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bioRxiv2024

When does sexual selection through mate choice deplete versus exaggerate genetic variation: is there a lek paradox?

The evolution of female preferences for male display traits relies on females receiving indirect benefits from their mate. This requires substantial genetic variation in display traits or male quality. Nevertheless, sexual selection through mate choice has been assumed to deplete this genetic variation, ultimately diminishing strong preferences. However, sexual traits often have higher genetic variation than non-sexual traits. This contradiction, and, relatedly, how costly preferences and display traits are maintained, is called the "lek paradox". Using infinitesimal models, we show that sexual selection through mate choice allows variation in male display traits and female preferences to mutually exaggerate each other, in a process analogous to runaway sexual selection but in terms of genetic variation. Therefore, contrary to prior suppositions, sexual selection may increase equilibrium genetic variance in display traits and preferences over that under random mating, provided that the variance of female preferences relative to male traits during mate choice is not too small and preferences are not too weak. Notably, even if equilibrium preference variation is substantially smaller than trait variation, trait variation can still increase over that under random mating, provided selection on the trait compared to the preference is sufficiently strong. Furthermore, when trait variation does decrease, this reduction is generally slight. It is under situations such as lekking, where females can simultaneously choose from many males so that mate discrimination is effectively strong and fitness costs of choice weak, that sexual selection through mate choice may be most powerful in exaggerating genetic variance in male displays. Significance statementThe "lek paradox"--the dissonance between a hypothesized loss of variation in sexual display traits due to mate choice, leading to the subsequent cessation of sexual selection, and evidence of high variation in such traits in nature, accompanied by the long-term persistence of sexual selection--is an enduring mystery of the sexual selection literature. We clarify and quantify multiple pathways by which sexual selection via mate preferences alters genetic variance in both display traits and female preferences. Using mathematical models, we show the lek paradox is built upon a false premise. We find a wide range of conditions under which sexual selection increases or minimally reduces variation in display traits, allowing the maintenance of substantial variance in traits and preferences.

evolutionary biology↗

bioRxiv2024

Evolution of genetic variance and its consequences oneco-evolutionary response in complex mutualistic networks

Rising temperatures threaten biodiversity and ecosystem resilience by disrupting phenological synchrony in plant-pollinator networks. These interactions, essential for ecosystem functioning, are sensitive to temperature shifts. We model species eco-evolutionary responses to an abrupt temperature increase, comparing evolution in mean trait alone versus evolution involving both the mean and genetic variance. We show that networks where species evolve in both their mean phenotype and genetic variance exhibit increased resilience to temperature shifts. Hyper-generalist species, engaged in extensive mutualistic interactions, accumulate greater genetic variance, thereby facilitating faster evolutionary rescue under strong selective pressures. Specialists also benefit by interacting with these hyper-generalists, which stabilize adaptation to new temperatures. We observe emergence in opposing selection pressures in complex networks that promote increases in genetic variance ("evolvability"), reducing trait lag, enabling faster adaptation, and increasing survival. Our findings highlight the role of evolving genetic variance and network architecture in mitigating plant-pollinator phenotypic mismatches under rising environmental temperatures. This study provides insights into the adaptive capacity of mutualistic networks, highlighting dynamic genetic variance changes as key to resilience amid accelerating climate warming. Our study highlights the importance of feedbacks between network topology and genetic architecture for conservation under climate change.

evolutionary biology↗

bioRxiv2025

Genetic control of the leaf ionome in pearl millet and correlation with root and agromorphological traits

Pearl millet (Pennisetum glaucum) thrives in arid and nutrient-poor environments, establishing its role as a crucial cereal crop for food security in sub-Saharan Africa. Despite its remarkable adaptability, its yields remain below genetic potential, primarily due to limited water and nutrient availability. In this study, we conducted ionomic profiling and genome-wide association studies (GWAS) in field conditions across two growing seasons to unravel the genetic basis of nutrient acquisition in pearl millet. Soil ion content analyses revealed significant differences in nutrient distribution between field sites, while certain ions, such as phosphorus (P) and zinc (Zn), consistently displayed stratified accumulation patterns across years, suggesting stable depth-dependent trends. Evaluation of a genetically diverse panel of inbred lines revealed substantial variation in leaf ion concentrations, with high heritability estimates. Correlations between leaf ion content and root anatomical or agromorphological traits highlighted the intricate interplay between genetic and environmental factors shaping leaf ion accumulation. These analyses also uncovered potential trade-offs in nutrient acquisition strategies. GWAS identified genomic regions associated with leaf ion concentrations, and the integration of genetic and gene expression data facilitated the identification of candidate genes implicated in ion transport and homeostasis. Our findings provide valuable insights into the genetic regulation of nutrient acquisition in pearl millet, offering potential targets for breeding nutrient-efficient and climate-resilient varieties. This study underscores the importance of integrating genetic, physiological, and root architectural traits to enhance agricultural productivity and sustainability in resource-constrained environments.

