates of depression, presenting biomarkers to capture genetic vulnerability of depression severity. However, heritability varies within brain regions, so a high-resolution genetic perspective is needed.\n\nMethod In a sample of 258 same-sex twin pairs from the Colorado Longitudinal Twin Study (LTS), we developed a toolbox that maps genetic and environmental associations between brain and behavior at high resolution. We used this toolbox to estimate brain areas that are genetically associated with both depressive symptoms and CU. We then overlapped the two maps to generate coordinates that allow for tests of downstream effects of genes influencing our clusters.\n\nResults Genetic variance influencing cortical thickness in the right dorsal lateral prefrontal cortex (DLFPC) sulci and gyri, ventral posterior cingulate cortex (PCC), pre-somatic motor cortex (PreSMA), medial precuneus, left occipital-temporal junction (OTJ), parietal-temporal junction (PTJ), ventral somatosensory cortex (vSMA), and medial and lateral precuneus were genetically associated with both depression and CU. Split-half replication found support for both DLPFC clusters. Meta-analytic term search identified \"theory of mind\", \"inhibit\", and \"pain\" as likely functions. Gene and transcript mapping/enrichment analyses implicated calcium channels.\n\nConclusionsCU reflects genetic vulnerability to depression that likely involves executive and social functioning in a distributed process across the cortex. This approach works to unify neuroimaging, neuroinformatics, and genetics to discover pathways to psychiatric vulnerability.

neuroscience↗

bioRxiv2018

In situ estimation of genetic variation of functional and ecological traits in Quercus petraea and Q. robur

BackgroundPredicting the evolutionary potential of natural tree populations requires the estimation of heritability and genetic correlations among traits on which selection acts, as differences in evolutionary success between species may rely on differences for these genetic parameters. In situ estimates are expected to be more accurate than measures done under controlled conditions which do not reflect the natural environmental variance.\n\nAimsThe aim of the current study was to estimate three genetic parameters (i.e. heritability, evolvability and genetic correlations) in a natural mixed oak stand composed of Quercus petraea and Quercus robur about 100 years old, for 58 traits of ecological and functional relevance (growth, reproduction, phenology, physiology, resilience, structure, morphology and defence).\n\nMethodsFirst we estimated genetic parameters directly in situ using realized genomic relatedness of adult trees and parentage relationships over two generations to estimate the traits additive variance. Secondly, we benefited from existing ex situ experiments (progeny tests and conservation collection) installed with the same populations, thus allowing comparisons of in situ heritability estimates with more traditional methods.\n\nResultsHeritability and evolvability estimates obtained with different methods varied substantially and showed large confidence intervals, however we found that in situ were less precise than ex situ esti-mates, and assessments over two generations (with deeper relatedness) improved estimates of heritability while large sampling sizes are needed for accurate estimations. At the biological level, heritability values varied moderately across different ecological and functional categories of traits, and genetic correlations among traits were conserved over the two species.\n\nConclusionWe identified limits for using realized genomic relatedness in natural stands to estimate the genetic variance, given the overall low variance of genetic relatedness and the rather low sampling sizes of currently used long term genetic plots in forestry. These limits can be overcome if larger sample sizes are considered, or if the approach is extended over the next generation.

