Biology subjects

Kasimatis, K. R.

Publications and source records attributed to Kasimatis, K. R..

10 recordsLinked to original sources

bioRxiv2026

A Male Expressed Copulatory Plug Increases Female Fertility in Caenorhabditis Nematodes

The genomes of self-fertilizing hermaphrodites offer a unique opportunity to probe why some genes with sex-specific functions are lost while others are maintained. In the androdiecious species, Caenorhabditis elegans, the presence of mate plugging is polymorphic across genetic backgrounds. The production of a mating plug is controlled by a single gene, plg-1, which has male-specific expression. Given that males are present less than 1% of the time, this gene is likely lost through relaxed selection or purifying selection, especially if mate plugging is maintained through intrasexual selection in males as is often hypothesized. We capitalized on a diverse panel of almost 2,000 C. elegans natural strains to show that plg-1 is maintained in at least 61% of genetic backgrounds, despite the androdiecious mating system. Genetic diversity estimates suggest that the loss of plg-1 is correlated with species globalization. We show that hermaphrodite total fecundity is not correlated with plg-1 genotype, indicating that this gene is not being maintained through linkage to a hermaphrodite beneficial gene. We then demonstrate in both C. elegans and the obligate outcrossing species, C. remanei, that the presence of a mating plug does not assure paternity by preventing subsequent males from mating. Instead, females with a mating plug have an extended peak reproductive window and higher fecundity than females without a mating plug. Together, these results indicate that mate plugging is female beneficial. We suggest that this benefit is derived from mating plugs acting as a vulval cover that can inhibit sperm loss during egg laying, thus reducing sperm limitation. Our work indicates that mate plugging may not always invoke male competition and can instead represent reproductive cooperation. More broadly, it demonstrates that male-specific gene expression does not equate to male-specific function, especially in the context of reproductive interactions.

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

Post-insemination sexual selection in males indirectly masculinizes the female transcriptome

Sex-specific regulation of gene expression is the most plausible way for generating sexually differentiated phenotypes from an essentially shared genome. However, since genetic material is shared, sex-specific selection in one sex can have an indirect response in the other sex. From a gene expression perspective, this tethered response can move one sex away from their wildtype expression state and impact potentially many gene regulatory networks. Here, using experimental evolution in the model nematode Caenorhabditis elegans, we explore the coupling of direct sexual selection on males with the transcriptomic response in males and females over microevolutionary timescales to uncover the extent to which post-insemination reproductive traits share a genetic basis between the sexes. We find that differential gene expression evolved in a sex-specific manner in males, while in females indirect selection causes an evolved response. Almost all differentially expressed genes were downregulated in both evolved males and females. Moreover, 97% of significantly differentially expressed genes in males and 69% of significantly differentially expressed genes in females have wildtype female-biased expression profile. Changes in gene expression profiles were likely driven through trans-acting pathways that are shared between the sexes. We found no evidence that the core dosage compensation machinery was impacted by experimental evolution. Together these data suggest a de-feminization of the male transcriptome and masculinization of the female transcriptome driven by direct selection on male sperm competitive ability. Our results indicate that on short evolutionary timescales sexual selection can generate putative sexual conflict in expression space.

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↗

bioRxiv2021

Post-Insemination Selection Dominates Pre-Insemination Selection in Driving Rapid Evolution of Male Competitive Ability

Sexual reproduction is a complex process that contributes to differences between the sexes and divergence between species. From a males perspective, sexual selection can optimize reproductive success by acting on the variance in mating success (pre-insemination selection) as well as the variance in fertilization success (post-insemination selection). The balance between pre- and post-insemination selection has not yet been investigated using a strong hypothesis-testing framework that directly quantifies the effects of post-insemination selection on the evolution of reproductive success. Here we use experimental evolution of a uniquely engineered genetic system that allows sperm production to be turned off and on in obligate male-female populations of Caenorhabditis elegans. We show that enhanced post-insemination competition increases the efficacy of selection and surpasses pre-insemination sexual selection in driving a polygenic response in male reproductive success. We find that after 30 generations post-insemination selection increased male reproductive success by an average of 5- to 7-fold. Contrary to expectation, enhanced pre-insemination competition hindered selection and slowed the rate of evolution. Furthermore, we found that post-insemination selection resulted in a strong polygenic response at the whole-genome level. Our results demonstrate that post-insemination sexual selection plays a critical role in the rapid optimization of male reproductive fitness. Therefore, explicit consideration should be given to post-insemination dynamics when considering the population effects of sexual selection.

