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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 433 records · Page 24Linked to original sources

bioRxiv2025

Chromatin accessibility differences between the hybrids of nasuta-albomicans complex of Drosophila

Understanding how chromosomal rearrangements (CRs) interact with epigenetic changes to drive speciation is a fundamental question in evolutionary biology. CRs are key contributors to chromosome evolution and can play a pivotal role in reproductive isolation. The Drosophila nasuta-albomicans species complex presents an ideal model to explore this, as D. albomicans possesses neo-sex chromosomes formed by Robertsonian fusion of chr3L, chr3R, and a sex chromosome, unlike its sister species D. nasuta. In this study, we investigate CRs influence on accessible chromatin (AC) and its relationship with genetic differentiation. We used ATAC-seq to decipher ACs of testis in two hybrids of D. albomicans and D. nasuta, and genome-wide fixation index (FST) scans of D. albomicans and D. nasuta to identify regions of genetic differentiation. Our analyses revealed that chromosome 4 (Muller F) harbors the largest number of differentially accessible regions ([~]97 Kb), which coincide with peaks in FST. Moreover, changes in ACs were associated with differential transcription factor (TF) binding across the genome. These results suggest that CRs can drive epigenomic divergence in hybrids, particularly on Muller F, and chromatin-level changes may play a key role in reproductive isolation. Our study provides an example of how chromosomal and epigenetic architecture interact in the early stages of speciation.

evolutionary biology↗

bioRxiv2026

Neo-sex Chromosomes Anchor a Sex-Limited Polymorphism Under Gene Flow

How polymorphic traits are maintained despite the homogenizing forces of gene flow and recombination is a central question in evolutionary biology. While the accumulation of locally adaptive alleles within chromosomal inversions is well established, the role of sex chromosomes in local adaptation has received comparatively less empirical support. Here, we show that a male-limited color polymorphism in an Anolis distichus contact zone is anchored by a neo-sex chromosome. Across a narrow environmental gradient, an abrupt transition between yellow and orange dewlaps--extensible throat fans used for signaling--is driven by distinct pigmentation profiles we characterize via histological and chromatographic analyses. Integrating genomics and association mapping, we demonstrate this divergence relies on an additive, oligogenic architecture. Alternative neo-Y haplotypes track the phenotypic cline and combine additively with autosomal variants near a putative ketolase and a lipid regulator to determine color, jointly explaining a significant portion of the phenotypic variance. Furthermore, we identify a copy number variant near an X-linked visual processing gene, indicating simultaneous sensory divergence. This concerted evolution suggests the local light environment drives adaptation of the communication system. Ultimately, this study demonstrates that degrading neo-sex chromosomes act as non-recombining hubs for locally adaptive alleles, preserving phenotypic diversity under gene flow.

evolutionary biology↗

bioRxiv2018

On the timing of bill length evolution in British great tits: A comment on Bosse et al. 2017.

Long-term field studies coupled with quantitative genomics offer a powerful means to understand the genetic bases underlying quantitative traits and their evolutionary changes. However, analyzing and interpreting the time scales at which adaptive evolution occurs is challenging. First, while evolution is predictable in the short term, with strikingly rapid phenotypic changes in data series, it remains unpredictable in the long term. Second, while the temporal dynamics of some loci with large effect on phenotypic variation and fitness have been characterized, this task can be complicated in cases of highly polygenic trait architecture implicating numerous small effect size loci, or when statistical tests are sensitive to the heterogeneity of some key characteristics of the genome, like recombination rate variations. After introducing these aforementioned challenges, we discuss a recent investigation of the genomic architecture and spatio-temporal variation in great tit bill length, which was related to the recent use of bird feeders. We discuss how this case study illustrates the importance of considering different temporal scales and evolutionary mechanisms both while analyzing trait temporal trends and when searching for and interpreting the signals of putative genomic footprints of selection. More generally this commentary discusses interesting challenges for unraveling the time scale at which adaptive traits evolve and their genomic bases.\n\nImpact summaryAn important goal in evolutionary biology is to understand how individual traits evolve, leading to fascinating variations in time and space. Long-term field studies have been crucial in trying to understand the timing, extent, and ecological determinants of such trait variation in wild populations. In this context, recent genomic tools can be used to look for the genetic bases underlying such trait variation and can provide clues on the nature and timing of their evolution. However, the analysis and the interpretation of the time scales at which evolution occurs remain challenging. First, analyzing long-term data series can be tricky; short-term changes are highly predictable whereas long-term evolution is much less predictable. A second difficult task is to study the architecture of complex quantitative traits and to decipher the timing and roles of the several genomic mechanisms involved in their evolution. This commentary introduces these challenges and discusses a recent investigation of the nature and timing of ecological and genomic factors responsible for variation in great tit bill length. Overall, we raise cautionary warnings regarding several conceptual and technical features and limitations when coupling analyses of long-term and genomic data to study trait evolution in wild populations.

