Biology subjects

Cutter, A. D.

Publications and source records attributed to Cutter, A. D..

At least 19 recordsLinked to original sources

bioRxiv2026

Gene regulatory divergence underlies tissue-specific and sex-specific misexpression in interspecies nematode hybrids

Gene regulatory divergence has emerged as a key feature in speciation, influencing gene expression differences that accumulate between diverging populations. Transcriptional regulation, mediated by cis- and trans-acting factors, modulates diverse developmental processes and is responsible for distinct species-specific gene expression profiles. Within interspecies hybrid individuals, negative interactions between divergent cis- and trans-acting factors can lead to gene misregulation and hybrid dysfunction at the organismal level. Such gene regulatory mismatch might disproportionately impact sex-biased and tissue-biased gene regulatory networks due to their unique selective pressures. To address these issues, we investigated the role of regulatory divergence in asymmetric hybrid incompatibility between sister species of Caenorhabditis nematodes (C. remanei, C. latens) by analyzing gene expression of reciprocal hybrids for each sex and key tissue types. Despite severe hybrid male sterility, hybrid males showed less misexpression of sex-biased genes than hybrid females, suggesting that the organismal phenotypic outputs of male-biased gene regulatory networks are more vulnerable to disruption than female-biased genetic networks. Additionally, we found more genes associated with cis- than trans-regulatory divergence, supporting the notion of a disproportionate role for cis-regulatory divergence between species. Moreover, we document extensive cis-trans compensatory X-linked regulatory divergence specifically from male transcriptomes, indicating distinct molecular evolutionary outcomes of stabilizing selection on regulatory controls in males and females. These insights derived from asymmetric hybrid misexpression expand our understanding of the evolution sex-biased gene regulation in the face of stabilizing selection and identify candidate genes contributing to Caenorhabditis post-zygotic reproductive isolation.

evolutionary biology↗

bioRxiv2026

Global genomic diversity of the selfing nematode Caenorhabditis tropicalis correlates with geography

Self-fertilization reduces genetic diversity compared to outcrossing and hypothetically decreases the ability to adapt to diverse environments. Among Caenorhabditis nematodes, self-fertilization evolved three times independently in Caenorhabditis elegans, Caenorhabditis briggsae, and the more recently discovered Caenorhabditis tropicalis. To survey C. tropicalis genetic relatedness, the influence of geography and niche on species-wide variation, and the signatures of selection, we collected 785 wild strains, sequenced their genomes, and identified 622 distinct genotypes (isotypes). In contrast to C. elegans and C. briggsae, C. tropicalis relatedness shows substantial association with geography and no transcontinental selective sweeps or broadly sampled isotypes. Populations from the Hawaiian Islands or Taiwan harbor more genetic variation than populations from the Caribbean or Americas, suggesting a Pacific species origin similar to other members of the Elegans subclade. Punctuated genomic regions of extreme genetic variation pervade the genome. These hyper-divergent regions (HDRs) comprise less than 6% of the reference genome in any given strain despite harboring 73% of all variant sites and are enriched for genes likely involved in environmental adaptation. HDRs represent a shared genomic feature of self-fertilizing Caenorhabditis nematodes despite their independent evolutionary origins and suggest a mechanism to explain worldwide distributions despite low species-wide levels of genetic variation.