evolutionary biology↗

bioRxiv2019

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation

Gene transcription profiles across tissues are largely defined by the activity of regulatory elements, most of which correspond to regions of accessible chromatin. Regulatory element activity is in turn modulated by genetic variation, resulting in variable transcription rates across individuals. The interplay of these factors, however, is poorly understood. Here we characterize expression and chromatin state dynamics across three tissues--liver, lung, and kidney--in 47 strains of the Collaborative Cross (CC) mouse population, examining the regulation of these dynamics by expression quantitative trait loci (eQTL) and chromatin QTL (cQTL). QTL whose allelic effects were consistent across tissues were detected for 1,101 genes and 133 chromatin regions. Also detected were eQTL and cQTL whose allelic effects differed across tissues, including local-eQTL for Pik3c2g detected in all three tissues but with distinct allelic effects. Leveraging overlapping measurements of gene expression and chromatin accessibility on the same mice from multiple tissues, we used mediation analysis to identify chromatin and gene expression intermediates of eQTL effects. Based on QTL and mediation analyses over multiple tissues, we propose a causal model for the distal genetic regulation of Akr1e1, a gene involved in glycogen metabolism, through the zinc finger transcription factor Zfp985 and chromatin intermediates. This analysis demonstrates the complexity of transcriptional and chromatin dynamics and their regulation over multiple tissues, as well as the value of the CC and related genetic resource populations for identifying specific regulatory mechanisms within cells and tissues.\n\nAuthor summaryGenetic variation can drive alterations in gene expression levels and chromatin accessibility, the latter of which defines gene regulatory elements genome-wide. The same genetic variants may associate with both molecular events, and these may be connected within the same causal path: a variant that reduces promoter region chromatin accessibility, potentially by affecting transcription factor binding, may lead to reduced expression of that gene. Moreover, these causal regulatory paths can differ between tissues depending on functions and cellular activity specific to each tissue. We identify cross-tissue and tissue-selective genetic regulators of gene expression and chromatin accessibility in liver, lung, and kidney tissues using a panel of genetically diverse inbred mouse strains. Further, we identify a number of candidate causal mediators of the genetic regulation of gene expression, including a zinc finger protein that helps silence the Akr1e1 gene. Our analyses are consistent with chromatin accessibility playing a role in the regulation of transcription. Our study demonstrates the power of genetically diverse, multi-parental mouse populations, such as the Collaborative Cross, for large-scale studies of genetic drivers of gene regulation that underlie complex phenotypes, as well as identifying causal intermediates that drive variable activity of specific genes and pathways.

genomics↗

bioRxiv2019

Pleiotropy or linkage? Their relative contributions to the genetic correlation of quantitative traits and detection by multi-trait GWA studies

Genetic correlations between traits may cause correlated responses to selection. Previous models described the conditions under which genetic correlations are expected to be maintained. Selection, mutation and migration are all proposed to affect genetic correlations, regardless of whether the underlying genetic architecture consists of pleiotropic or tightly-linked loci affecting the traits. Here, we investigate the conditions under which pleiotropy and linkage have differential effects on the genetic correlations between traits by explicitly modeling multiple genetic architectures to look at the effects of selection strength, degree of correlational selection, mutation rate, mutational variance, recombination rate, and migration rate. We show that at mutation-selection(-migration) balance, mutation rates differentially affect the equilibrium levels of genetic correlation when architectures are composed of pairs of physically linked loci compared to architectures of pleiotropic loci. Even when there is perfect linkage (no recombination within pairs of linked loci), a lower genetic correlation is maintained than with pleiotropy, with a lower mutation rate leading to a larger decrease. These results imply that the detection of causal loci in multi-trait association studies will be affected by the type of underlying architectures, whereby pleiotropic variants are more likely to be underlying multiple detected associations. We also confirm that tighter linkage between non-pleiotropic causal loci maintains higher genetic correlations at the traits and leads to a greater proportion of false positives in association analyses.

evolutionary biology↗

bioRxiv2019

The Evolution of Fluoroquinolone-Resistance in Mycobacterium tuberculosis is Modulated by the Genetic Background