plant biology↗

bioRxiv2025

Encoded and non-genetic alternative protein variants expand human functional proteome

Each stage of the Central Dogma contributes to proteome diversity through mechanisms such as heterozygosity, somatic mutations, transcriptional errors, and translational errors. As a result, a diverse array of protein variants can coexist within a single proteome, such as that of humans. However, until now, methods to detect, quantify, and evaluate the functional consequences of these variants have been lacking. Here we examined a large-scale proteogenomic dataset from 29 healthy human tissues and uncovered 13,910 confidently localized variants representing 7,215 unique single amino acid substitutions co-existing alongside their corresponding reference proteoforms. We found that the abundance of both genetic (SNPs, somatic mutations) and mistranslated protein variants mirrors their allele frequencies in the human population. Moreover, we show that non-genetic substitutions may provide a distinct route for exploring protein sequence space, circumventing the mutational constraints imposed by the genetic code. In addition, we provide experimental validation of non-genetic substitution on selected purified proteins. We demonstrate specific and recurring non-genetic variation patterns upon amino acid starvation in proteome-wide analyses of cancer-derived cell lines and identify hundreds of substituted non-genetic proteoforms that recur consistently in multiple healthy individuals or map to annotated protein functional sites. We propose that these substitutions constitute a novel class of functional protein phenotypic variants. Collectively, our findings indicate that non-genetic amino acid substitutions in human proteins provide an abundant source to expanding the functional proteome.

molecular biology↗

bioRxiv2025

Chlamydomonas chloroplast genes tolerate compression of the genetic code to just 51 codons

Genome scale engineering has enabled codon compression of the universal genetic code of up to three codons in E. coli, providing the means for genetic code expansion. To go much beyond this number, smaller and simpler genetic systems are needed to avoid significant technical challenges. Chloroplast genomes offer multiple advantages for codon compression and reassignment. Here we report a recoding scheme for the Chlamydomonas reinhardtii chloroplast genome, in which two stop codons and one or more of the codons for arginine, glycine, isoleucine, leucine and serine, all of which have two cognate tRNAs, are absent, compressing the genetic code to 51 codons. Firstly, several recoding strategies were tested on the essential rpoA gene, encoding a subunit of the chloroplast RNA polymerase. A defined compression scheme, which relied on swapping the target codons with the permitted frequent codons, could replace the native protein coding sequence without affecting chloroplast protein expression levels or the strain fitness. The same strategy was successfully used for codon compression of ycf1, encoding a subunit of the chloroplast translocon, psaA and psbA, intron-containing highly expressed genes encoding reaction centres subunits of both photosystems, and an 8.5 kb operon encoding essential and non-essential genes. Finally, we tested degeneracy of the 51-codon genetic code by exploring the combinatorial design for the large subunit of RuBisCO, relying on restoration of photosynthesis in an rbcL mutant strain. More than 70 functional sequences with diverse codon adaptation indices were recovered. In all codon-compressed genes there was no observable penalty on photosynthetic growth. Significance StatementWe demonstrate the use of a chloroplast genome as a synthetic biology platform to test modifications of the universal genetic code. Elimination of 13 of the 64 possible triplet codes (codons) was possible for several essential and/or highly expressed genes without affecting chloroplast function. The technology is mature, paving the way for codon compression of the entire genome and thus enabling further radical rearrangement or expansion of the genetic code.

synthetic biology↗

bioRxiv2025

Recent divergence and microgeographic genetic structure in an endangered Australian songbird: the southern black-throated finch

