SEARCH · Search bioRxiv

Results for “Evolutionary Biology”

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources

bioRxiv2024

Loci associated with cave-derived traits concentrate in specific regions of the Mexican cavefish genome

A major goal of modern evolutionary biology is connecting phenotypic evolution with its underlying genetic basis. The Mexican cavefish (Astyanax mexicanus), a characin fish species comprised of a surface ecotype and a cave-derived ecotype, is well suited as a model to study the genetic mechanisms underlying adaptation to extreme environments. Here we map 206 previously published quantitative trait loci (QTL) for cave-derived traits in A. mexicanus to the newest version of the surface fish genome assembly, AstMex3. This analysis revealed that QTL cluster in the genome more than expected by chance, and this clustering is not explained by the distribution of genes in the genome. To investigate whether certain characteristics of the genome facilitate phenotypic evolution, we tested whether genomic characteristics, such as highly mutagenic CpG sites, are reliable predictors of the sites of trait evolution but did not find any significant trends. Finally, we combined the QTL map with previously collected expression and selection data to identify a list of 36 candidate genes that may underlie the repeated evolution of cave phenotypes, including rgrb which is predicted to be involved in phototransduction. We found this gene has disrupted exons in all non-hybrid cave populations but intact reading frames in surface fish. Overall, our results suggest specific "evolutionary hotspots" in the genome may play significant roles in driving adaptation to the cave environment in Astyanax mexicanus and demonstrate how this compiled dataset can facilitate our understanding of the genetic basis of repeated evolution in the Mexican cavefish.

evolutionary biology↗

bioRxiv2025

Copy number variation facilitates rapid toggling between ecological strategies

A central question in evolutionary biology is how different types of mutations shape ecological strategy. Whereas both single nucleotide variants (SNVs) and copy number variants (CNVs) can alter gene dosage, it remains unclear whether CNVs confer unique adaptive advantages. Here, we show that CNVs do not mediate adaptive tracking in fluctuating environments, but instead act as reversible toggles between ecological strategies. Using a dual-fluorescent CNV reporter system in Saccharomyces cerevisiae, we tracked CNV dynamics at two transporter loci during long-term evolution under static and fluctuating nitrogen limitation. CNVs arose with high repeatability in static conditions but showed dampened or divergent dynamics in fluctuating environments, suggesting they do not track environmental change. Instead, we found that the ratio of copy number between the two loci, but not copy number at either locus alone, predicted ecological strategy: imbalanced CNV ratios defined specialists, while balanced ratios defined generalists. Evolution in static environments favored specialists whereas fluctuating environments favored generalists. Applying this framework to over 3,000 sequenced yeast genomes, we found generalist CNV signatures in both wild and domesticated strains, but specialist signatures exclusively in domesticated strains. These findings introduce a generalizable framework for predicting ecological strategy from genome structure, positioning CNV ratios as a molecular signature of niche breadth across evolutionary and ecological contexts.

evolutionary biology↗

bioRxiv2019

Sex enhances survival in Paramecium

The pervasiveness of sex despite its well-known costs is a long-standing puzzle in evolutionary biology. Current explanations for the success of sex in nature largely rely on the adaptive significance of the new or rare genotypes that sex may generate. Less explored is the possibility that sex-underlying molecular mechanisms can enhance fitness and convey benefits to the individuals that bear the immediate costs of sex. Here we show that self-fertilization can increase stress resistance in the ciliate Paramecium tetraurelia. This advantage is independent of new genetic variation, coupled with a reduced nutritional input, and offers fresh insights into the mechanistic origin of sex. In addition to providing evidence that the molecular underpinnings of sexual reproduction and the stress response are linked in P. tetraurelia, these findings supply an explanation for the persistence of self-fertilization in this ciliate.

evolutionary biology↗

bioRxiv2017

Dramatic evolution of body length due to post-embryonic changes in cell size in a newly discovered close relative of C. elegans