Fluoroquinolones (FQ) form the backbone in experimental treatment regimens against drug-susceptible tuberculosis. However, little is known on whether the genetic variation present in natural populations of Mycobacterium tuberculosis (Mtb) affects the evolution of FQ-resistance (FQ-R). To investigate this question, we used a set of Mtb strains that included nine genetically distinct drug-susceptible clinical isolates, and measured their frequency of resistance to the FQ ofloxacin (OFX) in vitro. We found that the Mtb genetic background led to differences in the frequency of OFX-resistance (OFX-R) that spanned two orders of magnitude and substantially modulated the observed mutational profiles for OFX-R. Further in vitro assays showed that the genetic background also influenced the minimum inhibitory concentration and the fitness effect conferred by a given OFX-R mutation. To test the clinical relevance of our in vitro work, we surveyed the mutational profile for FQ-R in publicly available genomic sequences from clinical Mtb isolates, and found substantial Mtb lineage-dependent variability. Comparison of the clinical and the in vitro mutational profiles for FQ-R showed that 45% and 19% of the variability in the clinical frequency of FQ-R gyrA mutations in Lineage 2 and Lineage 4 strains, respectively, can be attributed to how Mtb evolves FQ-R in vitro. As the Mtb genetic background strongly influenced the evolution of FQ-R in vitro, we conclude that the genetic background of Mtb also impacts the evolution of FQ-R in the clinic.\n\nSignificanceNewer generations of fluoroquinolones form the backbone in many experimental treatment regimens against M. tuberculosis (Mtb). While the genetic variation in natural populations of Mtb can influence resistance evolution to multiple different antibiotics, it is unclear whether it modulates fluoroquinolone-resistance evolution as well. Using a combination of in vitro assays coupled with genomic analysis of clinical isolates, we provide the first evidence illustrating the Mtb genetic backgrounds substantial role in fluoroquinolone-resistance evolution, and highlight the importance of bacterial genetics when studying the prevalence of fluoroquinolone-resistance in Mtb. Our work may provide insights into how to maximize the timespan in which fluoroquinolones remain effective in clinical settings, whether as part of current standardized regimens, or in new regimens against Mtb.

microbiology↗

bioRxiv2019

High genetic diversity can contribute to extinction in small populations

Human-driven habitat fragmentation and loss have led to a proliferation of small and isolated plant and animal populations with high risk of extinction. One of the main threats to extinction in these populations is inbreeding depression, which is primarily caused by the exposure of recessive deleterious mutations as homozygous by inbreeding. The typical approach for managing these populations is to maintain high genetic diversity, often by translocating individuals from large populations to initiate a genetic rescue. However, the limitations of this approach have recently been highlighted by the demise of the gray wolf population on Isle Royale, which was driven to the brink of extinction soon after the arrival of a migrant from the large mainland wolf population. Here, we use a novel population genetic simulation framework to investigate the role of genetic diversity, deleterious variation, and demographic history in mediating extinction risk due to inbreeding depression in small populations. We show that, under realistic models of dominance, large populations harbor high levels of recessive strongly deleterious variation due to these mutations being hidden from selection in the heterozygous state. As a result, when large populations contract, they experience a substantially elevated risk of extinction after these strongly deleterious mutations are exposed by inbreeding. Moreover, we demonstrate that although translocating individuals to small populations is broadly effective as a means to reduce extinction risk, using small or moderate-sized source populations rather than large source populations can greatly increase the effectiveness of genetic rescue due to greater purging in these smaller populations. Our findings challenge the traditional conservation paradigm that focuses on maximizing genetic diversity to reduce extinction risk in favor of a view that emphasizes minimizing strongly deleterious variation. These insights have important implications for managing small and isolated populations in the increasingly fragmented landscape of the Anthropocene. Impact SummaryNumerous threats to extinction exist for small populations, including the detrimental effects of inbreeding. Although much of the focus in reducing these harmful effects in small populations has been on maintaining high genetic diversity, here we use simulations to demonstrate that emphasis should instead be placed on minimizing strongly deleterious variation. More specifically, we show that historically-large populations with high levels of genetic diversity also harbor elevated levels of recessive strongly deleterious mutations hidden in the heterozygous state. Thus, when these populations contract, inbreeding can expose these strongly deleterious mutations as homozygous and lead to severe inbreeding depression and rapid extinction. Moreover, we demonstrate that, although translocating individuals to these small populations to perform a genetic rescue is broadly beneficial, the effectiveness of this strategy can be greatly increased by targeting historically-smaller source populations where recessive strongly deleterious mutations have been purged. These results challenge long-standing views on how to best conserve small and isolated populations facing the threat of inbreeding depression, and have immediate implications for preserving biodiversity in the increasingly fragmented landscape of the Anthropocene.

