Biology subjects

Stelkens, R.

Publications and source records attributed to Stelkens, R..

18 recordsLinked to original sources

bioRxiv2026

Strong habitat-associated differentiation of microbial communities across a fine-scale land-water interface

Microbial communities can remain strongly differentiated across environmental boundaries despite their potential for widespread dispersal. However, the extent to which habitat differences structure microbial communities at fine spatial scales remains poorly understood. Here, we investigated bacterial and fungal communities across a 350-m land-water interface in Lake Vanern, Sweden, including mainland soil, two small terrestrial islands and lake water. Using 16S and ITS amplicon sequencing, we compared microbial diversity and community composition across habitats and with increasing distance from the shoreline. Both bacterial and fungal communities showed pronounced habitat-associated differentiation, with the strongest contrasts between terrestrial and aquatic samples. Despite being surrounded by lake water, island communities were compositionally more similar to mainland soil communities, suggesting that geographic proximity alone does not necessarily lead to microbial community homogenization. Fungal, but not bacterial community composition varied significantly with shoreline position within both terrestrial and aquatic habitats, indicating contrasting spatial patterns between the two groups. Fungal genera also showed greater taxonomic overlap between terrestrial and aquatic habitats than bacterial genera, although overall community composition remained distinct. Taxonomically inferred functional profiles and ecological guilds further reflected habitat-associated differences. Together, our findings reveal strong microbial community differentiation across a fine-scale land-water interface and highlight how habitat identity and spatial context are associated with distinct patterns of bacterial and fungal community assembly.

microbiology↗

bioRxiv2026

Mitochondrial inheritance as an important parameter for the rational design of synthetic yeast polyploids

Synthetic allopolyploidization is a powerful strategy for generating strains with novel industrially relevant traits. During the design of select, hybridize, evolved and learn cycle, the mitochondrial inheritance is considered neutral and most studies overcome their phenotypic impact. Here, we generated 168 synthetic allotetraploid strains representing all pairwise parental combinations of eight wild Saccharomyces species, and systematically controlled mitochondrial inheritance in these crosses. These allopolyploids were phenotyped across 31 environmental conditions relevant to biotechnology. In ~50% of all condition-strain combinations conditions, allotetraploids exhibited mid-parent heterosis. In approximately 25% of conditions, we found crosses with hybrid vigor, particularly in combinations involving Saccharomyces arboricola x Saccharomyces mikatae . However, allotetraploids were highly unstable and rapidly sporulated. Our analyses revealed that environmental conditions accounted for the largest effects, follow by its interaction with mitotype. However, mitotype alone showed small effects but significantly affected 42% of the tested conditions, underscoring the importance of mitochondrial inheritance as a key determinant of allopolyploid performance. These findings demonstrate that mitochondrial inheritance is a key, environment-dependent determinant of allopolyploid fitness and should be considered alongside nuclear genome composition in the rational design of industrial allopolyploid strains

microbiology↗

bioRxiv2026

The mode and repeatability of thermal adaptation in gene expression in the seed beetle Callosobruchus maculatus

Transcriptional plasticity can maintain organismal homeostasis but its potential to buffer negative effects from climate change remains contentious and may rely on genetic adaptation. Theory predicts two general outcomes: genetic reinforcement, where adaptive plasticity is enhanced by genetic adaptation; or genetic compensation, where genetic adaptation reverses maladaptive plasticity. Here, we explored the prevalence, repeatability, and molecular basis of compensation and reinforcement of gene expression responses to temperature using experimental evolution in the beetle pest, Callosobruchus maculatus. We evolved lines from three genetic backgrounds under hot or cold conditions and compared them to ancestral lines after 80-135 generations. Cold adaptation was dominated by genetic compensation, revealing a highly repeatable mode of adaptation across backgrounds, however, the underlying genes and their biological functions were largely idiosyncratic. In contrast, heat adaptation showed a less consistent mode, combining compensation and reinforcement, but greater repeatability at the level of genes and their functions. Network analysis identified many heat reinforcement genes as hubs and strongly temperature dependent, suggestive of roles in orchestrated adaptive thermal plasticity, potentially explaining their high repeatability. Genomic analyses identified repeatable allele frequency changes at both hot and cold compensation and reinforcement genes during experimental evolution. However, these were not causally linked to changes in expression levels, suggesting trans-regulation. There was also no broader correspondence between the level of repeatability of sequence and expression evolution across gene categories. Our findings suggest that the predictability of evolution under climate change might critically depend on the thermal range and the level of the genotype-phenotype map that is studied.

