Biology subjects

Schwander, T.

Publications and source records attributed to Schwander, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Drivers of tandem repeats variation within and between stick insect genomes

Tandemly repeated sequences are noncoding, highly variable, yet integral components of eukaryotic genomes. Empirical research has so far largely focused on a few well-characterized, functional tandem repeats (TRs) or documented the broad diversity and rapid evolution of these repeats without explicitly testing the forces driving their evolution. By characterizing TR abundance and TR sequence composition within and between chromosomes and species in the stick insect genus Timema, we uncover that TR loads are enriched in genomic regions of high recombination but tend to be reduced in species with higher effective population sizes. These results suggest that there is a mutational effect of recombination that generates increased TR loads and that the bulk of TRs experience weak selection, leading to their rapid turnover over short evolutionary timescales. Finally, comparisons of centromere and non-centromere TRs reveal that the rapid divergence of centromeres is best explained by the combination of the fast-evolving nature of TRs per se and centromere-specific evolutionary forces. Overall, this study provides the first in-depth investigation of genome-wide TR evolution, while integrating the effects of recombination, genetic drift, and centromeric position along the genome.

evolutionary biology↗

bioRxiv2026

Widespread but cryptic introgression shapes genetic diversity in natural populations

Introgression following hybridization is increasingly recognized as a major driver of evolution. However, its importance depends on its frequency in nature, which remains to be quantified. To address this, we provide a snapshot of ongoing introgression in a whole species assemblage (4126 ant colonies). 23% of all 82 local species show signs of introgression, which is more than twice previous estimates. Introgression is typically subtle, yet contributes measurably to genetic diversity. Species divergence, rather than classical prezygotic reproductive barriers (mating phenology, ecological niche, fine-scale habitat use) constrains introgression, suggesting that the main reproductive barriers are postzygotic at this stage of divergence. Our results indicate that introgression may be a common but often overlooked feature of natural communities.

evolutionary biology↗

bioRxiv2026

Wolbachia facilitates the reproduction of a parthenogenetic ladybug

Wolbachia is a bacterial endosymbiont that is primarily transmitted from mother to offspring. To increase their transmission, some strains manipulate their hosts reproduction to favor female offspring, such as by inducing parthenogenesis. Here, we assess whether Wolbachia induces parthenogenesis in recently discovered parthenogenetic populations of the ladybug Nephus voeltzkowi by treating females with an antibiotic. Females from sexual populations, which we show are not infected by Wolbachia, serve as a control. Our results demonstrate that the treatment decreases Wolbachia load, subsequently reducing egg production and development among parthenogenetic females, while having no effect on sexual females. Wolbachia load and reproduction then rebound when the treatment is removed. This suggests that the Wolbachia infection is necessary for successful reproduction in the parthenogenetic females, and it may play a two-part role by facilitating egg laying and late embryo development. The cooccurrence of Wolbachia infection and parthenogenesis in N. voeltzkowi, as well as Wolbachias manipulation of host reproduction makes this a likely candidate of Wolbachia-induced parthenogenesis outside of haplo-diploids. Understanding how Wolbachia can impact diverse insect reproductive systems can shed a light on the extent in which these bacteria can manipulate hosts for their own gain.

evolutionary biology↗

bioRxiv2026

Alternative splicing shapes sexual dimorphism and erodes following the loss of sex in stick insects

