Biology subjects

Paaby, A. B.

Publications and source records attributed to Paaby, A. B..

11 recordsLinked to original sources

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

Nuclear-encoded tRNA genes harbor substantial allelic diversity in three nematode species

Cytosolic transfer RNAs, which are encoded as hundreds of genes in nuclear genomes, experience exceptionally high mutation rates and have been hypothesized to confer substantial mutational load in natural populations. Although this phenomenon appears universal across multicellular eukaryotes, a comprehensive characterization of standing variation in tRNA repertoires is still lacking in any system. Here, we resolve within-species allelic variation in nuclear-encoded tRNAs in three nematode species: Caenorhabditis elegans, C. briggsae, and C. tropicalis. We show that these genes carry signatures of high rates of historical transcription-associated mutagenesis and of purifying selection, resulting in allelic variation that includes pervasive instances of within-gene mismatches between the amino acid recognized by the tRNA backbone and that indicated by the anticodon. Furthermore, patterns of tRNA genomic organization and variation differ markedly from those of protein-coding regions. Individual genomes harbor distinct complements of tRNA genes with predicted functional differences, an observation that coincides with recent evidence that variation in tRNA expression and regulation contributes to human disease. Our findings offer an entry point for identifying the micro-evolutionary processes that act on tRNA repertoires, and in turn connecting those processes to the macro-evolutionary patterns that have more frequently been the focus of study. Significance statementTransfer RNAs (tRNAs) are ancient and essential molecules that deliver amino acids to the growing polypeptide chain during protein synthesis. Despite their importance, little is known about how the genes encoding tRNAs vary among individuals, even though they accumulate large numbers of mutations due to their high rates of expression. Here, we report that three nematode species, including the model organism C. elegans, show within-species variation in their tRNA gene repertoires, which may cause differences in protein synthesis across individuals. Our findings may represent patterns common across multicellular species and they set the stage for future investigation into how this diversity influences cellular function and organismal fitness.

genetics↗

bioRxiv2025

Variation in inbreeding depression within and among Caenorhabditis species

Outbreeding populations harbor large numbers of recessive deleterious alleles that reduce the fitness of inbred individuals, and this inbreeding depression potentially shapes the evolution of mating systems, acting as a counterweight to the inherent selective advantage of self-fertilization. The population biological factors that influence inbreeding depression are numerous and often difficult to disentangle. We investigated the utility of obligately-outcrossing (gonochoristic) Caenorhabditis nematodes as models for inbreeding depression. By systematically inbreeding lines from ten populations and tracking line extinction, we found that inbreeding depression is universal but highly variable among species and populations. Inbreeding depression was detected across the life cycle, from mating to embryo production to embryonic viability and larval growth, and reciprocal crosses implicated female-biased effects. In most cases, the surviving inbred lines have dramatically reduced fitness, but the variance among inbred lines is substantial and compatible with the idea that inbreeding depression need not be an obstacle to the evolution of selfing in these worms. Populations of some species, including Caenorhabditis becei, exhibited modest inbreeding depression and could be tractable laboratory models for gonochoristic Caenorhabditis.

evolutionary biology↗

bioRxiv2025

How much is Transcription-associated Mutagenesis Driving tRNA Microevolution?

Transfer RNAs (tRNAs) are among the most highly conserved and frequently transcribed genes. Recent studies have demonstrated that tRNAs experience exceptionally high rates of transcription-associated mutagenesis (TAM) as well as strong purifying selection. How the mutational input of TAM, which induces a non-uniform distribution of nucleotide substitutions, affects the fitness of tRNA molecules is unclear. Secondary structure in tRNAs is strongly conserved over macro-evolutionary time, suggesting that mutations that disrupt paired sites may be especially deleterious, but TAM-induced mutations primarily involve nucleotide transitions, which tend to preserve base-pairing stability. To examine how TAM affects tRNA molecule fitness and shapes tRNA evolution over short timescales, we analyzed tRNA allelic variation in contemporary Caenorhabditis elegans strains. We propose a model of tRNA microevolution driven by TAM and demonstrate that the observed secondary structure characteristics align with our predicted TAM-biased patterns. Furthermore, we developed a continuous Markov substitution model that incorporates TAM-specific mutational biases. This TAM-biased model fits the C. elegans tRNA data more effectively than standard models, such as the general time-reversible (GTR) model. Based on these results, we conclude that tRNAs in natural populations carry substantial levels of structure-destabilizing mutations, which may be tolerated but nevertheless likely induce meaningful fitness costs. Our findings are consistent with recent experimental studies on tRNA fitness in yeast but challenge prior theoretical and computational analyses that emphasize RNA base-pairing as a primary determinant in genotype-phenotype systems. 1 Significance StatementTransfer RNAs (tRNAs) are ancient molecules, encoded as genes in all living systems. tRNA genes are known to experience exceptionally high rates of both mutation and purifying selection, but how these opposing evolutionary forces shape tRNA evolution is unclear. We developed a sequence substitution model specific to tRNA mutagenesis and applied it to standing variation in a natural population in order to infer how mutation and selection affect the structural stability of tRNA molecules.