evolutionary biology↗

bioRxiv2019

A phenotypically plastic magic trait promoting reproductive isolation in sticklebacks?

This study identifies one possible mechanism whereby gene flow is interrupted in populations undergoing evolutionary divergence in sympatry; this is an important issue in evolutionary biology that remains poorly understood. Variation in trophic morphology was induced in three-spined stickleback by exposing them from an early age either to large benthic or to small pelagic prey. At sexual maturity, females given a choice between two breeding males, showed positive assortative mate choice for males raised on the same diet as themselves. The data indicate that this was mediated through a preference for males with trophic morphology similar to that of fish with which the females were familiar (from their pre-testing holding tanks). In trials where the female did not choose the most familiar male, the evidence suggests that either she had difficulty discriminating between two similar males or was positively choosing males with more extreme morphologies (more benthic-like or pelagic -like). This study has shown for the first time that expression of a plastic trait induced at an early age, not only results in specialisation for local foraging regimes but can also play a significant role in mate choice. This is equivalent to an environmentally induced, plastic version of the \"magic traits\" that promote ecologically-driven divergence in sympatry, hence the proposed descriptor \"plastic magic trait\".

evolutionary biology↗

bioRxiv2021

Genes encoding teleost orthologs of human haplo-insufficient and monoallelic genes remain in duplicate more frequently than the whole genome

Gene dosage is important is an important issue both in cell and evolutionary biology. Most genes are present in two copies in eukaryotic cells. The first outstanding exception is monoallelic gene expression (MA) that concerns genes localized on the X chromosome or in regions undergoing parental imprinting in eutherians, and many other genes scattered throughout the genome. The second exception concerns haploinsufficiency (HI), responsible for the fact that a single functional copy of a gene in a diploid organism is insufficient to ensure a normal biological function. One of the most important mechanisms ensuring functional innovation during evolution is Whole genome duplication (WGD). In addition to the two WGDs that have occurred in vertebrate genomes, the teleost genomes underwent an additional WGD, after their divergence from tetrapod. In the present work, we have studied on 57 teleost species whether the orthologs of human MA or HI genes remain more frequently in duplicates or returned more frequently in singleton than the rest of the genome. Our results show that the teleost orthologs of HI human genes remained more frequently in duplicate than the rest of the genome in all the teleost species studied. No signal was observed for the orthologs of genes localized on the human X chromosome or subjected to parental imprinting. Surprisingly, the teleost orthologs of the other human MA genes remained in duplicate more frequently than the rest of the genome for most teleost species. These results suggest that the teleost orthologs of MA and HI human genes also undergo selective pressures either related to absolute protein amounts and/or of dosage balance issues. However, these constraints seem to be different for MA genes in teleost in comparison with human genomes.

evolutionary biology↗

bioRxiv2024

Convergent evolution of plant prickles is drivenby repeated gene co-option over deep time

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. Here we genetically dissected repeated origins and losses of prickles, sharp epidermal projections, that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus Solanum. Strikingly, homologs promote prickle formation across angiosperms that collectively diverged over 150 million years ago. By developing new Solanum genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone-activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.

evolutionary biology↗

bioRxiv2018

No Cost of Complexity in Bacteriophages Adapting to a Complex Environment

A longstanding prediction in evolutionary biology is that organisms experience a so-called \"cost of complexity\" manifested as a decreasing rate of adaptation in populations as organisms or selective environments become increasingly complex. This theory assumes the ubiquity of antagonistic pleiotropy, or tradeoffs in fitness, for mutations affecting multiple traits or phenotypes. A particular manifestation of antagonism thought to be at play in adaptive dynamics involves the relationship between viral growth rate and capsid stability, an interaction that may impede the adaptation of viral pathogens to novel hosts and environments. Here, we present a comparison of the genetics of adaptation for populations of bacteriophages undergoing complete adaptive walks under both simple and complex selective conditions, with complexity being determined by the number of traits under directional selection. We found no evidence for a long-term cost of complexity in viruses experiencing complex selection, with on average at least as great a rate of adaptation under more complex conditions, and rampant evidence for synergistic, rather than antagonistic, pleiotropy. The lack of evident tradeoffs between multiple phenotypes implies that emerging pathogens may be able to improve their growth in many different hosts or environments simultaneously and to do so at a faster rate than previously anticipated.