Sexually dimorphic traits emerge from divergent selective pressures acting on males and females and are facilitated by gene regulatory mechanisms. While gene expression differences have been the subject of considerable focus in the evolution of sexual dimorphism, other regulatory processes remain comparatively understudied. One such mechanism is alternative splicing, whereby a single gene can encode multiple distinct transcripts, which can lead to functional diversification of the proteome. Leveraging long-read PacBio Iso-sequencing, we examine patterns of sex differences in gene expression and alternative splicing under different selection regimes. Alternative splicing is widespread in Timema, with the greatest isoform complexity found in the male gonad tissue. We observe similar rates of sex differences in gene expression and splicing, and a core set of genes involved in sexual differentiation and germline development that have conserved differential splicing patterns across the Timema phylogeny. Beyond this, however, differentially spliced genes undergo faster lineage-specific turnover and are subject to greater pleiotropic and purifying constraints than differentially expressed genes. Following the transition from sexual reproduction to asexuality, there is a systematic reduction in isoform diversity and erosion of sex-specific splicing variation. Taken together, our findings suggest a role for sexual selection in maintaining splicing complexity in sexual Timema species.

evolutionary biology↗

bioRxiv2025

Feminization of sex-biased gene expression in a parthenogenetic stick insect suggests unresolved sexual antagonism in early development

Sexual antagonism arises when males and females experience opposing selection on traits controlled by shared genetic architectures. For gene expression, such conflicts are typically resolved through the evolution of sex-biased regulation. Although sexual antagonism is often assumed to peak in adults, its developmental dynamics remain poorly understood. We investigated the ontogeny of sex-biased gene expression in the sexual stick insect Timema poppense and contrasted it with its parthenogenetic sister species to identify signatures of unresolved antagonism. Using RNA-seq across somatic tissues (brain, gut, legs, antennae) and reproductive tracts throughout post-embryonic development, we found that sex-biased expression in T. poppense is limited in somatic tissues but extensive in reproductive tracts from the earliest stages. Nearly half of the expressed genes are already sex-biased in first-instar gonads, with male- and female-biased genes largely stage-specific. Parthenogenetic females show masculinized expression in somatic tissues throughout development and in adult reproductive tracts, consistent with decay of sexual traits in the absence of mating. By contrast, they show feminized early gonadal expression, likely reflecting unresolved antagonism in the sexual ancestor. Our results reveal the ontogeny of sexual dimorphism in a hemimetabolous insect and suggest that focusing solely on adults underestimates the prevalence of unresolved sexual antagonism.

evolutionary biology↗

bioRxiv2025

Hybridogenesis as an intermediate step between sexual reproduction and parthenogenesis

Many organisms reproduce through non-canonical modes such as parthenogenesis or hybridogenesis (clonal transmission of one parents chromosomes), but whether these arise abruptly or stepwise from each other remains unclear. We address this in the stick-insect genus Bacillus, which harbors several hybrid lineages with diverse reproductive modes. From haplotype-resolved phylogenies of >500 wild-caught individuals, we infer a single, recent ([~]8,000 years) origin of all hybrids. The ancestral hybrid reproduced via hybridogenesis, which subsequently diversified into parthenogenesis and, twice independently, into triploid lineages. Laboratory crosses recapitulate this trajectory, where each step facilitated the next. These findings reveal how a single genomic perturbation can act as a catalyst for evolutionary innovation, turning the loss of sex into a driver of diversification rather than a dead end.

evolutionary biology↗

bioRxiv2025

Dosage compensation and meiotic sex chromosome inactivation are maintained in the absence of selection