Anthropogenic habitat loss and climate change threaten global biodiversity. Effective conservation management requires a detailed understanding of geographic structure, genetic diversity, and demography of threatened species. The black-throated finch, Poephila cincta, is an Australian songbird with two subspecies: atropygialis and cincta. The southern subspecies, cincta, has experienced an [~]80% range contraction over the last century and is listed as endangered but genetic surveys of it are incomplete. Here, we use a combination of reduced representation and whole genome sequencing to examine genetic differentiation, spatial genetic structure, and demographic history in both forms of this species. We find that atropygialis and cincta are genetically distinct despite a history of divergence with gene flow and geographically isolated by a biogeographic barrier known as the Einasleigh Uplands. Since they last shared a common ancestor [~]400,000 years ago, the two subspecies have experienced distinct demographic trajectories: population expansion in atropygialis and population decline in cincta. We find that the two remnant population centers of cincta, from the Galilee Basin and the Townsville Coastal Plain, each represent genetically distinct lineages that last shared appreciable levels of gene flow [~]4,000 years ago. Moreover, we report striking microgeographic genetic structure from the Townsville Coastal Plain between populations <20 km apart associated with barriers to dispersal caused by anthropogenic habitat modification over the last 50 years: namely the construction of the Ross River Dam. Our findings highlight the urgent need for a conservation approach that prioritizes habitat restoration to re-establish population connectivity in the endangered southern black-throated finch.

evolutionary biology↗

bioRxiv2025

Increased clonality, decreased allele diversity and high genetic structure in tetraploid sea anemone Aulactinia stella populations from North Pacific to Atlantic across the Arctic Ocean

Reproductive mode is a key factor shaping genetic diversity, evolutionary potential, and the processes of dispersal and colonization. Clonality is particularly common in harsh environments and at the margins of species ranges, where it supports persistence, enables rapid growth, and promotes the maintenance of locally adapted genotypes. In the rapidly changing Arctic, increasing ecological connectivity is eroding historical barriers for sessile species. Evaluating genetic diversity in this context, before global change further alters Arctic ocean, is essential for understanding evolutionary dynamics during range expansion and for informing conservation strategies. Aulactinia stella is a circumpolar sea anemone with physiological characteristics in laboratory conditions suggesting a potential for clonal reproduction. In this study, we investigated its reproductive modes in natural populations across the Arctic ocean, from the northern Pacific to the Atlantic, and examined how genetic diversity is structured between adults and juveniles at five sampled sites. Across all study sites, we observed only females or individuals lacking gonads, with the exception of Kamchatka, where males were also present. Genetic indices and changes in genotype frequencies between adults and juveniles confirmed that this species reproduces partially by parthenogenesis. Populations on the Atlantic side were highly clonal with clonal rates (c) estimated at 80-99%, whereas populations on the Pacific side reproduced more sexually (c around 50%). Allelic diversity was twice as high in Kamchatka and Kuril populations, suggesting North Pacific coasts being the main last glacial refugia of A. stella. We found a stepping-stone pattern of genetic structure from Kamchatka to Atlantic populations, consistent with contemporary ocean currents and melted summer sea ice. Only a subset of the juvenile genetic diversity, mostly of local origin, was found in the established adults, while juveniles exhibited lower levels of genetic differentiation across the Arctic Ocean. Our findings underscore the need for further ecological and behavioral investigations to elucidate the mechanisms allowing the current possibilities of dispersal of this species across the Arctic Ocean. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/650399v4_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@b395e6org.highwire.dtl.DTLVardef@364804org.highwire.dtl.DTLVardef@1b22eeeorg.highwire.dtl.DTLVardef@1272ae6_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract (photo: Ekaterina Bocharova)

evolutionary biology↗

bioRxiv2025

Differing drivers of range-wide genetic diversity across previously glaciated Northern hemisphere landscapes

O_LIThe latitudinal gradient (LG) hypothesis predicts a poleward decrease of genetic diversity. Similarly, the central-marginal hypothesis (CMH) predicts higher genetic diversity in range centres than margins. We examined these patterns in Europe (EU), North America (NA) and East Asia (EA), which experienced contrasting patterns of landscape fragmentation. C_LIO_LIWe compiled genetic variation data for 445 plant species and 8,530 populations. We calculated ecological metrics comprising distance to the range margin and native climatic niche margin, distance to refugia, latitude and altitude. We applied Bayesian inference to evaluate the relationships between genetic variation and ecological metrics. C_LIO_LIWe found universal support for the CMH, with populations at the centres of species ranges and/or native climatic niches exhibiting higher genetic diversity than those at the margins and stronger patterns in woody versus herbaceous plants. Evidence for a LG in diversity was less consistent with latitude: negatively correlated with genetic diversity in EU, positively correlated in EA, and no correlation in NA. C_LIO_LIOur analysis supports the view that the LG is largely driven by latitudinal trends in glaciation, particularly in EU, but highlights that glaciation patterns and their resulting impacts on landscape genetic diversity were more heterogeneous in NA and EA. C_LI

evolutionary biology↗

bioRxiv2025

Genetic Gains from Sixty Years of Spring Wheat Breeding in the Northern Plains of the US