evolutionary biology↗

bioRxiv2019

Demography, genetic, and extinction process in a spatially structured population of lekking bird

Understanding the mechanisms underlying biological extinctions is a critical challenge for conservation biologists. Both deterministic (e.g. habitat loss, fragmentation) and stochastic (i.e. demographic stochasticity, Allee effect) demographic processes are involved in population decline. Simultaneously, a decrease of population size has far-reaching consequences for genetics of populations by increasing the risk of inbreeding and the effects of genetic drift, which together inevitably results in a loss of genetic diversity and a reduced effective population size (Ne). These genetic factors may retroactively affect vital rates (a phenomenon coined inbreeding depression), and therefore reduce population growth and accelerate the extinction process of small populations. To date, few studies have simultaneously examined the demographic and genetic mechanisms driving the extinction of wild populations, and have most of the time neglected the spatial structure of populations. In this study, we examined demographic and genetic factors involved in the extinction process of a spatially structured population of a lekking bird, the western capercaillie (Tetrao urogallus). To address this issue, we collected capture-recapture and genetic data over a 6-years period in Vosges mountains, France. Our study showed that the population of T. urogallus experienced a severe decline between 2010 and 2015. We did not detect any Allee effect on survival and recruitment. By contrast, individuals of both sexes dispersed to avoid small leks, suggesting a behavioral response to a mate finding Allee effect. In parallel to this demographic decline, the population showed a low genetic diversity and high inbreeding. In addition, the effective population sizes at both lek and population levels was low. Despite this, we did not detected evidence of inbreeding depression: neither survival nor recruitment were affected by individual inbreeding level. Our study underlines the benefit from combining demographic and genetic approaches to investigate processes that are involved in biological extinctions.

ecology↗

bioRxiv2019

Somatic genetic drift and multi-level selection in modular species

Cells in multicellular organisms are genetically heterogeneous owing to somatic mutations. The accumulation of somatic genetic variation in species undergoing asexual (or clonal) reproduction (termed modular species) may lead to phenotypic heterogeneity among modules. However, abundance and dynamics of somatic genetic variation under clonal growth, a widespread life history in nature, remain poorly understood. Here we show that branching events in a seagrass clone or genet leads to population bottlenecks at the cellular level and hence the evolution of genetically differentiated modules. Studying inter-module somatic genetic variation, we uncovered thousands of SNPs that segregated among modules. The strength of purifying selection on mosaic genetic variation was greater at the intra-module comparing with the inter-module level. Our study provides evidence for the operation of selection at multiple levels, of cell population and modules. Somatic genetic drift leads to the emergence of genetically unique modules; hence, modules in long-lived clonal species constitute an appropriate elementary level of selection and individuality.

evolutionary biology↗

bioRxiv2019

Genetic diversity and population structure of the endangered endemic species Paeonia decomposita from China and implications for its conservation