evolutionary biology↗

bioRxiv2018

Sex allocation conflict and sexual selection throughout the lifespan of eusocial colonies

Models of sex allocation conflict are central to evolutionary biology but have mostly assumed static decisions, where resource allocation strategies are constant over colony lifespan. Here, we develop a model to study how the evolution of dynamic resource allocation strategies is affected by the queen-worker conflict in annual eusocial insects. We demonstrate that the time of dispersal of sexuals affects the sex allocation ratio through sexual selection on males. Furthermore, our model provides three predictions that depart from established results of classic static allocation models. First, we find that the queen wins the sex allocation conflict, while the workers determine the maximum colony size and colony productivity. Second, male-biased sex allocation and protandry evolve if sexuals disperse directly after eclosion. Third, when workers are more related to new queens, then the proportional investment into queens is expected to be lower, which results from the interacting effect of sexual selection (selecting for protandry) and sex allocation conflict (selecting for earlier switch to producing sexuals). Overall, we find that colony ontogeny crucially affects the outcome of sex-allocation conflict because of the evolution of distinct colony growth phases, which decouples how queens and workers affect allocation decisions and can result in asymmetric control.

evolutionary biology↗

bioRxiv2019

Range-wide spatial mapping reveals convergent character displacement of bird song

A long-held view in evolutionary biology is that character displacement generates divergent phenotypes in closely related coexisting species to avoid the costs of hybridisation or ecological competition, whereas an alternative possibility is that signals of dominance or aggression may instead converge to facilitate coexistence among ecological competitors. Although this counter-intuitive process--termed convergent agonistic character displacement--is supported by recent theoretical and empirical studies, the extent to which it drives spatial patterns of trait evolution at continental scales remains unclear. By modeling variation in song structure of two ecologically similar species of Hypocnemis antbird across western Amazonia, we show that their territorial signals converge such that trait similarity peaks in the sympatric zone, where intense interspecific territoriality between these taxa has previously been demonstrated. We also use remote sensing data to show that signal convergence is not explained by environmental gradients and is thus unlikely to evolve by sensory drive (i.e. acoustic adaptation to the sound transmission properties of habitats). Our results suggest that agonistic character displacement driven by interspecific competition can generate spatial patterns opposite to those predicted by classic character displacement theory, and highlight the potential role of social selection in shaping geographical variation in signal phenotypes of ecological competitors.

evolutionary biology↗

bioRxiv2026

Homologous ABA-independent kinase tracks coalesced into osmotic stress circuits during plant terrestrialization

Land plants possess a unique system for responding to environmental stressors. How this system evolved during plant terrestrialization remains one of the major questions in plant evolutionary biology. To retrace this process, it is essential to study both land plants and their closest algal relatives, the zygnematophytes. Using the single-celled zygnematophyte Mesotaenium, we integrated physiological stress experiments with phosphoproteomics, genome-wide transcription factor binding analyses, and protein-protein interaction studies to investigate the architecture of a key stress response pathway: the signaling cascade homologous to the plant abscisic acid (ABA)-mediated pathway. Our results highlight the roles of histidine kinases (HKs) and calcium-dependent protein kinases (CDPKs) in osmotic stress signaling. Focusing on SnRK2 and ABF, key components at the downstream end of the canonical ABA signaling pathway, we provide evidence that ABF plays a central role in osmotic stress responses even in the absence of ABA. Together, our data reveal the coordinated action of parallel functional modules that were likely integrated into the ABA response cascade during plant terrestrialization.

evolutionary biology↗

bioRxiv2021

Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

Understanding the genetic mechanisms leading to new traits is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different stickleback fish species to alter the length and number of bony dorsal spines. In Gasterosteus aculeatus, a variant HOXDB allele is genetically linked to shortening an existing spine and adding a spine. In Apeltes quadracus, a variant allele is associated with lengthening an existing spine and adding a spine. The alleles alter the same conserved non-coding HOXDB enhancer by diverse molecular mechanisms, including SNPs, deletions, and transposable element insertions. The independent cis-acting regulatory changes are linked to anterior expansion or contraction of HOXDB expression. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key morphological patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/472698v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@8e6675org.highwire.dtl.DTLVardef@e89e13org.highwire.dtl.DTLVardef@1e1f1dcorg.highwire.dtl.DTLVardef@cdb6f8_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2022