Evaluating genetic gains over time is essential for assessing the success of breeding programs and refining strategies for ongoing improvement. Hard red spring (HRS) wheat is an important wheat class in the US and is primarily grown in the Northern Great Plains. Despite a long history of breeding efforts in this region, long-term quantification of genetic gains for key traits has remained limited. This study analyzes over sixty years of data from the USDA-coordinated Hard Red Spring Wheat Uniform Regional Nursery (HRSWURN) to evaluate genetic advancements in agronomic traits across multiple phases. A significant positive genetic gain of 0.61% per annum was observed for grain yield in HRS wheat released in the Northern US region, which is lower than the expected gains needed to meet future wheat demand. The change was 0.07% for test weight, -0.04% for days to heading, and -0.16% for plant height. Notably, sustained yield improvements have not affected grain protein levels since they were first measured in 1995, indicating that ongoing selection has effectively balanced grain yield and protein despite their negative correlation (r = -0.31). Assessment of genetic gains over 20-year phases suggested slowing rates of genetic gains for grain yield but did not indicate any plateaus. The realized genetic gains were generally higher for individual breeding programs when breeding for target environments, with the public breeding program in Minnesota observing gains of approximately 1% per annum. These findings highlight the significant impact of long-term breeding efforts and offer valuable insights for refining future breeding strategies.

plant biology↗

bioRxiv2025

The genetic architecture of quantitative variation in the self-incompatibility response within Phlox drummondii (Polemoniaceae)

Flowering plants display extensive variation in selfing rate, a trait with significant ecological and evolutionary consequences. Many species use genetic mechanisms to recognize and reject self-pollen (termed self-incompatibility or SI), and the loss of SI is one of the most common evolutionary transitions among flowering plants. Despite the ubiquity of transitions to self-compatibility (SC), little is known about the genetic architecture through which SC evolves. Specifically, it is important to determine if SC has a polygenic or simple genetic basis and if variation in compatibility localizes to the genomic locus causing self-pollen recognition (the "S-locus"). Phlox drummondii (Polemoniaceae) has been a model system for exploring mating system evolution and expresses extensive range-wide variation in the SI response. Here we investigate the genetic architecture of SC variants segregating within this otherwise SI species. Using multiple independent crosses, we uncover numerous QTLs associated with intraspecific variation in SI, consistent with a polygenic genetic architecture. While some QTLs overlap across mapping experiments, other QTLs are unique, suggesting that multiple genetic routes to SC exist. Through these crossing experiments, we demonstrate that P. drummondii has a sporophytic SI system, suggesting that an independent evolution of SI occurred in the lineage containing Phlox. We map this novel S-locus and find that the genomic region containing the S-locus is associated with intraspecific variation in SI in one of the three mapping populations. Although further work is necessary to clarify the conditions under which quantitative variation in SI represents a transitional pathway to complete SC, our study reveals the underlying genetic architecture upon which selection could act to drive this frequent and evolutionarily significant transition.

plant biology↗

bioRxiv2025

Genetic modulation of immune gene co-expression in the aged mouse hippocampus by the Apbb1ip locus