evolutionary biology↗

bioRxiv2026

Convergent targeting of conserved regulatory networks during thermal evolution across Saccharomyces

Whether evolution follows predictable genetic paths across species remains a central question in evolutionary biology, particularly as rising temperatures reshape species distributions worldwide. Despite its importance, the genetic basis of thermal adaptation remains poorly understood across divergent species. Here, we use the yeast genus Saccharomyces as a comparative model to investigate how species with contrasting thermal niches adapt to rising temperatures. We combined experimental evolution under progressively increasing temperatures for up to [~]600 generations with whole-genome sequencing of 256 evolved genotypes, followed by transcriptomic, functional, and physiological analyses across eight species. Despite large differences in ancestral thermal tolerance and evolutionary outcomes, selection repeatedly targeted the same conserved regulatory pathways across species. Independent lineages accumulated de novo mutations in central growth and stress response networks, particularly in TORC1, PKA, and MAPK signaling pathways, revealing striking molecular convergence across species occupying distinct thermal environments. However, these shared genetic targets produced divergent transcriptional and physiological responses depending on species background, indicating that thermal adaptation primarily proceeds through rewiring of conserved regulatory hubs rather than changes in temperature-specific enzymes. Cold-tolerant species frequently lost mitochondrial DNA during thermal evolution, yet loss alone was insufficient to reproduce the adaptive thermal phenotypes of evolved populations. Together, our results show that adaptation to increasing temperature is driven by predictable changes in conserved regulatory networks, while species-specific constraints shape divergent phenotypic outcomes. These findings reveal both the predictability and contingency of evolutionary responses to rising temperature across species.

genomics↗

bioRxiv2026

Repeated heat waves trigger divergent transcriptional responses in cold- and warm-adapted yeast species

Extreme climatic events such as heat waves pose major challenges to species survival and have profound impacts on evolutionary processes. Plasticity is thought to buffer organismal stress, yet the molecular mechanisms underlying plastic responses remain poorly understood. In particular, the role of transcriptional plasticity and stress memory in responding to repeated stress events remains unresolved. Here, we experimentally exposed clonal populations of eight divergent Saccharomyces yeast species with different thermal tolerances to repeated heat waves. We compared their phenotypic and transcriptomic profiles after a few generations of mitotic growth, reflecting transcriptional changes. Warm-adapted species maintained higher growth than cold-adapted species across heat wave exposures. Thermo-generalist species showed intermediate outcomes with one species improving growth across repeated heat waves. To interpret transcriptomic results, we used a conceptual framework separating no-memory (gene expression independent from prior exposure) from memory-associated responses (expression modulated by prior exposure). No-memory responses showed conserved transcriptomic signatures of proteostasis induction, and reduced expression of ribosome biogenesis and translation upon repeated heat waves. Memory-associated responses were more rare and highly species-specific, showing opposite patterns of (de)sensitization in ribosomal and translational pathways in species at the two extremes of thermal tolerance. Together, our results show that thermal resilience can arise through alternative transcriptional changes and suggests that warm- and cold-temperature specialists adopt divergent gene regulatory strategies upon repeated heat waves. With climate change projections indicating more frequent and intense heat waves, understanding plastic responses across species with ecologically and genetically different backgrounds is crucial.

evolutionary biology↗

bioRxiv2025

Commercial Saccharomyces cerevisiae baker's yeasts: strain redundancy, genome plasticity, and colonization of the sourdough environment and the human body

Leavening dough is one of the most widespread applications of fermentative yeast and the most common practice for the general public to come into contact with microbial cultures. Saccharomyces cerevisiae is the typical species used for dough making, but the evolutionary origin of strains isolated from dough is mixed. Here, using 49 newly sequenced and 183 previously described isolates from the bakery environment, we show that the traditional strains used in Europe for sourdough making are more closely related to Chinese Mantou sourdough lineages than to commercially used baker yeast strains. Surprisingly, the expansion of these traditional European strains into other human-associated niches, including the human body, has been very limited. This is in stark contrast to the Mixed-origin clade commercial baking yeasts, which consists of only a few globally distributed clonal lineages that dominate the yeast market and recurrently colonize sourdoughs and human hosts. These clonal lineages consistently maintain their ploidy, unique heterozygous chromosomal rearrangements, and stable aneuploidies in addition to several diverse structural variants. In addition to the previously known diploid and tetraploid groups of commercial isolates, we describe a widely distributed stable triploid aneuploid clonal lineage. We show that company practices and global trade help the distribution of these clonal clusters and that these yeasts are characterized by their exclusively mitotic reproduction.