Geographic variability of hybridization between Red-breasted and Red-naped Sapsuckers

Hybrid zones reveal the strength of reproductive isolation between populations undergoing speciation and are thus a key tool used in evolutionary biology research. Multiple replicate transects across the same hybrid zone offer further insight into the dynamics of hybridization in different environments, clarifying the role of extrinsic forces on the speciation process. Red-breasted and Red-naped Sapsuckers (Sphyrapicus ruber and S. nuchalis) have a long zone of contact over approximately 1,600 km from central British Columbia, Canada to central California, USA. We compared Genotyping-by-Sequencing data from three independent sapsucker hybrid zone transects to compare hybridization dynamics between the same species under variable geoclimatic conditions. We then generated geographic clines of the genomic data to compare hybrid zone widths and used Random Forest models and linear regression to assess the relationship between climate and sapsucker ancestry along each transect. Our results show variation in symmetry and directionality of back crossing, patterns often indicative of moving hybrid zones. We note variable cline widths among transects, indicating differences in the selection maintaining hybrid zone dynamics. Furthermore, Random Forest models identified different variables in close association with sapsucker ancestry across each transect. These results indicate a lack of repeatability across replicate transects and a strong influence of the local environment on hybrid zone dynamics.

evolutionary biology↗

bioRxiv2021

Genomic insights into variation in thermotolerance between hybridizing swordtail fishes

Understanding how organisms adapt to changing environments is a core focus of research in evolutionary biology. One common mechanism is adaptive introgression, which has received increasing attention as a potential route to rapid adaptation in populations struggling in the face of ecological change, particularly global climate change. However, hybridization can also result in deleterious genetic interactions that may limit the benefits of adaptive introgression. Here, we used a combination of genome-wide quantitative trait locus mapping and differential gene expression analyses between the swordtail fish species Xiphophorus malinche and X. birchmanni to study the consequences of hybridization on thermotolerance. While these two species are adapted to different thermal environments, we document a complicated architecture of thermotolerance in hybrids. We identify a region of the genome that contributes to reduced thermotolerance in individuals heterozygous for X. malinche and X. birchmanni ancestry, as well as widespread misexpression in hybrids of genes that respond to thermal stress in the parental species, particularly in the circadian clock pathway. We also show that a previously mapped hybrid incompatibility between X. malinche and X. birchmanni contributes to reduced thermotolerance in hybrids. Together, our results highlight the challenges of understanding the impact of hybridization on complex ecological traits and its potential impact on adaptive introgression.

evolutionary biology↗

bioRxiv2025

Ancient origin of an urban underground mosquito

Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. Here we investigate a widely cited example of urban adaptation, Culex pipiens form molestus, also known as the London Underground Mosquito. Population genomic analysis of [~]350 contemporary and historical samples counter the popular hypothesis that molestus originated belowground in London less than 200 years ago. Instead, we show that molestus first adapted to human environments aboveground in the Middle East over the course of >1000 years, likely in concert with the rise of agricultural civilizations. Our results highlight the role of early human society in priming taxa for contemporary urban evolution and have important implications for understanding arbovirus transmission.

evolutionary biology↗

bioRxiv2026

Genomic signatures of reproductive isolation are decoupled from floral divergence in a long-standing hybrid zone

A central goal in evolutionary biology is to understand how species boundaries are maintained despite gene flow. Two North American wildflower species with divergent floral syndromes, Penstemon davidsonii (bee syndrome) and P. newberryi (bird syndrome), have formed hybrid zones in the eastern Sierra Nevada for at least 85 years. We combined multiple approaches to test whether divergent floral syndromes enforce reproductive isolation as predicted by classic models of pollinator-driven ecological speciation. The two parent species exhibited strong divergence across multivariate trait space and have maintained genomic differentiation despite persistent hybridization. Floral hue, a key component of pollination syndrome, mapped to a single genomic region containing two candidate genes with large effects on anthocyanin pigment composition. Pollinator visual models indicated that genetic variation at this region affects detectability to hummingbirds, but not bees. Genomic cline analyses identified many significantly steep clines, suggesting a polygenic basis to reproductive isolation. Surprisingly, these barriers appear unrelated to floral isolation; the major floral hue locus exhibits a strikingly shallow genomic cline and elevated heterozygosity, suggesting pervasive gene flow. Our results reveal that conspicuous trait divergence can be decoupled from reproductive barriers, challenging assumptions about how reproductive isolation is maintained in hybridizing populations.