evolutionary biology↗

bioRxiv2020

Sexually Antagonistic Selection on Genetic Variation is Rare in Humans

Sex and sexual differentiation are ubiquitous across the tree of life. Because females and males often have substantially different functional requirements, we expect selection to differ between the sexes. Recent studies in diverse species, including humans, suggest sexually antagonistic viability selection creates allele frequency differences between the sexes at many different loci. However, theory and population-level simulations indicate that sex-specific differences in viability would need to be very extreme in order to produce and maintain reported levels of between-sex allelic differentiation. We address this paradox between theoretical predictions and empirical observations by evaluating evidence for sexually antagonistic viability selection on autosomal loci in humans using the largest cohort to date (UK Biobank, n=438,427) along with a second large, independent cohort (BioVU, n=93,864). We performed association tests between genetically ascertained sex and genotypes. Although we found dozens of genome-wide significant associations, none replicated across samples. Moreover, closer inspection revealed that all associations are likely due to cross-hybridization with sex chromosome regions during genotyping. We report loci with potential for mis-hybridization found on commonly used genotyping platforms that should be carefully considered in future genetic studies of sex-specific differences. Despite being well-powered to detect allele frequency differences of up to 0.8% between the sexes, we do not detect evidence for this signature of sexually antagonistic viability selection on autosomal variation. These findings suggest a lack of strong ongoing sexually antagonistic viability selection acting on single locus autosomal variation in humans.

evolutionary biology↗

bioRxiv2019

Limits to Genomic Divergence Under Sexually Antagonistic Selection

Since the autosomal genome is shared between the sexes, sex-specific fitness optima present an evolutionary challenge. While sexually antagonistic selection might favor different alleles within females and males, segregation randomly reassorts alleles at autosomal loci between sexes each generation. This process of homogenization during transmission thus prevents between-sex allelic divergence generated by sexually antagonistic selection from accumulating across multiple generations. However, recent empirical studies have reported high male-female FST statistics. Here, we use a population genetic model to evaluate whether these observations could plausibly be produced by sexually antagonistic selection. To do this, we use both a single-locus model with nonrandom mate choice, and individual-based simulations to study the relationship between strength of selection, degree of between-sex divergence, and the associated genetic load. We show that selection must be exceptionally strong to create measurable divergence between the sexes and that the decrease in population fitness due to this process is correspondingly high. Individual-based simulations with selection genome-wide recapitulate these patterns and indicate that small sample sizes and sampling variance can easily generate substantial male-female divergence. We therefore conclude that caution should be taken when interpreting autosomal allelic differentiation between the sexes.

evolutionary biology↗

bioRxiv2018

Proteomic and Evolutionary Analyses of Sperm Activation Identify Uncharacterized Genes in Caenorhabditis Nematodes

BackgroundNematode sperm have unique and highly diverged morphology and molecular biology. In particular, nematode sperm contain subcellular vesicles known as membranous organelles that are necessary for male fertility, yet play a still unknown role in overall sperm function. Here we take a novel proteomic approach to characterize the functional protein complement of membranous organelles in two Caenorhabditis species: C. elegans and C. remanei.\n\nResultsWe identify distinct protein compositions between membranous organelles and the activated sperm body. Two particularly interesting and undescribed gene families--the Nematode-Specific Peptide family, group D and the here designated Nematode-Specific Peptide family, group F--localize to the membranous organelle. Both multigene families are nematode-specific and exhibit patterns of conserved evolution specific to the Caenorhabditis clade. These data suggest gene family dynamics may be a more prevalent mode of evolution than sequence divergence within sperm. Using a CRISPR-based knock-out of the NSPF gene family, we find no evidence of a male fertility effect of these genes, despite their high protein abundance within the membranous organelles.\n\nConclusionsOur study identifies key components of this unique subcellular sperm component and establishes a path toward revealing their underlying role in reproduction.

evolutionary biology↗

bioRxiv2018

Auxin-Mediated Sterility Induction System for Longevity and Mating Studies in Caenorhabditis elegans

The ability to control both the means and timing of sexual reproduction provides a powerful tool to understand not only fertilization, but also life history trade-offs resulting from sexual reproduction. However, precisely controlling fertilization has proved a major challenge across model systems. An ideal sterility induction system should be external, non-toxic, and reversible. Using the auxin-inducible degradation system targeting the spe-44 gene within the nematode Caenorhabditis elegans, we designed a means of externally inducing spermatogenesis arrest. We show that exposure to auxin during larval development induces both hermaphrodite self-sterility and male sterility. Moreover, male sterility can be reversed upon cessation of auxin exposure. The sterility induction system developed here has multiple applications in the fields of spermatogenesis and mating systems evolution. Importantly, this system is also a highly applicable tool for aging studies. We show that auxin-induced self-sterility is comparable to the commonly used chemically-induced FUdR sterility, while offering multiple benefits, including being less labor intensive, being non-toxic, and avoiding compound interactions with other experimental treatments.

genetics↗

bioRxiv2017

Quantifying male and female pheromone-based mate choice in Caenorhabditis nematodes using a novel microfluidic technique

Pheromone cues are an important component of intersexual communication, particularly in regards to mate choice. Caenorhabditis nematodes predominant rely on pheromone production for mate finding and mate choice. Here we describe a new microfluidic paradigm for studying mate choice in nematodes. Specifically, the Pheromone Arena allows for a constant flow of small molecule signals to be passed in real time from signaling worms to those making a choice without any physical contact. We validated this microfluidic paradigm by corroborating previous studies in showing that virgin C. remanei and C. elegans males have a strong preference for virgin females over mated ones. Moreover, our results suggest that the strength of attraction is an additive effect of male receptivity and female signal production. We go on to explicitly examine female choice and find that females are more attracted to virgin males. However, a females mate choice is strongly dependent on her mating status.

animal behavior and cognition↗