microbiology↗

bioRxiv2025

Divergent ecological selection causes partial reproductive isolation and vast genomic instability in yeast

Populations evolving independently in divergent environments accumulate genetic differences and potentially evolve reproductive isolation as a by-product of divergence. The speed and mechanisms underlying this process are difficult to investigate because we rarely get the opportunity to witness them in natural settings, and histories of selection and gene flow between populations are often unknown. Here, we experimentally evolved yeast for 1000 generations of evolution in both divergent and parallel environments. At regular time points during experimental evolution, we made crosses between parallel- and divergent-evolving populations to measure postzygotic reproductive isolation (gamete viability). We used whole genome population sequencing to determine the mutational load, the number and types of structural variation, and other genomic features of the parent, F1, and F2 intraspecific hybrids. We found evidence for large scale phenotypic and genome-wide differentiation in response to divergent laboratory selection. Divergent-selected populations produced hybrids with reduced gamete viability - a classic signature of postzygotic reproductive isolation in the form of hybrid breakdown. Parallel-selected populations on the other hand remained more reproductively compatible (with exceptions). We found that F2 hybrid genomes contained vast genomic instability, i.e., new structural variants (especially insertions, deletions, and interchromosomal translocations) that were not observed in parent and F1 genomes, which is likely a result of chromosome missegregation and recombination errors in hybrid meiosis. Our results provide phenotypic and genomic evidence that partial reproductive isolation evolved due to adaptation to divergent environments, consistent with predictions of ecological speciation theory.

evolutionary biology↗

bioRxiv2025

Fermentative yeast diversity at the northern range limit of their oak tree hosts

Fermentative yeasts play important roles in both ecological and industrial processes but their distribution and abundance in natural environments is not well understood. We investigated the diversity of yeast species associated with oak trees (Quercus spp.) in the northern range limit of oak in Sweden, and identified climatic and ecological conditions governing their distribution. We isolated yeasts from oak bark collected from 28 forests and identified them to the species level using metabarcoding. Most communities were dominated by species in the Saccharomycetaceae family, especially by species of Saccharomyces, Kluyveromyces, and Pichia. Each of these genera showed a distinct latitudinal and longitudinal distribution, and both temperature and precipitation metrics predicted significant variation in their abundance. Consistent with this, laboratory assays revealed significant effects of temperature on the growth of strains collected from different longitudes and latitudes. We further found that older trees harbour more diverse and more balanced microbial communities with more evenly distributed species abundances, and that communities across trees were more similar when sharing a common dominant genus. This work provides a baseline for future studies on the impact of climate change on the microbial biodiversity of temperate forests in northern latitudes, and contributes to a growing collection of fermentative yeasts isolated from the wild with potential for biotechnological applications.

microbiology↗

bioRxiv2025

Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing

NOD-like receptors (NLRs) are intracellular immune receptors that detect pathogen-associated cues and trigger defense mechanisms, including regulated cell death. In filamentous fungi, some NLRs mediate heterokaryon incompatibility, a self/non-self recognition process that prevents the vegetative fusion of genetically distinct individuals, reducing the risk of parasitism. The het-d and het-e NLRs in Podospora anserina are highly polymorphic incompatibility genes (het genes) whose products recognize different alleles of the het-c gene via a sensor domain composed of WD40 repeats. These repeats display unusually high sequence identity maintained by concerted evolution. However, some sites within individual repeats are hypervariable and under diversifying selection. Despite extensive genetic studies, inconsistencies in the reported WD40 domain sequence have hindered functional and evolutionary analyses. Here we demonstrate that the WD40 domain can be accurately reconstructed from long-read sequencing (Oxford Nanopore and PacBio) data, but not from Illumina-based assemblies. Functional alleles are usually formed by 11 highly conserved repeats, with different repeat combinations underlying the same phenotypic het-d and het-e incompatibility reactions. Protein structure models suggest that their WD40 domain folds into two 7-blade {beta}-propellers composed of the highly conserved repeats, as well as three cryptic divergent repeats at the C-terminus. We additionally show that one particular het-e allele does not have an incompatibility reaction with common het-c alleles, despite being 11-repeats long. Our findings provide a robust foundation for future research into the molecular mechanisms and evolutionary dynamics of het NLRs, while also highlighting both the fragility and the flexibility of {beta}-propellers as immune sensor domains.