Ageing is a major risk factor for many neurodegenerative diseases, and the hippocampus is particularly vulnerable to the effects of ageing. To define the transcriptomic changes related to ageing and the impact of genetic variation, we analysed hippocampal gene expression data generated from a genetically diverse panel of inbred mouse strains belonging to the BXD Family. We applied a combination of differential expression, differential correlation, and weighted gene co-expression network analyses, followed by genetic mapping to delineate age-associated transcriptomic patterns and genetic modulators. This study revealed an upregulation in immune response and microglial genes. We identified a key age-associated co-expression module enriched in immune related genes, and quantitative trait locus mapping of this module uncovered a genetic regulatory locus in which Apbb1ip was the primary candidate gene. Additionally, gene level differential correlation analysis identified a substantial restructuring of the hippocampal transcriptome during ageing. Notably, Ywhab, an important signalling chaperone displayed altered gene expression correlations with >70 genes, between young and aged mice. These results provide novel insights into transcriptional dynamics of hippocampal ageing and identified the immune gene Apbb1ip as a potential modulator of immune response and microglial gene upregulation with implications for neurodegenerative disease pathogenesis. HighlightsO_LIComplementary gene expression analyses indicated an upregulation of immune responses in the ageing hippocampus of a genetically diverse mouse cohort, likely driven by microglia subtypes. C_LIO_LIA systems genetics approach revealed the Apbb1ip locus as a modulator of immune gene co-expression, highlighting a novel candidate regulator of age-associated neuroimmune dynamics. C_LIO_LISignalling chaperone Ywhab gene expression was highly differentially correlated with other transcripts during ageing which may underlie widespread age-associated molecular perturbations in the hippocampus. C_LI

bioinformatics↗

bioRxiv2025

Genetic affinities between an ancient Greek colony and its metropolis: the case of Amvrakia in western Greece

BackgroundDuring the Ancient Greek colonization, Corinth established a stable network of economic and political ties, by founding colonies connecting southern Greece with the mainland of Epirus and reaching as far as the east Adriatic coast. Amvrakia, one of the main Corinthian colonies founded during the 7th century BCE, was characterized by its strong dependence on its metropolis. Here, we aim to investigate the genetic relationships between the Corinthian metropolis and the Amvrakia colony, the contribution of the local population to the founding genetic pool, as well as the demography of Amvrakia in subsequent periods. ResultsDuring its foundation in the Archaic period, Amvrakia appears to have been shaped by genetic influences from at least two different sources. The first source migrated from the Corinth territory, represented by the Archaic Tenea population and is supported via an Identity By Descent (IBD) analysis. The second source shows a direct ancestry from Late Bronze Age (LBA) / Iron Age Greece, including a local LBA population represented by the Ammotopos site located in close proximity to Amvrakia, as shown by a plethora of independent population genomics analyses. During the subsequent Classical and Hellenistic periods, the population of Amvrakia appears to have slightly differentiated, yet evidence of genetic continuity over time is observed. ConclusionsThe migration of Corinthians to Amvrakia contributed to the initial genetic pool of the colony along with the local genetic pool, indicating that the Corinthian colonization included both genetic and cultural transmission between the metropolis and its colony.

evolutionary biology↗

bioRxiv2025

First insight into genetic diversity of two sympatric marten species between the Alps and Adriatic islands

Closely related species occupying the same geographical area may exhibit markedly different genetic patterns due to differences in evolutionary history, ecology and behaviour. In this study, a landscape genetics approach is applied to investigate the genetic structure, diversity, and connectivity of two sympatric carnivore species, i.e. the European pine marten (Martes martes) and the stone marten (Martes foina) in Croatia and Slovenia. We analysed mitochondrial DNA sequences for both species and additionally used nuclear microsatellite markers for the pine marten. A total of 211 individuals (29 pine martens and 182 stone martens) from both mainland and island populations were analysed. For pine marten, we found a significant genetic structuring, with pronounced differentiation between island and mainland populations, and a further substructure within the mainland. No significant isolation by distance was detected (Mantel test, p = 0.15), suggesting that genetic differentiation is driven more by habitat discontinuities and anthropogenic barriers rather than geographical distance alone. In contrast, stone marten exhibited weak genetic structure and high genetic diversity, indicating gene flow and potential landscape permeability for this more synanthropic species. These contrasting patterns underscore species-specific responses to landscape fragmentation and highlight the need to tailor management strategies accordingly.

zoology↗

bioRxiv2025

Tumor clone dynamics in gastro-esophageal cancer organoids reveal a non-genetic memory of neoadjuvant chemotherapy via downregulation of NFκB signaling