evolutionary biology↗

bioRxiv2024

Stabilizing selection and adaptation shape cis and trans gene expression variation in C. elegans

An outstanding question in the evolution of gene expression is the composition of the underlying regulatory architecture and the processes that shape it. Mutations affecting a genes expression may reside locally in cis or distally in trans; the accumulation of these changes, their interactions, and their modes of inheritance influence how traits are expressed and how they evolve. Here, we interrogated gene expression variation in C. elegans, including the first allele-specific expression analysis in this system, capturing effects in cis and in trans that govern gene expression differences between the reference strain N2 and seven wild strains. We observed extensive compensatory regulation, in which opposite effects in cis and trans at individual genes mitigate expression differences among strains, and that genes with expression differences exhibit strain specificity. As the genomic distance increased between N2 and each wild strain, the number of genes with expression differences also increased. We also report for the first time that expression-variable genes are lower expressed on average than genes without expression differences, a trend that may extend to humans and Drosophila melanogaster and may reflect the selection constraints that govern the universal anticorrelation between gene expression and rate of protein evolution. Together, these and other observed trends support the conclusion that many C. elegans genes are under stabilizing selection for expression level, but we also highlight outliers that may be biologically significant. To provide community access to our data, we introduce an easily accessible, interactive web application for gene-based queries: https://wildworm.biosci.gatech.edu/ase/. Author SummaryGenes are first expressed as RNAs, which act as templates in the synthesis of proteins, the workhorse molecules of the cell. Naturally-occurring mutations can influence how RNA expression occurs; to evaluate how RNA expression varies among individuals and how such patterns evolve, the authors measured expression in wild strains of the nematode C. elegans and in offspring derived from crosses between them. This study describes the architecture of RNA expression variation in this essential model organism and reports novel patterns that may extend to insects and humans.

genetics↗

bioRxiv2023

Beyond the reference: gene expression variation and transcriptional response to RNAi in C. elegans

A universal feature of living systems is that natural variation in genotype underpins variation in phenotype. Yet, research in model organisms is often constrained to a single genetic background, the reference strain. Further, genomic studies that do evaluate wild strains typically rely on the reference strain genome for read alignment, leading to the possibility of biased inferences based on incomplete or inaccurate mapping; the extent of reference bias can be difficult to quantify. As an intermediary between genome and organismal traits, gene expression is well positioned to describe natural variability across genotypes generally and in the context of environmental responses, which can represent complex adaptive phenotypes. C. elegans sits at the forefront of investigation into small-RNA gene regulatory mechanisms, or RNA interference (RNAi), and wild strains exhibit natural variation in RNAi competency following environmental triggers. Here, we examine how genetic differences among five wild strains affect the C. elegans transcriptome in general and after inducing RNAi responses to two germline target genes. Approximately 34% of genes were differentially expressed across strains; 411 genes were not expressed at all in at least one strain despite robust expression in others, including 49 genes not expressed in reference strain N2. Despite the presence of hyper-diverse hotspots throughout the C. elegans genome, reference mapping bias was of limited concern: over 92% of variably expressed genes were robust to mapping issues. Overall, the transcriptional response to RNAi was strongly strain-specific and highly specific to the target gene, and the laboratory strain N2 was not representative of the other strains. Moreover, the transcriptional response to RNAi was not correlated with RNAi phenotypic penetrance; the two germline RNAi incompetent strains exhibited substantial differential gene expression following RNAi treatment, indicating an RNAi response despite failure to reduce expression of the target gene. We conclude that gene expression, both generally and in response to RNAi, differs across C. elegans strains such that choice of strain may meaningfully influence scientific conclusions. To provide a public, easily accessible resource for querying gene expression variation in this dataset, we introduce an interactive website at https://wildworm.biosci.gatech.edu/rnai/.

genetics↗

bioRxiv2022

A Toxin-Antidote Selfish Element Increases Fitness of its Host

Selfish genetic elements can promote their transmission at the expense of individual survival, creating conflict between the element and the rest of the genome. Recently, a large number of toxin-antidote (TA) post-segregation distorters have been identified in non-obligate outcrossing nematodes. Their origin and the evolutionary forces that keep them at intermediate population frequencies are poorly understood. Here, we study a TA element in C. elegans called peel-1/zeel-1. Two major haplotypes of this locus, with and without the selfish element, segregate in C. elegans. Here we study the fitness consequences of the peel-1/zeel-1 element outside of its role in gene drive in non-outcrossing animals. We demonstrate that loss of the toxin peel-1 decreased fitness of hermaphrodites and resulted in reductions in fecundity and body size. This fitness advantage is independent of the antidote zeel-1, suggesting that a distinct peel-1 pathway plays a biological role. This work demonstrates that a TA element can provide a fitness benefit to its hosts, either during their initial evolution or by being co-opted by the animals following their selfish spread. These findings guide our understanding on how TA elements can remain in a population where gene drive is minimized, helping resolve the mystery of prevalent TA elements in selfing animals.

evolutionary biology↗

bioRxiv2022

Caenorhabditis nematodes colonize ephemeral resource patches in neotropical forests.