evolutionary biology↗

bioRxiv2024

Plant hormone manipulation impacts salt spray tolerance, which preempts herbivory as a driver of local adaptation in the yellow monkeyflower, Mimulus guttatus

A major challenge in evolutionary biology is identifying the selective agents and phenotypes underlying local adaptation. Local adaptation along environmental gradients may be driven by trade-offs in allocation to reproduction, growth, and herbivore resistance. To identify environmental agents of selection and their phenotypic targets, we performed a manipulative field reciprocal transplant experiment with coastal perennial and inland annual ecotypes of the common yellow monkeyflower (Mimulus guttatus). We manipulated herbivory with exclosures built in the field and exogenously manipulated gibberellin and jasmonic acid to shift allocation of plant resources among growth, reproduction, and herbivore resistance. Our hormone treatments influenced the timing of allocation to reproduction and allocation to phytochemical defense, but this shift was small relative to ecotype differences in allocation. Herbivore exclosures reduced herbivory and increased fitness of plants at the coastal site. However, this reduction in herbivory did not decrease the homesite advantage of coastal perennials. Unexpectedly, we found that the application of exogenous gibberellin increased mortality due to salt spray at the coastal site for both ecotypes. Our results suggest that divergence in salt spray tolerance, potentially mediated by ecotype differences in gibberellin synthesis or bioactivity, is a strong driver of local adaptation and preempts any impacts of herbivory in coastal habitats that experience salt spray.

evolutionary biology↗

bioRxiv2026

Genomic and phenotypic consequences of long-term isolation and small population size in Yakushima macaques

The relative roles of genetic drift, inbreeding, and natural selection in island evolution have been fundamental themes in evolutionary biology for nearly a century. However, empirical studies have yet to reach a consensus, and research integrating both genotypes and phenotypes in primates remains limited. The present study aims to estimate the demographic history of an island primate population, the Yakushima macaque (Macaca fuscata yakui), and evaluate the genomic and morphological consequences of its isolation. To this end, we conducted population genetic analyses based on whole-genome sequencing and geometric morphometric analyses of cranial shape. Our results indicate that M. f. yakui has been isolated with an effective population size of several thousand individuals for over 100,000 years. Although we detected signatures of purifying selection, deleterious alleles have not been sufficiently purged. The degree of fluctuating asymmetry in males was slightly, yet significantly, higher in M. f. yakui than in mainland populations, whereas this trend was not observed in females. Marginal evidence of directional selection was found for cranial size, but not for shape. Overall, our findings suggest that due to long-term isolation, genetic drift and inbreeding have exerted a substantial influence on shaping genotypic and phenotypic variation in this island population.

evolutionary biology↗

bioRxiv2023

Competition-driven eco-evolutionary feedback reshapes bacteriophage lambda's fitness landscape and enables speciation

A major challenge in evolutionary biology is explaining how populations navigate rugged fitness landscapes without getting trapped on local optima. One idea illustrated by adaptive dynamics theory is that as populations adapt, their newly enhanced capacities to exploit resources alter fitness payoffs and restructure the landscape in ways that promote speciation by opening new adaptive pathways. While there have been indirect tests of this theory, none have measured how fitness landscapes deform during adaptation, or test whether these shifts promote diversification. Here, we achieve this by studying bacteriophage , a virus that readily speciates into co-existing receptor specialists under controlled laboratory conditions. We used a high-throughput gene editing-phenotyping technology to measure s fitness landscape in the presence of different evolved- competitors and found that the fitness effects of individual mutations, and their epistatic interactions, depend on the competitor. Using these empirical data, we simulated s evolution on an un-changing landscape and one that recapitulates how the landscape deforms during evolution. heterogeneity only evolved in the shifting landscape regime. This study provides a test of adaptive dynamics, and, more broadly, shows how fitness landscapes dynamically change during adaptation, potentiating phenomena like speciation by opening new adaptive pathways.

evolutionary biology↗