Dosage compensation and meiotic sex chromosome inactivation (MSCI) are key mechanisms regulating gene expression from the X chromosome in male-heterogametic species. While the convergent evolution of these mechanisms is well-documented, their evolutionary fate under relaxed selection remains poorly understood. Here, we test whether dosage compensation and MSCI persist following three independent transitions to parthenogenesis in stick insects, where selection on male phenotypes is relaxed. Using rare males occasionally produced by parthenogenetic females, chromosome-level genome assemblies, RNA-seq from multiple tissues, and immunocytochemistry, we find that dosage compensation is fully conserved across all nine studied somatic tissues. This is even the case in the oldest, approximately 1.5 million years old all-female lineage, and for tissue-specific genes for which dosage variation is not expected to be very deleterious. Meiotic X inactivation in the germline is also conserved. Surprisingly however, expression data and cytological markers indicate that MSCI signatures are even stronger in parthenogenetic males, a pattern likely driven by prolonged autosomal transcription during meiosis. These results indicate that X-targeting dosage compensation and MSCI are highly stable over evolutionary time and may be maintained in all-female lineages by a combination of evolutionary constraint, pleiotropy, or very weak selection, whereas autosomal expression during meiosis shifts rapidly under relaxed selection. Significance StatementSex chromosomes are regulated by specialized mechanisms that balance gene expression between males and females in somatic tissues (dosage compensation) and silence the X chromosome during male meiosis (meiotic sex chromosome inactivation, MSCI). These processes are thought to decay when they become redundant, yet suitable systems to test this prediction are scarce. We studied rare males from parthenogenetic stick insect lineages that have been evolving without sex for up to 1.5 million years. Surprisingly, both dosage compensation and MSCI remain fully functional, despite relaxed selection. Instead, we find altered autosomal expression during meiosis. Our results reveal that sex chromosome regulation is evolutionarily stable and constrained, persisting even after the loss of its purpose.

evolutionary biology↗

bioRxiv2025

Convergent Evolution of H4K16ac-mediated Dosage Compensation Shapes Sex-dependent Lifespan in a ZW Species

Sex chromosomes impact chromatin organization and histone modification dynamics differently between males and females, particularly those involved in dosage compensation (DC). The stability of DC mechanisms may shape sex-specific phenotypes and traits such as lifespan. However, the tissue- and age-dependent variations as well as the evolutionary diversity of DC mechanisms are incompletely understood. Here, we investigate the occurrence of histone H4 lysine 16 acetylation (H4K16ac), previously known for its role in sex chromosome DC in the male-heterogametic fruit fly Drosophila melanogaster and the green anole lizard Anolis carolinensis. By sampling multiple arthropods, we find the convergent evolution of H4K16ac for DC in a female-heterogametic (ZW) species, the crustacean Artemia franciscana. CUT&Tag analysis demonstrates that H4K16ac is confined to the non-recombining stratum of the Z chromosome in females. H4K16ac-mediated DC is established during embryogenesis, sustained until adulthood, but then becomes reconfigured and variable in aged females. Interfering with acetylation alleviates male-female differences in lifespan. Our findings shed light on the evolutionary diversity of DC across species. They highlight histone acetylation as a sex-specific vulnerability linked to the chromatin landscape of sex chromosomes and its potential role in driving male-female differences.

evolutionary biology↗

bioRxiv2024

Do morphologically distinct groups correspond to reproductively isolated species? A case study in Myrmica ants from Switzerland

The most widely used definition of a species is that it is reproductively isolated from other populations. Yet, most species are described on the basis of morphological criteria, and reproductive isolation is seldom tested. Using the ant genus Myrmica Latreille (Hymenoptera, Formicidae) as a model, we ask whether species described as distinct based on (often subtle) morphological differences indeed form reproductively isolated lineages. We collected and morphologically identified 918 Myrmica ants from a 3212 km2 area in Switzerland. We then combined DNA barcoding (based on COI) and RAD sequencing to identify genetically isolated lineages. Out of the 14 morphological species identified, 13 formed genetically differentiated lineages, while the last one was not supported by our genetic data. Overall, the morphological identification was congruent with genetic lineage delineation for 94.9% of individuals. Our dataset also allowed us to screen for cryptic lineages in the five most frequent species, including in M. scabrinodis where cryptic lineages were previously suggested, but we found no evidence for cryptic species. Overall, our results indicate that morphology parallels genetic isolation in the studied species. However, an integrative approach combining morphological identification with nuclear marker genotyping is necessary for confident species identification of all individuals. Finally, our results provide a library of validated COI barcodes for future Myrmica specimen identification.

evolutionary biology↗

bioRxiv2024

Decontaminating genomic data for accurate species delineation and hybrid detection in the Lasius ant genus