genomics↗

bioRxiv2025

Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes

Comparative genomics provides a powerful framework to uncover the molecular and evolutionary mechanisms that shape genetic diversity within and across species, revealing how shared and lineage-specific processes influence their evolutionary trajectories through time. The nematode Caenorhabditis briggsae is distributed world-wide and is a comparative model to Caenorhabditis elegans in the biology of development, cellular mechanisms, neurobiology, genetic mappings of complex traits, and genome evolution. Following massive collection efforts by the nematode research community, we present the isolation of over 2,000 wild strains and analyses of genome sequences that catalog over six million single-nucleotide and insertion-deletion variants. This genome and strain resource provide a powerful means to interrogate the causal genetic bases of phenotypic variation for diverse traits. Additionally, we describe its global population structure and discover new and genetically distinct groups within this primarily self-fertilizing species, including groups of highly related strains that were sampled across different continents. We leverage expansive genetic variation to decipher the effects of linkage and selection on the distribution of genetic diversity across the genome and across geographic regions. Within the species, we find genomic regions with extremely high levels of genetic variation similar to hyper-divergent regions found in C. elegans and other species. These regions harbor new genes and variation enriched for environmental sensing and pathogen responses. In comparison to the outbreeding sister species Caenorhabditis nigoni, we conclude that long-term balancing selection has maintained substantial functional variation since the divergence from their outbreeding ancestor, likely in response to differences in the ecological niche. Overall, this massive strain resource enables future comparative genetics and genomics studies, including genome-wide association studies between Caenorhabditis species.

genomics↗

bioRxiv2025

An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal

Introns play a critical role in regulating alternative splicing. However, identifying functional intronic motifs is challenging due to their short and degenerate sequence composition. Massively parallel reporter assays have provided insights into cis-regulatory logic governing alternative splicing, but these approaches are generally performed in cell culture, limiting their ability to capture tissue-specific contexts. Here, we implemented in vivo Parallelized Reporter Assays in C. elegans neurons and muscle cells to screen for intronic enhancer and silencer motifs among thousands of randomized sequences. We identified nearly 200 sequences regulating splicing in these tissues. We uncovered core sub-sequences with tissue-biased enhancing and silencing activity, including motifs recognized by well-characterized RNA-binding proteins, and orphan motifs with no obvious cognate binding protein. Mapping our PRA-derived motifs to native introns flanking tissue-biased alternative exons revealed their conservation across nematodes, supporting their functional relevance. Additionally, individual intronic regions frequently contained diverse combinations of these motifs, indicative of complex engagement of these sequences by RNA-binding proteins. Finally, we performed targeted mutagenesis of PRA-derived intronic enhancers flanking a neuronal microexon, identifying key cis-regulatory determinants of microexon splicing. Together, our study provides a framework to explore the role of intronic regions in tissue-specific splicing regulation within a multicellular organism. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/670696v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@84d5daorg.highwire.dtl.DTLVardef@f3f625org.highwire.dtl.DTLVardef@a53739org.highwire.dtl.DTLVardef@ccbb03_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Conserved gene expression plasticity in development is more pervasive than expression divergence between species of Caenorhabditis nematodes

Diverse regulatory mechanisms enable precise spatio-temporal control of gene expression across developmental stages, tissues, and sexes, contributing to the proper development of the organism. Evolutionary divergence leads to species-specific gene expression patterns, even in preserved developmental structures, due to regulatory changes that can disproportionately influence subsets of developmental genetic networks. Here we quantify the evolution of sex-biased and tissue-biased transcriptomes from two tissue types (gonad and soma) for each of two sexes (male and female) from two of the closest known sister species of Caenorhabditis nematodes (C. remanei and C. latens). Differential gene expression and co-expression network analyses identify gene sets with distinct transcriptomic profiles, revealing widespread divergence between these morphologically and developmentally cryptic sister species. The transcriptomic divergence occurs despite most genes showing conserved expression across tissues and sexes. These observations implicate shared selection pressures related to tissue and sex differences as outweighing species-specific selection and developmental system drift in shaping overall transcriptome profiles. Although developmentally-plastic tissue-biased expression profiles are mostly conserved between species, we find that sex-biased genes, particularly male-biased genes, contribute disproportionately to species-differences in gene expression, consistent with a disproportionate role for male-biased selection driving gene expression divergence.

evolutionary biology↗

bioRxiv2025

Phylogenomic timetree-calibrated speciation clocks for Caenorhabditis nematodes reveal slow but disproportionate accumulation of post-zygotic reproductive isolation