genomics↗

bioRxiv2024

The long-term evolutionary potential of four yeast species and their hybrids in extreme temperature conditions

Accelerating climate change and extreme temperatures urge us to better understand the potential of populations to tolerate and adapt to thermal challenges. Interspecific hybridization can facilitate adaptation to novel or extreme environments. However, predicting the long-term fitness effects of hybridization remains a major challenge in evolutionary and conservation biology. Experimental evolution with microbes provides a powerful tool for tracking adaption, across generations and in real time. We investigated the thermal adaptation dynamics of four species of budding yeast (Saccharomyces) and their interspecific F2 hybrids, for 140 generations under cold (5{degrees}C) and warm (31{degrees}C) conditions.We found significant variation in the evolutionary potential of species and hybrids, strongly determined by their natural temperature tolerance. The largest fitness improvements occurred in hybrids, with some populations nearly quadrupling in fitness in the cold environment, exceeding both parents in thermal adaptive potential. Reciprocal transplanting of evolved populations from the endpoint of evolution into opposite temperatures revealed that hybrids had greater resilience when challenged with sudden temperature shifts. Our results highlight that hybridization alters the fitness outcomes of long-term adaptation to extreme environments and may render populations more resilient to sudden environmental change, presenting both opportunities and challenges for conservation and sustainable agriculture.

evolutionary biology↗

bioRxiv2024

Strong Selection, but low repeatability: Temperature-specific effects on genomic predictions of adaptation

Climate warming is threatening biodiversity by increasing temperatures beyond the optima of many ectotherms. Due to the inherent non-linear relationship between temperature and the rate of cellular processes, such shifts towards hot temperature are predicted to impose stronger selection compared to corresponding shifts toward cold temperature. This suggests that when adaptation to warming occurs, it should be relatively rapid and predictable. Here, we tested this hypothesis from the level of single-nucleotide polymorphisms to life-history traits, by conducting an evolve-and-resequence experiment on three genetic backgrounds of the beetle, Callosobruchus maculatus. Indeed, phenotypic evolution was faster and more repeatable at hot, relative to cold, temperature. However, at the genomic level, adaptation to heat was less repeatable when compared across genetic backgrounds. As a result, genomic predictions of phenotypic adaptation in populations exposed to hot temperature were accurate within, but not between, backgrounds. These results seem best explained by genetic redundancy and an increased importance of epistasis during adaptation to heat, and imply that the same mechanisms that exert strong selection and increase repeatability of phenotypic evolution at hot temperature, reduce repeatability at the genomic level. Thus, predictions of adaptation in key phenotypes from genomic data may become increasingly difficult as climates warm.

evolutionary biology↗

bioRxiv2024

Wild Patagonian yeast improve the evolutionary potential of novel interspecific hybrid strains for Lager brewing

ABSTRACTLager yeasts are limited to a few strains worldwide, imposing restrictions on flavour and aroma diversity and hindering our understanding of the complex evolutionary mechanisms during yeast domestication. The recent finding of diverse S. eubayanus lineages from Patagonia offers potential for generating new Lager yeasts and obtaining insights into the domestication process. Here, we leverage the natural genetic diversity of S. eubayanus and expand the Lager yeast repertoire by including three distinct Patagonian S. eubayanus lineages. We used experimental evolution and selection on desirable traits to enhance the fermentation profiles of novel S. cerevisiae x S. eubayanus hybrids. Our analyses reveal an intricate interplay of pre-existing diversity, selection on species-specific mitochondria, de-novo mutations, and gene copy variations in sugar metabolism genes, resulting in high ethanol production and unique aroma profiles. Hybrids with S. eubayanus mitochondria exhibited greater evolutionary potential and superior fitness post-evolution, analogous to commercial Lager hybrids. Using genome-wide screens of the parental subgenomes, we identified genetic changes in IRA2, SNF3, IMA1 and MALX genes that influence maltose metabolism, and increase glycolytic flux and sugar consumption in the evolved hybrids. Functional validation and transcriptome analyses confirmed increased maltose-related gene expression, influencing grater maltotriose consumption in evolved hybrids. This study demonstrates the potential for generating industrially viable Lager yeast hybrids from wild Patagonian strains. Our hybridization, evolution, and mitochondrial selection approach produced hybrids with high fermentation capacity, expands Lager beer brewing options, and deepens our knowledge of Lager yeast domestication.