Understanding morphological diversity--and morphological constrainto--has been a central question in evolutionary biology since its inception. Nematodes of the genus Caenorhabditis, which contains the well-studied model system C. elegans, display remarkable morphological consistency in the face of extensive genetic divergence. Here, we provide a description of the broad developmental patterns of a recently discovered species, C. sp. 34, which was isolated from fresh figs in Okinawa and which is among the closest known relatives of C. elegans. C. sp. 34 displays an extremely large body size and can grow to be nearly twice as long as C. elegans and all other known members of the genus. Observations of the timing of developmental milestones reveal that C. sp. 34 develops about twice as slowly as C. elegans. Measurements of embryo and larval size show that the size difference between C. sp. 34 and C. elegans is largely due to post-embryonic events, particularly during the transition from larval to adult stages. This difference in size is not attributable to differences in germ line chromosome number or the number of somatic cells. The overall difference in body size is therefore largely attributable to changes in cell size via increased cytoplasmic volume. Because of its close relationship to C. elegans, the distinctness of C. sp. 34 provides an ideal system for the detailed analysis of evolutionary diversification. The context of over forty years of C. elegans developmental genetics also reveals clues into how natural selection and developmental constraint act jointly to promote patterns of morphological stasis and divergence in this group.

evolutionary biology↗

bioRxiv2022

Distinct Effects of the Male-Killing Bacteria Wolbachia and Spiroplasma and a Partiti-Like Virus in the Tea Pest Moth, Homona magnanima

Male killing, the phenomenon of male death during development, is considered to be one of the advantageous strategies exerted by maternally transmitted microbes. Male killing has attracted interest in the fields of evolutionary biology and ecology for decades; however, little is known about its mechanism and origin. Here, we characterized and compared the effects of three distinct male killers, Wolbachia (Alphaproteobacteria), Spiroplasma (Mollicutes), and Osugoroshi virus (OGV) (Partitiviridae) in the tea pest moth Homona magnanima (Lepidoptera, Tortricidae). Regardless of the genetic sex (male: ZZ; female: ZW), female specific splice variants of the doublesex gene (dsx), a downstream regulator of the sex-determining gene cascade, was expressed in H. magnanima harbored either male-killing Wolbachia or Spiroplasma. However, OGV and non-male-killing Wolbachia did not alter dsx splicing. RNA sequencing and quantitative PCR assays demonstrated that male-killing Wolbachia impaired the hosts dosage compensation system by altering the global gene expression of the Z chromosome (corresponding to Bombyx mori chromosome 1 and 15) in males, whereas Spiroplasma did not affect dosage compensation. In contrast, the partiti-like virus OGVs did not affect sex-determination cascades or dosage compensation systems. Besides, male killers distinctly altered host gene expression and metabolomes associated with physiology, morphology, and diverse metabolic pathways. Moreover, Wolbachia and Spiroplasma infections triggered abnormal apoptosis only in male embryos. These findings suggest that distantly related microbes employ distinct machineries to kill identical host males, which have been acquired through independent evolutionary processes. ImportanceMale-killing caused by diverse microbes has attracted substantial attention. However, it remains unclear how such male killers have evolved similar phenotypes, in part because male-killing mechanisms have been studied using different insect models. Here, by comparing three phylogenetically distinct male killers, Wolbachia, Spiroplasma, and a partiti-like virus, in an identical host, we provide evidence that microbes can affect male viability through distinct machinery, demonstrating distinct evolutionary scenarios for microbes to acquire make-killing ability. These findings provide insight into new directions for studying microbe-host interactions.

evolutionary biology↗

bioRxiv2023

Manipulating multi-level selection in a fungal entomopathogen reveals social conflicts and a method for improving biocontrol traits