Reproductive isolation and genomic divergence both accumulate over time in the formation and persistence of distinct biological species. The pace of "speciation clocks" quantified with pre-zygotic and post-zygotic reproductive isolation, however, differs among taxa, with pre-zygotic isolation tending to evolve sooner in some but not all taxa. To address this issue in nematodes for the first time, here we infer the species tree and divergence times across the phylogeny of 51 species of Caenorhabditis. We incorporate several molecular evolutionary strategies in phylogenomic dating to account for complications in this group due to lack of fossil calibration, deep molecular divergence with synonymous-site saturation, and codon usage bias. By integrating divergence times with experimental data on pre- and post-zygotic reproductive isolation, we infer that post-zygotic isolation accumulates faster than pre-zygotic isolation in Caenorhabditis and that hybrid sterility evolves sooner than hybrid inviability. These findings are consistent with speciation being driven principally by intrinsic isolating barriers and the disproportionate fragility of germline developmental programs to disruption. We estimate that it takes approximately 50 million generations for intrinsic post-zygotic reproductive compatibility to be reduced by half, on average, between diverging pairs of Caenorhabditis. The protracted reproductive isolation clocks in Caenorhabditis may, in part, reflect the capacity to retain population genetic hyperdiversity, the incomplete sampling of global biodiversity, and as-yet uncharacterized incipient or cryptic species.

evolutionary biology↗

bioRxiv2025

Divergent organelle allocation in the evolution of sperm gigantism revealed from subcellular quantification of nematode sperm with electron microscopy

Sperm gigantism evolved multiple times independently among Caenorhabditis nematodes, raising the question of whether intracellular allocation strategies evolved in concert with cell size. Allocation to intracellular components might evolve from direct selection on specific subcellular constituents that affect cell size indirectly, or instead as a byproduct of selection on cell size per se. We used transmission electron microscopy of spermatozoa to quantify investment in pseudopods, mitochondria, and membranous organelles (MOs) from C. macrosperma and C. nouraguensis, related species divergent in sperm size. We demonstrate that C. macrosperma allocates more to mitochondria, in both total and relative terms, consistent with larger sperm cells having greater energetic demands associated with longevity, adhesion, and motility functions. Similar relative pseudopod sizes between species, however, is consistent with an optimal pseudopod:cell body ratio. MO size and distribution patterns within cells implicate C. macrosperma having lower relative investment in MO contributions to seminal fluid, thus excluding increased investment in MOs and pseudopod as drivers of sperm gigantism in C. macrosperma. We conclude that cell size per se likely represents the primary target of selection in the evolution of sperm gigantism, with mitochondrial traits likely evolving as a consequence of increased energetic demands of giant sperm cells.

evolutionary biology↗

bioRxiv2025

A constellation of dysfunctional hybrid phenotypes enforces reproductive isolation between Caenorhabditis nematode species

The evolution of complete reproductive isolation hinges on the cumulative action of reproductive isolating barriers that can manifest throughout the life cycle of an organism. Consequently, a comprehensive understanding of the features underlying the origin and maintenance of species requires assessing the relative contributions of distinct barriers to overall reproductive isolation. Here we characterize multiple interrelated isolating barriers across various developmental stages of nematode sister species Caenorhabditis remanei and Caenorhabditis latens. We quantified F1 hybrid male sterility and characterized multiple phenotypic causes associated with developmental abnormalities in the germline as well as non-germline gonad and somatic tissues, uncovering a complex suite of developmental defects contributing to strong postzygotic reproductive isolation. Despite these multifarious isolating barrier traits, assays testing for interspecies sperm transfer under "choice" conditions did not yield evidence of premating isolation. In contrast to other Caenorhabditis species pairs, we also found no evidence that ectopic sperm migration acts as a postmating-prezygotic barrier. The constellation of phenotypic defects in hybrids points to a polygenic or highly pleiotropic basis for hybrid dysfunction and implicates more rapid evolution of intrinsic postzygotic reproductive isolation than prezygotic isolation in these organisms.