microbiology↗

bioRxiv2024

Adaptation to complex environments reveals pervasive trade-offs and genomic targets with large pleiotropic effects

Much of our knowledge on the dynamics of adaptation comes from experimental evolution studies that expose populations to a single selective pressure. However, populations in nature rarely adapt to a single stress at a time. Instead, various biotic and abiotic factors come together to produce complex selective environments. Here, we used experimental evolution to describe adaptive dynamics in the presence of simultaneous stressors, and to quantify the evolution of trade-offs between stressors in a complex environment. We adapted populations of the yeast Saccharomyces cerevisiae to a full-factorial combination of four stressors over the course of 15 serial transfers. Rapid fitness increases were accompanied by the accumulation of mutations in genes and pathways related to specific stressors. Trade-offs evolved rapidly, with the order and mode of trade-off evolution varying between environments due to the inherent physiological and genetic basis of resistance to each stressor. Compensatory evolution for maladaptation as a result of initial trade-offs was typically mediated by fine-tuning of genes associated with the initially adapted environmental component, rather than those associated with the maladapted trait. As environmental complexity increased, mutations had increasingly broader effects across multiple biological processes. Although shared mutations at the individual SNP level were rare, recurrent mutations affecting the same genes and putative biological processes were abundant across environmental complexity. Our results suggest that adaptation in complex environments follows genetic trajectories shaped by pleiotropy and trade-offs, but these trajectories may impose lasting constraints on future adaptation.

evolutionary biology↗

bioRxiv2023

Hybrid adaptation is hampered by Haldane's sieve

Hybrids between species exhibit plastic genomic architectures that foster phenotypic diversity. Their genomic instability also incurs costs, potentially limiting adaptation. When challenged to evolve in an environment containing a UV mimetic drug, yeast hybrids have reduced adaptation rates compared to parents. We hypothesized that this reduction could result from a faster accumulation of genomic changes, but we found no such association. Alternatively, we proposed that hybrids might lack access to adaptive mutations occurring in the parents, yet, we identified mutations in the same genes (PDR1 and YRR1), suggesting similar molecular adaptation mechanisms. However, mutations in these genes tended to be homozygous in the parents but heterozygous in the hybrids. We hypothesized that a lower rate of loss of heterozygosity (LOH) in hybrids could limit fitness gain. Using genome editing, we demonstrated that mutations display incomplete dominance, requiring homozygosity to show full impact and to circumvent Haldanes sieve, which favors the fixation of dominant mutations. We used frozen fossils to track genotype frequency dynamics and confirmed that LOH occurs at a slower pace in hybrids than in parents. Together, these findings show that Haldanes sieve slows down adaptation in hybrids, revealing an intrinsic constraint of hybrid genomic architecture that can limit the role of hybridization in adaptive evolution.

evolutionary biology↗

bioRxiv2022

The dynamics of adaptation to stress from standing genetic variation and de novo mutations

Adaptation from standing genetic variation is an important process underlying evolution in natural populations but we rarely get the opportunity to observe the dynamics of fitness changes in real time. Here, we used the power of microbial experimental evolution and whole population sequencing to track the phenotypic and genomic changes of genetically diverse yeast populations in environments with different stress levels. We found that populations rapidly and in parallel increased in fitness in stressful environments. The founders genetic diversity was quickly depleted, however, not to the same degree in all populations and environments. Some populations fixed all ancestral variation in < 30 generations while others maintained diversity across hundreds of generations. We also observed parallelism at the gene and pathway level. Specifically, we detected up to seven genes harbouring multiple independent mutations in different populations, and a general enrichment for mutations affecting downstream effectors of the high-osmolarity-glycerol pathway in three out of four environments. Adaptation to the most stressful environment was characterised by the fast evolution of functional haploidy, likely driven by standing genetic variation. Almost 40% of all populations contained aneuploidies (losses or gains of chromosomes) at least once during experimental evolution. Some aneuploidies were maintained for hundreds of generations in parallel in different replicates, suggesting they were adaptive. This work shows that experimental evolution is a great tool to address the interplay between standing variation and the influx of de novo mutations, leading to a better understanding of the demographic and environmental drivers and constraints of a populations capacity to adapt to environmental change.