Changes in parasite virulence are commonly expected to lead to trade-offs in other life history traits that can affect fitness. Understanding these trade-offs is particularly important if we want to manipulate the virulence of microbial biological control agents. Theoretically, selection across different spatial scales, i.e. between- and within-hosts, shapes these trade- offs. However, trade-offs are also dependent on parasite biology. Despite their applied importance the evolution of virulence in fungal parasites is poorly understood: virulence can be unstable in culture and commonly fails to increase in simple passage experiments. We hypothesized that manipulating selection intensity at different scales would reveal virulence trade-offs in a fungal pathogen of aphids, Akanthomyces muscarius. Starting with a genetically diverse stock we selected for infectivity, parasite yield or speed of kill by manipulating competition within and between hosts and between groups of hosts over 7 rounds of infection. We characterized ancestral and evolved lineages by whole genome sequencing and by measuring virulence, growth rate, sporulation and fitness. While several lineages showed increases in virulence, we saw none of the trade-offs commonly found in obligately-killing parasites. Phenotypically similar lineages within treatments often shared multiple single-nucleotide variants, indicating strong convergent evolution. The most dramatic phenotypic changes were in timing of sporulation and spore production in vitro. We found that early sporulation led to reduced competitive fitness but could increase yield of spores on media, a trade-off characteristic of social conflict. Notably, the selection regime with strongest between-group competition and lowest genetic diversity produced the most consistent shift to early sporulation, as predicted by social evolution theory. Mutli-level selection therefore revealed social interactions novel to fungi and showed that these biocontrol agents have the genomic flexibility to improve multiple traits -virulence and spore production - that are often in conflict in other parasites. Author summaryUnderstanding the ecological forces that shape virulence is a key challenge in evolutionary biology. Here we investigated how competition at different levels of selection (within-hosts, between-hosts, between populations) could alter investment in virulence in a fungal entomopathogen. We predicted that cooperative investment in virulence would increase at higher scales of competition and aimed to further our understanding of potential trade-offs shaping life-history of a fungal insect pathogens. We found moderate increases in virulence in different selection regimes but importantly, none of the commonly expected trade-offs, such as that between spore production and virulence or a relationship between virulence and growth rate, which is consistent with cooperation. However, we found convergent genetic changes and significant differences in timing and production of spores, dependent how we manipulated scales of selection. Our data suggests that this is driven by social conflict regarding the timing of sporulation. This carries fundamental importance for understanding how varying selection pressure at different scales shape pathogen life history. In addition, these results also have applied importance for understanding how to improve and select for beneficial traits in biocontrol agents.

evolutionary biology↗

bioRxiv2026

Rare sex punctuates strict asexual reproduction in the clonal raider ant, Ooceraea biroi

While asexual species can often outcompete their sexual counterparts over ecological timescales, their long-term evolutionary success is hindered by a diminished ability to purge deleterious mutations and to adapt to changing environments. However, some asexual species persist for millions of years, and a major question in evolutionary biology is how they do so. One solution is to occasionally reproduce sexually, as has been shown in a handful of primarily asexual species. Here, we investigate the possibility of rare sex in the clonal raider ant, Ooceraea biroi. We report the whole-genome sequence of a previously uncharacterized clonal line and, using population genetic and phylogenetic analyses, show that it originated through sexual reproduction between two extensively studied clonal lines. The mitochondrial genome of this clonal line differs from that of the maternal clonal line at only a single nucleotide, suggesting that the sexual reproduction event occurred within the past few hundred years. These results demonstrate that sex occurs sporadically in the clonal raider ant, allowing it to generate new genetic combinations and potentially to overcome some of the costs of asexuality.

evolutionary biology↗

bioRxiv2023

The Maintenance of Deleterious Variation in Wild Chinese Rhesus Macaques

Understanding how deleterious variation is shaped and maintained in natural populations is important in conservation and evolutionary biology, as decreased fitness caused by these deleterious mutations can potentially lead to an increase in extinction risk. It is known that demographic processes can influence these patterns. For example, population bottlenecks and inbreeding increase the probability of inheriting identical-by-descent haplotypes from a recent common ancestor, creating long tracts of homozygous genotypes called runs of homozygosity (ROH), which have been associated with an accumulation of mildly deleterious homozygotes. Counter intuitively, positive selection can also maintain deleterious variants in a population through genetic hitchhiking. Here we analyze the whole genomes of 79 wild Chinese rhesus macaques across five sub-species and characterize patterns of deleterious variation with respect to ROH and signals of recent positive selection. We show that the fraction of homozygotes occurring in long ROH is significantly higher for deleterious homozygotes than tolerated ones, whereas this trend is not observed for short and medium ROH. This confirms that inbreeding, by generating these long tracts of homozygosity, is the main driver of the high burden of homozygous deleterious alleles in wild macaque populations. Furthermore, we show evidence that homozygous LOF variants are being purged. Next, we identify 7 deleterious variants at high frequency in regions putatively under selection near genes involved with olfaction and other processes. Our results shed light on how evolutionary processes can shape the distribution of deleterious variation in wild non-human primates. SignificanceOur results offer insights into the relationship between demographic and evolutionary processes and the maintenance of deleterious alleles in wild rhesus macaques. We demonstrate how inbreeding and recent positive selection can contribute to the maintenance of deleterious variants in wild non-human primate populations. Given that deleterious variation can reduce individuals reproductive fitness and contribute to extinction risks, this study is particularly relevant in the context of conservation of wild endangered species.

evolutionary biology↗

bioRxiv2018

Does Adaptive Protein Evolution Proceed by Large or Small Steps at the Amino Acid Level?