evolutionary biology↗

bioRxiv2024

Dynamic birth and death of Argonaute gene family functional repertoire across Caenorhabditis nematodes

Diverse small RNA pathways, comprised of Argonaute effector proteins and their bound small RNA molecules, define critical systems for regulating gene expression in all domains of life. Some small RNA pathways have undergone significant evolutionary change in nematode roundworms, including gains of novel Argonaute genes and losses of entire pathways. Differences in the functional complement of Argonautes among species therefore profoundly influence the available repertoire of mechanisms for gene regulation. Despite intensive study of Argonaute function in Caenorhabditis elegans, the extent of Argonaute gene family dynamism and functional breadth remains unknown. We therefore comprehensively surveyed Argonautes across 51 Caenorhabditis species, yielding over 1200 genes from 11 subfamilies. We documented multiple cases of diversification, including the birth of a potentially novel Argonaute subfamily and the origin of the ALG-5 microRNA Argonaute near the base of the Caenorhabditis phylogeny, as well as evidence of adaptive sequence evolution and gain of a new splice isoform for CSR-1 in a clade of 31 species. We also detected repeated independent losses of multiple components of the piRNA pathway, mirroring other instances of piRNA pathway loss across the phylum. Gene gain and loss occurs significantly faster than expected within several Argonaute subfamilies, potentially associated with transposable element proliferation coevolving with WAGO-9/10/12 copy number variation. Our characterization of Argonaute diversity across Caenorhabditis demonstrates exceptional functional dynamism in the evolution of gene regulation, with broad implications for mechanisms of control over ontogenetic development and genome integrity. Author SummaryFor organisms to develop properly to survive and reproduce, they must express their genes in the right amount, in the appropriate cell types and time during development. One important mechanism that organisms use to regulate gene expression involves small RNA pathways, where short molecules of RNA serve as targeting guides by binding to Argonaute effector proteins. To understand how small RNA pathways evolve over time, we searched for Argonaute genes throughout the genomes of 51 species of Caenorhabditis nematode worms and found over 1200 Argonaute genes belonging to 11 different Argonaute subfamilies. We then documented cases where species have evolved potentially new types of Argonautes, or new protein isoforms of existing Argonautes. We also identified repeated cases of evolutionary loss of entire Argonaute subfamilies, including for the PRG-1 Argonaute needed in the piRNA regulatory pathway, and characterized how some Argonaute subfamilies gain and lose genes significantly faster than expected. Our findings demonstrate substantial variation in the functional repertoire of Argonaute genes found among Caenorhabditis species, with this evolutionary dynamism implicating fundamental differences between species in how they regulate gene expression across their genomes throughout development.

evolutionary biology↗

bioRxiv2023

Experimental evolution of hybrid populations to identify Dobzhansky-Muller incompatibility loci

Epistatic interactions between loci that reduce fitness in inter-species hybrids, Dobzhansky-Muller incompatibilities (DMIs), contribute genetically to the inviability and infertility within hybrid populations. It remains a challenge, however, to identify the loci that contribute to DMIs as causes of reproductive isolation between species. Here, we assess through forward simulation the power of evolve and resequence experimental evolution of hybrid populations to map DMI loci. We document conditions under which such a mapping strategy may be most feasible and demonstrate how mapping power is sensitive to biologically relevant parameters such as one-way versus two-way incompatibility type, selection strength, recombination rate, and dominance interactions. We also assess the influence of parameters under direct control of an experimenter, including duration of experimental evolution and number of replicate populations. We conclude that an evolve and re-sequence strategy for mapping DMI loci, and other cases of epistasis, can be a viable option under some circumstances for study systems with short generation times like Caenorhabditis nematodes.

evolutionary biology↗

bioRxiv2022

Genetic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes

Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being 10-fold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. Convolutional neural networks demonstrate the potential for classifying distinct evolutionary scenarios in simulated populations. Distinguishing these forces confidently with the empirical data, however, will benefit from larger population genomic samples from multiple populations and consideration of an even more extensive training set of simulations.