Factors shaping the distribution and abundance of species include life-history traits, population structure, and stochastic colonization-extinction dynamics. Field studies of model species groups help reveal the roles of these factors. Species of Caenorhabditis nematodes are highly divergent at the sequence level but exhibit highly conserved morphological uniformity, and many of these species live in sympatry on microbe-rich patches of rotten material. Here, we use field experiments and large-scale opportunistic collections to investigate species composition, abundance, and colonization efficiency of Caenorhabditis in two of the worlds best studied lowland tropical field sites: Barro Colorado Island in Panama and La Selva in Sarapiqui, Costa Rica. We observed seven species of Caenorhabditis, four of them known only from these collections. While these localities contain species from many parts of the phylogeny, both localities were dominated by globally distributed androdiecious species. We found that Caenorhabditis were able to colonize baits accessible only by phoresy, preferring to colonize baits making direct contact with the ground. We estimate founder numbers per colonization event to be low.

ecology↗

bioRxiv2021

Diversification of small RNA pathways underlies germline RNAi incompetence in wild C. elegans strains

The discovery that experimental delivery of dsRNA can induce gene silencing at target genes revolutionized genetics research, by both uncovering essential biological processes and creating new tools for developmental geneticists. However, the efficacy of exogenous RNAi varies dramatically within the C. elegans population, raising questions about our understanding of RNAi in the lab relative to its activity and significance in nature. Here, we investigate why some wild-type strains fail to mount a robust RNAi response to germline targets. We observe diversity in mechanism: in some strains, the response is stochastic, either on or off among individuals, while in others the response is consistent but delayed. Increased activity of the Argonaute PPW-1, which is required for germline RNAi in the laboratory strain N2, rescues the response in some strains, but dampens it further in others. Among wild-type strains, genes known to mediate RNAi exhibited very high expression variation relative to other genes in the genome as well as allelic divergence and strain-specific instances of pseudogenization at the sequence level. Our results demonstrate functional diversification in the small RNA pathways in C. elegans, and suggest that RNAi processes are evolving rapidly and dynamically in nature.

evolutionary biology↗

bioRxiv2019

A portable, low-cost device for precise control of specimen temperature under stereomicroscopes

To facilitate precise and convenient control of biological sample temperature, we developed a low-cost device that can be used independently or with any stereomicroscope. The purpose of the device is to control the thermal environment during experimental intervals in which a specimen must be manipulated outside of an incubator, e.g. for dissection or slide-mounting in preparation for imaging. Sample temperatures can be both cooled to below and heated to above room temperatures, and stably maintained at a precision of +/- 0.1{degrees}C. To demonstrate the utility of this device, we report improved characterization of the penetrance of a short-acting temperature-sensitive allele in C. elegans embryos, and identification of the upper temperature threshold for embryonic viability for six Caenorhabditis species. By controlling the temperature environment even as a specimen is manipulated, this device offers consistency and flexibility, reduces environmental noise, and enables precision timing in experiments requiring temperature shifts.

developmental biology↗

bioRxiv2019

Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping

Pleiotropy - when a single mutation affects multiple traits - is a controversial topic with far-reaching implications. Pleiotropy plays a central role in debates about how complex traits evolve and whether biological systems are modular or are organized such that every gene has the potential to affect many traits. Pleiotropy is also critical to initiatives in evolutionary medicine that seek to trap infectious microbes or tumors by selecting for mutations that encourage growth in some conditions at the expense of others. Research in these fields, and others, would benefit from understanding the extent to which pleiotropy reflects inherent relationships among phenotypes that correlate no matter the perturbation (vertical pleiotropy). Alternatively, pleiotropy may result from genetic changes that impose correlations between otherwise independent traits (horizontal pleiotropy). We distinguish these possibilities by using clonal populations of yeast cells to quantify the inherent relationships between single-cell morphological features. Then, we demonstrate how often these relationships underlie vertical pleiotropy and how often these relationships are modified by genetic variants (QTL) acting via horizontal pleiotropy. Our comprehensive screen measures thousands of pairwise trait correlations across hundreds of thousands of yeast cells and reveals ample evidence of both vertical and horizontal pleiotropy. Additionally, we observe that the correlations between traits can change with the environment, genetic background and cell-cycle position. These changing dependencies suggest a nuanced view of pleiotropy: biological systems demonstrate limited pleiotropy in any given context, but across contexts (e.g., across diverse environments and genetic backgrounds) each genetic change has the potential to influence a larger number of traits. Our method suggests that exploiting pleiotropy for applications in evolutionary medicine would benefit from focusing on traits with correlations that are less dependent on context.

evolutionary biology↗