A longstanding question in evolutionary biology is the relative contribution of large and small effect mutations to the adaptive process. We have investigated this question in proteins by estimating the rate of adaptive evolution between all pairs of amino acids separated by one mutational step using a McDonald-Kreitman type approach and genome-wide data from several Drosophila species. We find that the rate of adaptive evolution is higher amongst amino acids that are more similar. This is partly due to the fact that the proportion of mutations that are adaptive is higher amongst more similar amino acids. We also find that the rate of neutral evolution between amino acids is higher amongst similar amino acids. Overall our results suggest that both the adaptive and non-adaptive evolution of proteins is dominated by substitutions between amino acids that are more similar.

evolutionary biology↗

bioRxiv2020

Fitness dependence preserves selection for recombination across diverse mixed mating systems

Meiotic recombination and the factors affecting its rate and fate in nature have inspired many theoretical studies in evolutionary biology. Classical theoretical models have inferred that non-zero recombination can be favoured under a rather restricted parameter range. Thus, the ubiquity of recombination in nature remains an open question. However, these models assumed constant (uniform) recombination with an equal rate across all individuals within the population. Models of fitness-dependent recombination, with the rate varying among genotypes according to their fitness have shown that such a strategy can often be favoured over the best constant recombination. Here we use simulations to show that across a range of mating systems with varying frequencies of selfing and clonality, fitness-dependent recombination is often favoured even when any non-zero constant recombination is disfavoured. This recombination-protecting effect of fitness dependence is strongest under intermediate rates of selfing or high rates of clonality.

evolutionary biology↗

bioRxiv2023

The effects of mutations on gene expression and alternative splicing: a case study of EMS-induced heritable mutations in the microcrustacean Daphnia

Understanding the relationship between mutations and their genomic and phenotypic consequences has been a longstanding goal of evolutionary biology. However, few studies have investigated the impact of mutations on gene expression and alternative splicing on the genome- wide scale. In this study, we aim to bridge this knowledge gap by utilizing whole-genome sequencing data and RNA sequencing data from 16 OP Daphnia mutant lines to investigate the effects of EMS-induced mutations on gene expression and alternative splicing. Using rigorous analyses of mutations, expression changes, and alternative splicing, we show that trans-effects are the major contributor to the variance in gene expression and alternative splicing between the wildtype and mutant lines, whereas cis mutations only affected a limited number of genes and do not always alter gene expression. Moreover, we show that there is a significant association between DE genes and exonic mutations, indicating that exonic mutations are an important driver of altered gene expression.

evolutionary biology↗

bioRxiv2026

Rapid divergence in sperm morphology and transgressive segregation of hybrid sperm kinematics in a young pupfish radiation

Understanding how divergence in reproductive traits can promote speciation remains a fundamental question in evolutionary biology. Sperm morphology and kinematics diverge rapidly across species. However, the effect of hybridization between recently diverged species on sperm traits remains unclear, limiting our understanding of how reproductive isolation evolves. Here, we evaluated sperm morphology, kinematics, and trait integration in species of a young (~10,000 years), sympatric Cyprinodon pupfish radiation from San Salvador Island, Bahamas, as well as fertile advanced-generation hybrids between two of these species. We found significant divergence in flagellum length, midpiece area, and sperm velocity among species. In contrast, hybrids displayed transgressive kinematic profiles defined by high velocities, reduced path curvature, and distinct patterns of sperm kinematic integration. Our findings suggest that hybridization between recently diverged species may reorganize the underlying control of sperm locomotor mechanisms, generating novel phenotypes that could contribute to reproductive isolation in the early stages of speciation.

evolutionary biology↗

bioRxiv2026

A deep genetic structure phylogenomically frames the closest algal relatives of land plants