Adenocarcinomas of the gastroesophageal junction exhibit genetic and non-genetic heterogeneity that impact clinical outcomes, though the underlying mechanisms behind drug resistance remain poorly understood. We integrated bulk whole-genome sequencing (WGS) and single cell RNA sequencing (scRNA-seq) data from patient-derived organoid lines generated from drug resistant gastric tumors of three patients before and after chemotherapy with FLOT (5-fluorouracil, leucovorin, oxaliplatin, and docetaxel), investigating both in vivo and ex vivo treatment effects. We found that inter-patient variability of gene expression exceeds intra-patient differences and predominantly shapes the expression profiles. Integration of WGS-inferred cancer phylogenies with scRNA-seq data allowed us to associate genetic clones with the individual cells transcriptional program and to track the genetic and transcriptomic history of dominant genetic clones in post-treatment samples relative to the corresponding primary tumor. Notably, in vivo treated samples appeared to be transcriptionally distinct from the untreated counterparts, marked by sustained NF-{kappa}B down-regulation, which suggests that they retain an immune-mediated imprint of the prior therapy. Changes in the clonal composition of a tumor alone cannot explain the post-chemotherapy NF-{kappa}B-associated transcriptional reprogramming. Instead, non-genetic mechanisms shape the altered transcriptomic landscape, particularly a distinct subpopulation of epithelial cells that specifically express pro-inflammatory cytokines, key components of the NF-{kappa}B regulatory network. These observations support a model of transcriptional reprogramming after FLOT treatment, which is most likely independent of genetic evolution and consequently potentially reversible. Downregulated NF-{kappa}B signaling may thus represent a candidate pathway change for predictive response assessment and/or NF-{kappa}B-stimulating co-therapeutic strategies to overcome FLOT resistance.

cancer biology↗

bioRxiv2025

Changes in sea ice alter genetic structure of an iconic Arctic apex predator in less than three decades

Climate change is having profound effects on biodiversity and species distributions worldwide. Nowhere are these effects potentially more pronounced than in the Arctic, where warming is almost two times the global average, and where year-round sea ice extent has significantly decreased, affecting many ice-dependent species. The polar bear (Ursus maritimus) is a circumpolar, apex Arctic predator, a sentinel of climate change, and a symbol of conservation. It is of immense cultural and spiritual importance to Inuit peoples and is hunted across the Arctic. Declines in sea ice have caused habitat fragmentation and loss, disrupting movement and prey access, potentially altering genetic structure and influencing polar bears potential to persist. Using samples collected from 1997 to 2020 by Inuit across much of the Canadian Arctic, 322 genome-wide autosomal DNA markers specifically designed to quantify polar bear genetic structure and a very stringent spatial-temporal method, we compare polar bear spatial genetic structure and landscape features between two periods across a consistent distribution:1997-2008 and 2009-2020. We observe marked changes in spatial genetic structure across the Arctic Archipelago over just two decades, shifting the boundaries between polar bear genetic clusters by [~]250 km. Landscape resistance models reveal the importance of sea ice and land cover type for each period, with spatial lag models showing that genetic change is best predicted by sea ice shifts between periods. Our study reveals rapid changes in genetic structure of polar bears in the Canadian Arctic, helps to inform conservation and management, and offers insight on future polar bear persistence across its immense, remote distribution.

genomics↗

bioRxiv2025

Interstrain Recombinants of Human Cytomegalovirus Reveals Complex Genetic Correlates and Epistasis Influencing Glycoprotein Display, Virion Infectivity and Spread Characteristics.