evolutionary biology↗

bioRxiv2022

No evidence of sexual conflict for a novel sperm-derived seminal fluid protein in Caenorhabditis nematodes

Nematode sperm contain subcellular vesicles known as membranous organelles (MOs) that fuse with the cell membrane upon sperm activation to release their soluble contents into the extracellular space. The second most abundant proteins in the MOs belong to the conserved Nematode-Specific Peptide family, group F (NSPF) gene family. We hypothesize that these proteins contribute to seminal fluid and are part of post-insemination reproductive tract dynamics. We characterized the anatomical region where the NSPF proteins likely function during fertilization using whole-worm immunostaining of a His-tagged nspf-1 transgene. We confirmed that NSPF proteins are transferred to females during mating. NSPF proteins localize to the uterus lumen when transferred to mated females and in unmated adult hermaphrodites. These results suggest that the uterine localization of the NSPF proteins is likely a functional property of both male-derived sperm and self-sperm and not incidental to the point of transfer during mating. In males, we found that NSPF presence and abundance was correlated with reproductive maturity. We then used experimental evolution to compete the wildtype allele against a deletion allele in 10 replicate obligate-outcrossing populations. We calculated a mean selective disadvantage of 0.1% for the deletion allele, which indicated that the NSPF genes are beneficial to male fitness. This conclusion was reinforced by qualitative trends from lower powered single-generation fertility assays. Together we demonstrate that nematodes use a novel mechanism for generating seminal fluid proteins and show that the highly abundant NSPF proteins likely have a beneficial impact on fitness.

evolutionary biology↗

bioRxiv2022

Regulatory divergence as a mechanism for X-autosome incompatibilities in Caenorhabditis nematodes

The worlds astounding biodiversity results from speciation, the process of formation of distinct species. Hybrids between species often have reduced fitness due to negative epistatic interactions between divergent genetic factors, as each lineage accumulated substitutions independently in their evolutionary history. Such negative genetic interactions can manifest as gene misexpression due to divergence in gene regulatory controls from mutations in cis-regulatory elements and trans-acting factors. Gene misexpression due to differences in regulatory controls can ultimately contribute to incompatibility within hybrids through developmental defects such as sterility and inviability. We sought to quantify the contributions of regulatory divergence to post-zygotic reproductive isolation using sterile interspecies hybrids of two Caenorhabditis nematodes: C. briggsae and C. nigoni. We analysed previous transcriptome profiles for two introgression lines with distinct homozygous X-linked fragments from C. briggsae in a C. nigoni genomic background that confers male sterility, owing to defects in spermatogenesis (Li et al. 2016). Our analysis identified hundreds of genes that show distinct classes of non-additive expression inheritance and regulatory divergence. We find that these non-overlapping introgressions affect many of the same genes in the same way and demonstrate that the preponderance of transgressive gene expression is due to regulatory divergence involving compensatory and joint effects of cis- and trans-acting factors. The similar transcriptomic responses to non-overlapping genetic perturbations of the X-chromosome implicate multiway incompatibilities as an important feature contributing to hybrid male sterility in this system. Significance statementThe genetic causes of intrinsic post-zygotic reproductive isolation can arise from hybrids experiencing negative gene regulatory interactions. In Caenorhabditis nematodes, hybrid male sterility involves X-autosome incompatibilities that affect small-RNA regulatory pathways. We sought to understand the role of gene regulatory divergence as a related contributor to hybrid misexpression by analyzing transcriptomes of sterile males from two hybrid introgression lines, each containing distinct X-linked fragments from C. briggsae in a C. nigoni genomic background. We show that gene misexpression occurs due to extensive joint divergence of cis- and trans-acting regulatory factors and provide evidence for multiway incompatibilities as an important feature of this system.

evolutionary biology↗

bioRxiv2022

Temperature-dependent small RNA expression depends onwild genetic backgrounds of Caenorhabditis briggsae