Paeonia decomposita, endemic to China, has important ornamental, medicinal and economic value and is regarded as a threatened endangered plant. The genetic diversity and structure have seldom been described. A conservation management plan is not currently available. In present study, 16 pairs of SSR primers were used to evaluate genetic diversity and population structure. A total of 122 alleles were obtained with a mean of 7.625 alleles per locus. The expected heterozygosity (He) varied from 0.043 to 0.901 (mean 0.492). Moderate genetic diversity (He=0.405) among populations were revealed, with Danba identified as the center of genetic diversity. Mantel tests revealed a significant positive correlation between geographic and genetic distance among populations (r=0.592, P=0.0001), demonstrating consistency with the isolation by distance model. Analysis of molecular variance (AMOVA) results indicated that the principal genetic variation existed within populations (73.48%) rather than among populations (26.52%). Bayesian structure analysis and principal coordinate analysis (PCoA) supported classification of the populations into three clusters. Based on the level of observed genetic diversity, three management unints were proposed as conservation measures. The results will be beneficial for the conservation and exploitation of the species, providing a theoretical basis for further research on its evolution and phylogeography. HightlightsO_LIGenetic diversity among populations was moderate in Paeonia decomposita C_LIO_LIThere is significant positive correlation between geographic and genetic distance among populations, consistent with the isolation by distance model C_LIO_LIPrincipal genetic variation existed within populations rather than among populations. C_LIO_LIThe populations divided into three clusters. C_LIO_LIThree management unints were proposed as conservation measures. C_LI

plant biology↗

bioRxiv2019

Genetic profiling of 2,683 Vietnamese genomes from non-invasive prenatal testing data

The under-representation of several ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in many populations. Cost and technology limitations remain the challenges in performing large-scale genome sequencing projects in many developing countries, including Vietnam. As one of the most rapidly adopted genetic tests, non-invasive prenatal testing (NIPT) data offers an alternative untapped resource for genetic studies. Here we performed a large-scale genomic analysis of 2,683 pregnant Vietnamese women using their NIPT data and identified a comprehensive set of 8,054,515 single-nucleotide polymorphisms, among which 8.2% were new to the Vietnamese population. Our study also revealed 24,487 disease-associated genetic variants and their allele frequency distribution, especially 5 pathogenic variants for prevalent genetic disorders in Vietnam. We also observed major discrepancies in the allele frequency distribution of disease-associated genetic variants between the Vietnamese and other populations, thus highlighting a need for genome-wide association studies dedicated to the Vietnamese population. The resulted database of Vietnamese genetic variants, their allele frequency distribution, and their associated diseases presents a valuable resource for future genetic studies.

genomics↗

bioRxiv2026

Post-transcriptional control by RNA-binding proteins links local synaptic translation to schizophrenia genetic risk

BackgroundSynaptic function is increasingly recognized as a core property of genes implicated in psychiatric disorders. Defining the specific synaptic molecular systems underlying genetic risk is critical step toward therapeutic advances. Synaptic processes rely on rapid protein production driven by local translation of mRNA in context-specific synapses. Synaptic mRNA metabolism, transport and local translation is regulated by RNA-binding proteins (RBPs). Here, we hypothesized that genetic risk converges on localised transcripts with synaptic function and aimed to identify RBP regulatory systems that capture this shared schizophrenia genetic risk. MethodsWe use recent human and mouse bulk and single-synapse transcriptomic and proteomic datasets to test for enrichment of schizophrenia genetic risk among mRNAs stratified by localization and synaptic function employing gene set association (MAGMA) and heritability enrichment (S-LDSC) analyses. Prioritized transcripts were further analyzed for RBP control through motif enrichment analysis (Transite) of the 3UTRs of these transcripts. Candidate RBPs were then evaluated based on the strength of genetic association among their predicted binding targets. ResultsWe demonstrate that genes encoding localised mRNAs with synaptic function show significantly greater genetic association than other synaptic genes. We identified a subset of RBPs, RBFOX1/2/3, CELF4, HNRNPR, and nELAVL, whose motifs are enriched in localised synaptic mRNAs and whose targets are enriched for schizophrenia risk variants. These RBPs are prioritized as candidate regulatory systems through which genetic risk may converge on the transport, splicing and translation of localised transcripts with synaptic function. ConclusionsOur results highlight potential regulatory systems through which genetic variation influences synaptic mechanisms and provide a scalable framework for refining the link between genetic association and post-transcriptional regulation in neuropsychiatric disorders.

neuroscience↗