Most of the nucleotide diversity in the human cytomegalovirus (HCMV) genome is due to approximately 17 genes with 2-14 alleles each. These allelic genes are interspersed among longer stretches of highly conserved sequences with signatures of extensive recombination that would shuffle the allelic genes into a vast number of allelic haplotypes. Bacterial artificial chromosome clones derived from 3 independent clinical isolates (TB40/e (TB), TR and Merlin (ME)) display dramatic differences in the abundance of entry-mediating glycoproteins gH/gL/gO and gH/gL/UL128-131, virion infectivity and efficiency of cell-free and cell-to-cell modes of spread. Of these, TB and ME are the most phenotypically different and share only 2 of the 17 allelic genes. A set of recombinant HCMV was generated by coinfecting cells with TB and ME and restriction fragment length polymorphism (RFLP) analyses demonstrated complex crossover patterns. Most recombinants were either "TB-like" with much more gH/gL/gO than gH/gL/UL128-131, or "ME-like" with much more gH/gL/UL128-131. This correlated with a TB or ME UL128 sequence, consistent with a G/T polymorphism affecting UL128 pre-mRNA splicing. One recombinant had a gH/gL/gO:gH/gL/UL128-131 ratio of 0.8, suggesting genetic determinants beyond UL128. Virion infectivity correlated with TB versus ME-like glycoprotein display, but intragroup variability indicated additional factors and variability in spread efficiency and the contribution of cell-free and cell-to-cell spread modes indicated an influence of characteristics beyond virion infectivity. Results suggest that the relationships among these three phenotypes are not strictly causal and that all three phenotypes are genetically complex and influenced by epistasis among polymorphic loci across the genome. IMPORTANCEThe emerging picture of the genetic diversity of HCMV in vivo prompts a reevaluation of how in vitro characterized viral phenotypes, such as the abundance of the various glycoproteins displayed on the virion envelope and tendency towards cell-free or direct cell-to-cell spread, reflect viral characteristics in vivo. A small sampling of the in vivo genetic diversity of HCMV has been examined in the laboratory and the genetic correlates of in vitro phenotypes are unclear. Engineered mutations can yield different phenotypic effects when introduced on to different genetic backgrounds, suggesting complex epistasis among polymorphic loci across the genome. By generating a set of recombinants derived from two phenotypically and genotypically distinct parental clones, this work offers an approach to characterize complex genetic correlates of viral phenotypes, which in turn may enhance efforts to link genomics data with in vivo viral behavior and clinical outcomes.

microbiology↗

bioRxiv2025

Impact of selective logging on the population dynamics and genetic diversity in the neotropical timber tree Dicorynia guianensis

Selective logging is a widely applied forest management strategy in the tropics, yet it is insufficiently documented how it affects the genetic and demographic processes of seedling recruitment in timber species in the Guiana Shield. Our study investigates how selective logging influences genetic diversity, gene dispersal, and seedling establishment in Dicorynia guianensis by comparing a logged and an unlogged forest plot in French Guiana. We genotyped 703 individuals using 66 nuclear SSR markers and applied parentage analyses to infer dispersal patterns and reproductive success. We analyzed genetic diversity and spatial genetic structure across life stages, and tested whether seedling recruitment was associated with logging-related canopy openings. Genetic diversity indices were broadly similar between logged and unlogged plots, with no evidence of genetic erosion in adults or seedlings. Seedling establishment was associated with logging-induced canopy openings. Parentage analyses revealed shorter mean dispersal distances in the logged plot but substantial long-distance pollen flow, ensuring admixture and inter-plot connectivity. Reproductive success was more evenly distributed among mothers, whereas male contributions were skewed in the logged plot. Selective logging did not cause immediate genetic erosion but altered dispersal dynamics and reproductive patterns. These findings underline the resilience of D. guianensis under current management practices, while emphasizing the need for long-term monitoring of regeneration to ensure sustainable recruitment and evolutionary resilience across logging cycles.

ecology↗

bioRxiv2025

Genetic Erosion at the Edge: Landscape fragmentation and connectivity in sloth bears of the Indian terai

Habitat fragmentation is a major global threat to biodiversity, particularly for species at the periphery of their range where populations are smaller and historically more isolated. Fragmented landscapes reduce connectivity, erode genetic diversity, and elevate inbreeding risk, potentially leading to local extinction. Landscape genetics offers a powerful framework to assess how land-use patterns influence gene flow and population viability. We investigated the endemic sloth bear (Melursus ursinus) populations in the Indian Central Terai landscape, a multi-use, high human density region exemplifying fragmentation and range-edge pressures. Using a ddRAD-seq based approach on non-invasively collected faecal samples (n=209), we generated genomic data, and identified 66 individuals using 964 SNP markers. Despite weak spatial genetic structure, with Dudhwa populations showing the highest differentiation (FST = 0.30). The populations exhibited extremely low heterozygosity (HO = 0.073) and high fixation index (FIS = 0.45), indicating recent bottlenecks and isolation. Landscape genetic analyses revealed agriculture density as the primary barrier to gene flow, followed by road density. Compared to sloth bear populations in Central India and Nepal Terai, CTL bears exhibit markedly reduced genetic variation, likely driven by historic fragmentation and peripheral range effects. This study provides the first genomic baseline for sloth bears in the CTL and underscores the urgency of integrating genetic monitoring with habitat management to prevent further erosion of genetic diversity and ensure long-term population persistence.

ecology↗