To discern the nature of the closest streptophyte algal relatives of land plants (embryophytes) is a major question in the field of plant evolutionary biology; discerning that nature is essential for our ability to infer the last common ancestor of embryophytes and algae, allowing to retrace the adaptations that ushered in the conquest of land by plants. Albeit initially coming as a surprise, all major phylogenomic efforts have concluded that the Zygnematophyceae are the algal sisters to land plants1-6. The Zygnematophyceae are the streptophyte algal class with the greatest species richness7 and while we now have ample genome information on a few select members of zygnematophytes8-13, our understanding of the genetic and genomic divergence as well as potential is limited by a lack of phylodiverse data that accounts for this diversity and integrates it into a phylogenomic framework. We here sequenced 43 new transcriptome datasets for the Zygnematophyceae and built a phylogenomic tree based on a total of 104 zygnematophyceaen transcriptomes and 2243 loci. We recover a deep genetic structure for the Zygnematophyceae, revealing that this algal class is ancient. Despite the deep split between Spirogyrales and their unicellular sister group Desmidiales, most Spirogyrales emerged after pronounced genetic divergence, accommodating the attainment of multicellularity and divergent traits such as unique cell and plastid division13. Overall, our data capture signatures of massive ancient radiations. Zygnematophyceae are characterized by deep genetic divergences that necessitated a phylodiverse sampling to be revealed, together with their vast evolutionary history, and to illuminate the nature of the algal progenitors of land plants.

evolutionary biology↗

bioRxiv2024

Cross-Species Analysis Reveals No Universal Programmed Aging Mechanism: Insights from Single-Cell Transcriptomics in Zebrafish, Fruit Fly, and Nematode

The question of whether aging follows a universal programmed process has been a topic of debate for a long time. Previous arguments, either supporting or refuting programmed aging, were mainly based on different evolutionary biology theories. In this study, we analysed single-cell RNA sequencing data from zebrafish, fruit fly, and nematode at various stages of development to explore gene co-expression modules across these species. We successfully identified a co-expression module related to ribosomal protein genes that is shared across the early development stages in multiple tissues of all three species. However, we did not find any cross-species shared gene co-expression modules related to aging. Further analysis of gene regulatory networks (GRNs) demonstrated that although certain aging-related genes are conserved, their regulatory mechanisms vary significantly between species. These findings suggest that aging is not governed by a conserved universal program but rather by species-specific adaptations to damage and environmental conditions.

evolutionary biology↗

bioRxiv2020

A genotype-phenotype-fitness map reveals local modularity and global pleiotropy of adaptation

Building a genotype-phenotype-fitness map of adaptation is a central goal in evolutionary biology. It is notoriously difficult even when the adaptive mutations are known because it is hard to enumerate which phenotypes make these mutations adaptive. We address this problem by first quantifying how the fitness of hundreds of adaptive yeast mutants responds to subtle environmental shifts and then modeling the number of phenotypes they must collectively influence by decomposing these patterns of fitness variation. We find that a small number of phenotypes predicts fitness of the adaptive mutations near their original glucose-limited evolution condition. Importantly, phenotypes that matter little to fitness at or near the evolution condition can matter strongly in distant environments. This suggests that adaptive mutations are locally modular--affecting a small number of phenotypes that matter to fitness in the environment where they evolved--yet globally pleiotropic--affecting additional phenotypes that may reduce or improve fitness in new environments.

evolutionary biology↗

bioRxiv2026

Environmental feedback maintains cooperation in viruses

Cooperators that pay a cost to provide benefits to others are vulnerable to exploitation by defectors that reap the benefits while avoiding the costs. Thus selection on the individual level can lead to loss of cooperators while lowering overall population fitness. Accordingly, the maintenance of cooperation is a key problem in evolutionary biology. The puzzle of cooperation extends to viruses: cooperative viruses produce gene products that can be shared, while defector viruses produce less and instead use products made by cooperators. In coinfection, defectors are always advantaged, predicting the loss of cooperation. However, the fitness of cooperator and defector phenotypes is context dependent. Though defectors are advantaged in coinfection, they suffer reduced replication in single infections. Environmental feedback is the process by which changes in population composition alter viral densities and rates of coinfection, which in turn feed back to affect the fitness of each type. We show that environmental feedback maintains cooperation in viruses. We also find that defector emergence may interfere with phage therapy by disrupting the phage dynamics that cause host extinction, and demonstrate that the introduction of defectors lowers viral densities and drives viral extinction, suggesting that defectors that replicate alone could function as antiviral therapies.