evolutionary biology↗

bioRxiv2022

Harnessing the power of technical and natural variation in 116 yeast datasets to benchmark long read assembly pipelines

With increases in throughput and reductions in cost, long read sequencing has become the standard for most genome assembly projects and has opened up new avenues for large-scale genomic research. While more amenable to assembly than short-read sequence data, long-read datasets tend to have higher error rates. To address this problem numerous tools have been developed to correct reads before assembly and polish assembled contigs. Although, numerous studies have been conducted to assess or benchmark these tools, few capture the real variance in long read sequence data that might affect tool performance much less full pipeline performance. To address these shortcomings, we compiled a dataset containing long-read sequences of 116 different strains of brewers yeast, S. cerevisiae, gathered largely from public databases and evaluated different assembly-related tools as well as their interactions. We found that pre-assembly short-read error correction of long reads combined with post-assembly short-read polishing provided the best assemblies. We also found that correction/polishing steps with uncorrected long reads often lead to degradation of assembly quality. Finally, we show which tools and pipelines work best with different types of input data.

bioinformatics↗

bioRxiv2020

Tracking the origin of Baker's yeast: Seven new long-read genomes of highly divergent, wild Saccharomyces cerevisiae strains from East Asia

Comparative genome analyses have suggested East Asia to be the cradle of the domesticated microbe Brewers yeast (Saccharomyces cerevisiae), used in the food and biotechnology industry worldwide. Here, we provide seven new, high quality long read genomes of non-domesticated yeast strains isolated from primeval forests and other natural environments in China and Taiwan. In a comprehensive analysis of our new genome assemblies, along with other long read Saccharomycetes genomes available, we show that the newly sequenced East Asian strains are among the closest living relatives of the ancestors of the global diversity of Brewers yeast, confirming predictions made from short read genomic data. Three of these strains (termed the East Asian Clade IX Complex here) share a recent ancestry and evolutionary history suggesting an early divergence from other S. cerevisiae strains before the larger radiation of the species, and prior to its domestication. Our genomic analyses reveal that the wild East Asian strains contain elevated levels of structural variations. The new genomic resources provided here contribute to our understanding of the natural diversity of S. cerevisiae, expand the intraspecific genetic variation found in this this heavily domesticated microbe, and provide a foundation for understanding its origin and global colonization history. Significance statementBrewers yeast (Saccharomyces cerevisiae) is a domesticated microbe and research model organism with a global distribution, and suspected origin in East Asia. So far only limited genomic resources are available from non-domesticated lineages. This study provides seven new, high quality long read genomes of strains isolated from primeval forests and other natural environments in China and Taiwan. Comparative genomics reveal elevated levels of structural variation in this group, and early phylogenetic branching prior to the global radiation of the species. These new genomic resources expand our understanding of the evolutionary history of Brewers yeast, and illustrate what the ancestors of this highly successful microbe may have looked like.

genomics↗

bioRxiv2019

Recombining your way out of trouble: The genetic architecture of hybrid fitness under environmental stress

Hybridization between species is a fundamental evolutionary force that can both promote and delay adaptation. There is a deficit in our understanding of the genetic basis of hybrid fitness, especially in non-domesticated organisms. We also know little about how hybrid fitness changes as a function of environmental stress. Here, we made genetically variable F2 hybrid populations from two divergent Saccharomyces yeast species, exposed populations to ten toxins, and sequenced the most resilient hybrids on low coverage using ddRADseq. We expected to find strong negative epistasis and heterozygote advantage in the hybrid genomes. We investigated three aspects of hybridness: 1) hybridity, 2) interspecific heterozygosity, and 3) epistasis (positive or negative associations between non-homologous chromosomes). Linear mixed effect models revealed strong genotype-by-environment interactions with many chromosomes and chromosomal interactions showing species-biased content depending on the environment. Against our predictions, we found extensive selection against heterozygosity such that homozygous allelic combinations from the same species were strongly overrepresented in an otherwise hybrid genomic background. We also observed multiple cases of positive epistasis between chromosomes from opposite species, confirmed by epistasis- and selection-free simulations, which is surprising given the large divergence of the parental species (~15% genome-wide). Together, these results suggest that stress-resilient hybrid genomes can be assembled from the best features of both parents, without paying high costs of negative epistasis across large evolutionary distances. Our findings illustrate the importance of measuring genetic trait architecture in an environmental context when determining the evolutionary potential of hybrid populations.

evolutionary biology↗