Geographically distinct populations can adapt to the temperature conditions of their local environment, leading to temperature-dependent fitness differences between populations. Consistent with local adaptation, phylogeographically distinct Caenorhabditis briggsae nematodes show distinct fitness responses to temperature. The genetic mechanisms underlying local adaptation, however, remain unresolved. To investigate the potential role of small noncoding RNAs in genotype-specific responses to temperature, we quantified small RNA expression using high-throughput sequencing of C. briggsae nematodes from tropical and temperate strain genotypes reared under three temperature conditions (14{degrees}C, 20{degrees}C, 30{degrees}C). Strains representing both tropical and temperate regions showed significantly lower expression of PIWI-interacting RNAs (piRNAs) at high temperatures, primarily mapping to a large [~]7 Mb long piRNA cluster on chromosome IV. We also documented decreased expression of 22G-RNAs antisense to protein-coding genes and other genomic features at high rearing temperatures for the thermally-intolerant temperate strain genotype, but not for the tropical strain genotype. Reduced 22G-RNA expression was widespread along chromosomes and among feature types, indicative of a genome-wide response. Targets of the EGO-1/CSR-1 22G-RNA pathway were most strongly impacted compared to other 22G-RNA pathways, implicating the CSR-1 Argonaute and its RNA-dependent RNA polymerase EGO-1 in the genotype-dependent modulation of C. briggsae 22G-RNAs under chronic thermal stress. Our work suggests that gene regulation via small RNAs may be an important contributor to the evolution of local adaptations.

evolutionary biology↗

bioRxiv2021

COMPMAP: an allele-specific expression read-counter based on competitive mapping

SummaryChanges to regulatory sequences account for important phenotypic differences between species and populations. In heterozygote individuals, regulatory polymorphism typically manifests as allele-specific expression (ASE) of transcripts. ASE data from inter-species and inter-population hybrids, in conjunction with expression data from the parents, can be used to infer regulatory changes in cis and trans throughout the genome. Improper data handling, however, can create problems of mapping bias and excessive loss of information, which are prone to arise unintentionally from the cumbersome pipelines with multiple dependencies that are common among current methods. Here, we introduce a new, selfcontained method implemented in Python that generates allele-specific expression counts from genotype-specific map alignments. Rather than assessing individual SNPs, our approach sorts and counts reads within a given homologous region by comparing individual read-mapping statistics from each parental alignment. Reads that are aligned ambiguously to both references are resolved proportionally to the allele-specific matching read counts or statistically using a binomial distribution. Using simulations, we show CompMap has low error rates in assessing regulatory divergence. AvailabilityThe Python code with examples and installation instructions is available on the GitHub repository https://github.com/santiagosnchez/CompMap Contactsantiago.snchez@gmail.com Supplementary information

bioinformatics↗

bioRxiv2020

The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation

The distribution of fitness effects for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the distribution of fitness effects (DFE) from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, and non-random mating. Although inference methods aim to control for population size changes, the influence of non-random mating remains incompletely understood, despite being a common feature of many species. We report the distribution of fitness effects estimated from 326 genomes of Caenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history of C. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection can conspire to compromise estimates of the DFE from extant polymorphisms. These factors together tend to bias inferences towards weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species like C. elegans. Improved methods for inferring the distribution of fitness effects are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.

evolutionary biology↗

bioRxiv2020

Sex-specific and sex-chromosome regulatory evolution underlie widespread misregulation of inter-species hybrid transcriptomes