evolutionary biology↗

bioRxiv2017

Inferring Genetic Interactions From Comparative Fitness Data

AO_SCPLOWBSTRACTC_SCPLOWDarwinian fitness is a central concept in evolutionary biology. In practice, however, it is hardly possible to measure fitness for all genotypes in a natural population. Here, we present quantitative tools to make inferences about epistatic gene interactions when the fitness landscape is only incompletely determined due to imprecise measurements or missing observations. We demonstrate that genetic interactions can often be inferred from fitness rank orders, where all genotypes are ordered according to fitness, and even from partial fitness orders. We provide a complete characterization of rank orders that imply higher order epistasis. Our theory applies to all common types of gene interactions and facilitates comprehensive investigations of diverse genetic interactions. We analyzed various genetic systems comprising HIV-1, the malaria-causing parasite Plasmodium vivax, the fungus Aspergillus niger, and the TEM-family of {beta}-lactamase associated with antibiotic resistance. For all systems, our approach revealed higher order interactions among mutations.

evolutionary biology↗

bioRxiv2019

Symbiont-mediated protection varies with wasp genotype in the Drosophila melanogaster-Spiroplasma interaction

The ability of an insect to survive attack by natural enemies can be modulated by the presence of defensive symbionts. Study of aphid-symbiont-enemy interactions has indicated that protection may depend on the interplay of symbiont, host and attacking parasite genotypes. However, the importance of these interactions are poorly understood outside of this model system. Here, we study interactions within a Drosophila model system, in which Spiroplasma protect their host against parasitoid wasps and nematode attack. We examine whether the strength of protection conferred by Spiroplasma to its host, Drosophila melanogaster varies with strain of attacking Leptopilina heterotoma wasp. We perform this analysis in the presence and absence of ethanol, an environmental factor that also impacts the outcome of parasitism. We observed that Spiroplasma killed all strains of wasp. However, the protection produced by Spiroplasma following wasp attack depended on attacking wasp strain. A composite measure of protection, including both the chance of the fly surviving attack and the relative fecundity/fertility of the survivors, varied from a <4% positive effect of the symbiont following attack of the fly host by the Lh14 strain of wasp to 21% for the Lh-Fr strain in the absence of ethanol. Variation in protection provided was not associated with differences in the oviposition behaviour of the different wasp strains. We observed that environmental ethanol altered the pattern of protection against wasp strains, with Spiroplasma being most protective against the Lh-Mad wasp strain in the presence of ethanol. These data indicate that the dynamics of the Spiroplasma-Drosophila-wasp tripartite interaction depend upon the genetic diversity within the attacking wasp population, and that prediction of symbiont dynamics in natural systems will thus require analysis across natural enemy genotypes and levels of environmental ethanol.\n\nImpact SummaryNatural enemies - predators, parasites and pathogens - are a common source of mortality in animals, and this has driven the evolution of an array of mechanisms for preventing and surviving attack. Recently it has been observed that microbial symbionts form a component of insect defence against attack by pathogens and parasites. Whether an individual fly dies or lives following wasp attack, for instance, is partly determined by the presence or absence of Spiroplasma bacteria in the fly blood. The evolutionary biology of these protective symbioses will in part depend on the specificity of defence - does Spiroplasma defend against all wasp strains equally, or does defence vary between wasp strains? We investigated this in the model insect, Drosophila melanogaster. We observed that the defensive symbiont killed all strains of wasps tested. However, the capacity of the symbiont to rescue the fly varied - Spiroplasma rescued the flies for some attacking wasp strains, but not for others. These data mean that the degree to which symbionts protect their host will depend on the wasp strains circulating in nature. Our results are important in terms of understanding the forces that promote symbiont mediated protection and understanding the origins of diversity of circulating wasp strains. Further, these data indicate enemy diversity and their interaction with protective symbionts should be included in evaluation of the efficiency of biocontrol programmes involving natural enemies.

evolutionary biology↗