Advancements in genetic technologies have allowed us to generate large data sets relatively quickly and easily. However, without proper quality control checks, the inferences drawn from such data can be erroneous and go on to misinform further studies. DNA contamination between focal samples of the same or closely related species can have major impacts on downstream analyses, but their presence is seldom tested. Here, we created a pipeline combining competitive mapping to remove reads from intergeneric contamination, followed by a filtering method using allelic depth ratio frequencies to exclude intrageneric contamination. We then used a RADseq dataset of over 1,000 Swiss Lasius ants that were cross contaminated to various levels prior to sequencing to assess the impact of contamination on inferences of introgression. The original dataset presented widespread introgression between species in which hybridization has never been recorded. After thorough decontamination, we found only one individual with a strong signature of introgression, between the species L. emarginatus and L. platythorax, revealing that introgression is extremely rare in this genus. Implementing our method of filtering can significantly improve the robustness of biological findings based on genomic datasets. We recommend that systematically checking for the presence of cross contamination should be a key step in the preprocessing of genomic datasets.

genomics↗

bioRxiv2024

Dynamics of recombination, X inactivation and centromere proteins during stick insect spermatogenesis

In eukaryotes, the cellular processes contributing to gamete formation form the building blocks of genetic inheritance across generations. While traditionally viewed as conserved across model organisms, emerging studies reveal significant variation in meiotic and post-meiotic processes. Extending our knowledge to non-model organisms is therefore critical to improve our understanding of the evolutionary origin and significance of modifications associated with gamete formation. We describe the cytological patterns underlying chromosome segregation, recombination, and meiotic sex chromosome inactivation during male meiosis in the stick insect group Timema. Our results provide a detailed description of centromere protein loading dynamics during spermatogenesis, and further reveal that 1) recombination initiates before synapsis (unlike Drosophila meiosis), and 2) that the X remains actively silenced despite two waves of transcriptional activation in autosomes during spermatogenesis. Together, our observations help understand the evolutionary significance of key cellular events related to spermatogenesis and shed light on the diversity of their associated molecular processes among species, including Timema stick insects.

cell biology↗

bioRxiv2024

Dynamics of X chromosome hyper-expression and inactivation in male tissues during stick insect development

Differentiated sex chromosomes are frequently associated with major transcriptional changes: the evolution of dosage compensation (DC) to equalize gene expression between the sexes and the establishment of meiotic sex chromosome inactivation (MSCI). Our study investigates the mechanisms and developmental dynamics of dosage compensation and meiotic sex chromosome inactivation in the stick insect species T. poppense. Stick insects are characterized by XX/XO sex determination and an X chromosome which likely evolved prior to the diversification of insects over 450 Mya. We generated a chromosome-level genome assembly and analyzed gene expression from various tissues (brain, gut, antennae, leg, and reproductive tract) across developmental stages in both sexes. Our results show that complete dosage compensation is maintained in male somatic tissues throughout development, mediated by upregulation of the single X chromosome. Contrarily, in male reproductive tissues, dosage compensation is present only in the early nymphal stages. As males reach the 4th nymphal stage and adulthood, X-linked gene expression diminishes, coinciding with the onset of MSCI. This reduction is associated with histone modifications indicative of transcriptional silencing, aligning with meiotic progression. These findings reveal the dynamic regulation of X-linked gene expression in T. poppense, and suggest that reduced X-expression in insect testes is generally driven by MSCI rather than an absence of dosage compensation mechanisms. Our work provides critical insights into sex chromosome evolution and the complex interplay of dosage compensation and MSCI across tissues and developmental stages.

evolutionary biology↗

bioRxiv2024

Functional monocentricity with holocentric characteristics andchromosome-specific centromeres in a stick insect