When gene regulatory networks diverge between species, their dysfunctional expression in inter-species hybrid individuals can create genetic incompatibilities that generate the developmental defects responsible for intrinsic post-zygotic reproductive isolation. Both cis- and trans-acting regulatory divergence can be hastened by directional selection through adaptation, sexual selection, and inter-sexual conflict, in addition to cryptic evolution under stabilizing selection. Dysfunctional sex-biased gene expression, in particular, may provide an important source of sexually-dimorphic genetic incompatibilities. Here, we characterize and compare male and female/hermaphrodite transcriptome profiles for sibling nematode species Caenorhabditis briggsae and C. nigoni, along with allele-specific expression in their F1 hybrids, to deconvolve features of expression divergence and regulatory dysfunction. Despite evidence of widespread stabilizing selection on gene expression, misexpression of sex-biased genes pervades F1 hybrids of both sexes. This finding implicates greater fragility of male genetic networks to produce dysfunctional organismal phenotypes. Spermatogenesis genes are especially prone to high divergence in both expression and coding sequences, consistent with a "faster male" model for Haldanes rule and elevated sterility of hybrid males. Moreover, underdominant expression pervades male-biased genes compared to female-biased and sex-neutral genes and an excess of cis-trans compensatory regulatory divergence for X-linked genes underscores a "large-X effect" for hybrid male expression dysfunction. Extensive regulatory divergence in sex determination pathway genes likely contributes to demasculinization of XX hybrids. The evolution of genetic incompatibilities due to regulatory versus coding sequence divergence, however, are expected to arise in an uncorrelated fashion. This study identifies important differences between the sexes in how regulatory networks diverge to contribute to sex-biases in how genetic incompatibilities manifest during the speciation process. Authors summaryAs species diverge, many mutations that affect traits do so by altering gene expression. Such gene regulatory changes also accumulate in the control of static traits, due to compensatory effects of mutation on multiple regulatory elements. Theory predicts many of these changes to cause inter-species hybrids to experience dysfunctional gene expression that leads to reduced fitness, disproportionately affecting genes biased toward expression in one sex and that localize to sex chromosomes. Our analyses of genome-wide gene expression from Caenorhabditis nematode roundworms support these predictions. We find widespread rewiring of gene regulation, despite the extensive morphological stasis and conserved expression profiles that are hallmarks of these animals. Misregulation of expression in inter-species hybrids of both sexes is most severe for genes linked to the X-chromosome, but male organismal phenotypes are most disrupted in hybrids. This fragility of male genetic networks and sex differences in regulatory evolution of local versus distant elements may underlie feminized and sterile phenotypes among hybrids. Our work clarifies how distinct components of regulatory networks evolve and contribute to sex differences in the manifestation of genetic incompatibilities in the speciation process.

genomics↗

bioRxiv2019

Neuro-genetic plasticity of Caenorhabditis elegans behavioral thermal tolerance

BackgroundAnimal responses to thermal stimuli involve intricate contributions of genetics, neurobiology and physiology, with temperature variation providing a pervasive environmental factor for natural selection. Thermal behavior thus exemplifies a dynamic trait that requires non-trivial phenotypic summaries to appropriately capture the trait in response to a changing environment. To characterize the deterministic and plastic components of thermal responses, we developed a novel micro-droplet assay of nematode behavior that permits information-dense summaries of dynamic behavioral phenotypes as reaction norms in response to increasing temperature (thermal tolerance curves, TTC).\n\nResultsWe found that C. elegans TTCs shift predictably with rearing conditions and developmental stage, with significant differences between distinct wildtype genetic backgrounds. Moreover, after screening TTCs for 58 C. elegans genetic mutant strains, we determined that genes affecting thermosensation, including cmk-1 and tax-4, potentially play important roles in the behavioral control of locomotion at high temperature, implicating neural decision-making in TTC shape rather than just generalized physiological limits. However, expression of the transient receptor potential ion channel TRPA-1 in the nervous system is not sufficient to rescue rearing-dependent plasticity in TTCs conferred by normal expression of this gene, indicating instead a role for intestinal signaling involving TRPA-1 in the adaptive plasticity of thermal performance.\n\nConclusionsThese results implicate nervous system and non-nervous system contributions to behavior, in addition to basic cellular physiology, as key mediators of evolutionary responses to selection from temperature variation in nature.

genetics↗