Centromeres are specialized genomic regions that are critical for chromosome segregation in eukaryotes. However, how the diversity of centromeres evolved, ranging from localized centromeres in monocentric species to complex chromosome-wide distributed centromere regions in holocentric species, remains elusive. Our cellular and genomic analyses in Timema stick insects reveal that within cell variation of the major centromere protein CenH3 recapitulates the variation typically observed across species. While CenH3-containing nucleosomes are distributed in a monocentric fashion on autosomes and bind tandem repeat sequences specific to individual or small groups of chromosomes, they exhibit a holocentric-like distribution on the sex chromosome and bind to more complex intergenic regions. Despite this contrasting distribution, all chromosomes, including the sex chromosome, attach to spindle microtubules at a single location, marking the first instance of a functionally monocentric species with holocentric-like attributes. Together, our findings highlight the potential for gradual transitions towards holocentricity or CenH3-independent centromere determination, and help to understand the rapid centromere sequence divergence between species.

evolutionary biology↗

bioRxiv2024

Recent neo-X and Y sex chromosomes in an ant cricket

In eukaryotes with separate sexes, sex determination often involves heteromorphic sex chromosomes which have diverged as a consequence of recombination suppression. In species with very old heteromorphic sex chromosomes, mechanisms such as dosage compensation and meiotic sex chromosome inactivation adjust for the fact that sex chromosomes occur as a single copy in the heterogametic sex. However, how such mechanisms evolve remains largely unknown because species with young sex chromosomes characterised by recent recombination suppression remain understudied. We discovered such young neo-sex chromosomes in the ant cricket Myrmecophilus myrmecophilus, which displays a neo-XY system. We generated a chromosomal-level assembly of the female genome and compared it to male genomic data and identified four evolutionary strata on the X, with varying degrees of Y chromosome degeneration. Phylogenetic studies and genomic comparisons with closely related species revealed two cases of taxonomic synonymies and that the Myrmecophilus neo-sex chromosomes likely evolved approximately 7 million years ago from an X-autosome fusion. The X strata subsequently emerged as a consequence of two localised events of recombination suppression. Ant crickets thus represent a promising new model for studying the early stages of sex chromosome degeneration and the establishment of processes such as dosage compensation or meiotic sex chromosome inactivation.

evolutionary biology↗

bioRxiv2024

LEVERAGING CITIZEN SCIENCE TO ASSESS RICHNESS, DIVERSITY, AND ABUNDANCE IN ANT COMMUNITIES

AO_SCPLOWBSTRACTC_SCPLOWCitizen science is a key resource in overcoming the logistical challenges of monitoring biodiversity. While datasets collected by groups of volunteers typically have biases, recent methodological and technological advances provide approaches for accounting for such biases, particularly in the context of modelling species distributions and diversity. Specifically, data integration techniques allow for the combination of scientifically collected datasets with haphazardly sampled presence-only datasets created by most citizen science initiatives. Here, we use a hierarchical Bayesian framework to integrate a set of ant presences collected by citizen scientists in the Vaud canton (Switzerland) with ant colony density data collected concurrently in the same region following a scientific sampling design. The community-level Poisson point process model included species-specific responses to the local (1.2 m2) and regional (1 km2) environment, with the presence-only samples incorporated at the regional scale to predict local and regional ant communities. At the regional scale, species richness followed a hump-shaped pattern and peaked near 1000 m while abundance increased with elevation. Low elevation and montane ant communities were composed of distinct species assemblages. At the local scale, the link between elevation and richness, diversity, and abundance was weak. At low elevations, local plots varied both in total abundance and species composition, while at higher elevations, the species composition was less variable. The citizen science dataset showed a general tendency toward under-representation of certain species, and heavy spatial sampling bias. Nonetheless, the inclusion of the citizen science data improved predictions of local communities, and also reduced susceptibility to over-fitting. Additionally, the citizen science dataset included many rare species not detected in the structured abundance dataset. The model described here illustrates a framework for capitalizing on the efforts of citizen scientists to better understand the patterns and distribution of biodiversity.

ecology↗

bioRxiv2023

Ecological specialization and local adaptation in sympatric sexual and asexual grass thrips species

The maintenance of sex is difficult to explain in the face of the demographic advantages of asexuality, especially when sexual and asexual lineages co-occur and compete. Here, we test if niche divergence and specialization can contribute to the maintenance of sympatric populations of two closely related, sexual and asexual Aptinothrips grass thrips species. In mesocosm experiments, ecological niches and ecological specialization were inferred from thrips performances on different grass species used as hosts in natural populations. Sexual and asexual thrips performed best on different grass hosts, indicating niche differentiation. The asexual species was also characterized by a broader fundamental ecological niche than the sexual one. However, niche differentiation is unlikely to explain the maintenance of the two species in sympatry because the reproductive rate of asexual females generally exceeded that of sexual ones. Surprisingly, the asexual but not sexual species showed geographic variation in the fundamental niche. This geographic variation likely stems from different clonal assemblages at different locations because different asexual genotypes have different ecological niches. Across natural populations, the performance of asexual females on a specific grass species was further positively correlated with the frequency of that grass species, consistent with adaptation to locally abundant grasses. Altogether, our results suggest that niche differentiation contributes little to the maintenance of grass thrips species with different reproductive modes and that asexuality facilitates adaptation to a diversity of co-occurring host plants.

evolutionary biology↗

bioRxiv2023

Evolution of alternative reproductive systems in Bacillus stick insects

Reproduction is a key feature of all organisms, yet the way in which it is achieved varies greatly across the tree of life. One striking example of this variation is the stick insect genus Bacillus, in which five different reproductive modes have been described: sex, facultative and obligate parthenogenesis, and two highly unusual reproductive modes: hybridogenesis and androgenesis. Under hybridogenesis, the entire genome from the paternal species is eliminated, and replaced each generation by mating with the corresponding species. Under androgenesis, an egg is fertilized but the developing diploid offspring bear two paternal genomes, and no maternal genome, as a consequence of unknown mechanisms. Here, we re-evaluate previous descriptions of Bacillus lineages and the proposed F1 hybrid ancestries of the hybridogenetic and obligately parthenogenetic lineages (based on allozymes and karyotypes) from Sicily, where all these reproductive modes are found. We generate a chromosome-level genome assembly for a facultative parthenogenetic species (B. rossius) and combine extensive field sampling with RADseq and mtDNA data. We identify and genetically corroborate all previously described species and confirm the ancestry of hybrid lineages. All hybrid lineages have fully retained their F1 hybrid constitution throughout the genome, indicating that the elimination of the paternal genome in hybridogens is always complete and that obligate parthenogenesis in Bacillus hybrid species is not associated with an erosion of heterozygosity as known in other hybrid asexuals. Our results provide a stepping stone towards understanding the transitions between reproductive modes and the proximate mechanisms of genome elimination.

evolutionary biology↗

bioRxiv2023

Trophic eggs affect caste determination in the ant Pogonomyrmex rugosus

Understanding how a single genome creates distinct phenotypes remains a fundamental challenge for biologists. Social insects provide a striking example of polyphenism, with queen and worker castes exhibiting morphological, behavioural, and reproductive differences. Here we show that trophic eggs, which do not contain an embryo and are primarily regarded as a source of food, play a role in the process of caste determination in the harvester ant Pogonomyrmex rugosus. When first instar larvae were given access to trophic eggs, they mostly developed into workers. By contrast, larvae without access to trophic eggs developed into queens. We found that trophic eggs differ in many ways from viable eggs, including texture, morphology and their contents of protein, triglycerides, glycogen, sugar and small RNAs. Moreover, comparison of miRNA fragment size distributions suggests differences in the composition of miRNAs between the two egg types. This is the first demonstration of trophic eggs playing a role in caste determination in social insects.

evolutionary biology↗