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Intrinsic reproductive isolation occurs when genetic differences between populations disrupt the development of hybrid organisms, preventing gene flow and enforcing speciation. While prior studies have examined the genetic origins of hybrid incompatibility, the effects of incompatible factors on development remain poorly understood. Here, we investigate the mechanistic basis of hybrid incompatibility inCaenorhabditisnematodes by capitalizing on the ability ofC. brennerifemales to produce embryos after mating with males from several other species. Contrary to expectations, hybrid incompatibility was evident immediately after fertilization, suggesting that post-fertilization barriers to hybridization originate from physical incompatibility between sperm and oocyte-derived factors rather than from zygotic transcription, which starts after the 4-cell stage. Sperm deliver chromatin, which expands to form a pronucleus, and a pair of centrioles, which form centrosomes that attach to the sperm-derived pronucleus and signal to establish the embryo's anterior-posterior axis. InC. brennerioocytes fertilized withC. eleganssperm, sperm pronuclear expansion was compromised, frequent centrosome detachment was observed, and cortical polarity was disrupted. Live imaging revealed that defective polar body extrusion contributes to defects in mitotic spindle morphology.C. brennerioocytes fertilized withC. remaneiorC. sp. 48sperm showed similar defects, and their severity and frequency increased with phylogenetic distance. Defective expansion of the sperm-derived pronucleus and unreliable polar body extrusion immediately after fertilization generally underlie the inviability of hybrid embryos in this clade. These results indicate that physical mismatches between sperm and oocyte-derived structures may be a primary mechanism of hybrid incompatibility. 

Dormancy allows organisms to survive hostile conditions and is hypothesized to enable species to coexist in fluctuating environments. Although determining how species avoid extinction is critical to understanding the dynamics of natural populations, experimental work exploringifandwhendormancy rescues populations from extinction remains rare. We conducted an experiment, where we grew two species of nematode at three temperatures. Strains ofCaenorhabditiseleganshad mutations altering their propensity to enter a dormant stage andCaenorhabditis briggsaewas a single strain with a wildtype background. We used those empirical results to parameterize a model and simulate competitive outcomes in fluctuating environments between the two species. We show that upregulating the dormancy pathway rescues populations that would otherwise go extinct, thereby increasing coexistence between competing species. By leveraging the genetic tools available from a model system, this study provides experimental confirmation that dormancy specifically facilitates species coexistence and thereby promotes diversity. This study system could be used more expansively to explore the role of dormancy in species interactions. 

Abstract Although similar developmental regulatory networks can produce diverse phenotypes, different networks can also produce the same phenotype. In theory, as long as development can produce an acceptable end phenotype, the details of the process could be shielded from selection, leading to the possibility of developmental system drift, where the developmental mechanisms underlying a stable phenotype continue to evolve. Many examples exist of divergent developmental genetics underlying conserved traits. However, studies that elucidate how these differences arose and how other features of development accommodated them are rarer. InCaenorhabditis elegans, six GATA-type transcription factors (GATA factors) comprise the zygotic part of the endoderm specification network. Here we show that the core of this network - five of the genes - originated within the genus during a brief but explosive radiation of this gene family and that at least three of them evolved from a single ancestral gene with at least two different spatio-temporal expression patterns. Based on analyses of their evolutionary history, gene structure, expression, and sequence, we explain how these GATA factors were integrated into this network. Our results show how gene duplication fueled the developmental system drift of the endoderm network in a phylogenetically brief period in developmentally canalized worms. 

Abstract Transcription factors are defined by their DNA-binding domains (DBDs). The binding affinities and specificities of a transcription factor to its DNA binding sites can be used by an organism to fine-tune gene regulation and so are targets for evolution. Here we investigate the evolution of GATA-type transcription factors (GATA factors) in theCaenorhabditisgenus. Based upon comparisons of their DBDs, these proteins form 13 distinct groups. This protein family experienced a burst of gene duplication in several of these groups along two short branches in the species tree, giving rise to subclades with very distinct complements of GATA factors. By comparing extant gene structures, DBD sequences, genome locations, and selection pressures we reconstructed how these duplications occurred. Although the paralogs have diverged in various ways, the literature shows that at least eight of the DBD groups bind to similar G-A-T-A DNA sequences. Thus, despite gene duplications and divergence among DBD sequences, mostCaenorhabditisGATA factors appear to have maintained similar binding preferences, which could create the opportunity for developmental system drift. We hypothesize that this limited divergence in binding specificities contributes to the apparent disconnect between the extensive genomic evolution that has occurred in this genus and the absence of significant anatomical changes. 

Behavioral phenotyping of model organisms has played an important role in unravelling the complexities of animal behavior. Techniques for classifying behavior often rely on easily identified changes in posture and motion. However, such approaches are likely to miss complex behaviors that cannot be readily distinguished by eye (e.g., behaviors produced by high dimensional dynamics). To explore this issue, we focus on the model organism Caenorhabditis elegans , where behaviors have been extensively recorded and classified. Using a dynamical systems lens, we identify high dimensional, nonlinear causal relationships between four basic shapes that describe worm motion (eigenmodes, also called “eigenworms”). We find relationships between all pairs of eigenmodes, but the timescales of the interactions vary between pairs and across individuals. Using these varying timescales, we create “interaction profiles” to represent an individual’s behavioral dynamics. As desired, these profiles are able to distinguish well-known behavioral states: i.e., the profiles for foraging individuals are distinct from those of individuals exhibiting an escape response. More importantly, we find that interaction profiles can distinguish high dimensional behaviors among divergent mutant strains that were previously classified as phenotypically similar. Specifically, we find it is able to detect phenotypic behavioral differences not previously identified in strains related to dysfunction of hermaphrodite-specific neurons. 

Automated analysis of video can now generate extensive time series of pose and motion in freely-moving organisms. This requires new quantitative tools to characterise behavioural dynamics. For the model roundworm Caenorhabditis elegans , body pose can be accurately quantified from video as coordinates in a single low-dimensional space. We focus on this well-established case as an illustrative example and propose a method to reveal subtle variations in behaviour at high time resolution. Our data-driven method, based on empirical dynamic modeling, quantifies behavioural change as prediction error with respect to a time-delay-embedded ‘attractor’ of behavioural dynamics. Because this attractor is constructed from a user-specified reference data set, the approach can be tailored to specific behaviours of interest at the individual or group level. We validate the approach by detecting small changes in the movement dynamics of C. elegans at the initiation and completion of delta turns. We then examine an escape response initiated by an aversive stimulus and find that the method can track return to baseline behaviour in individual worms and reveal variations in the escape response between worms. We suggest that this general approach—defining dynamic behaviours using reference attractors and quantifying dynamic changes using prediction error—may be of broad interest and relevance to behavioural researchers working with video-derived time series. 

Abstract The cyanobacteriumSynechococcus elongatusis a model organism for the study of circadian rhythms. It is naturally competent for transformation—that is, it takes up DNA from the environment, but the underlying mechanisms are unclear. Here, we use a genome-wide screen to identify genes required for natural transformation inS. elongatus, including genes encoding a conserved Type IV pilus, genes known to be associated with competence in other bacteria, and others. Pilus biogenesis occurs daily in the morning, while natural transformation is maximal when the onset of darkness coincides with the dusk circadian peak. Thus, the competence state in cyanobacteria is regulated by the circadian clock and can adapt to seasonal changes of day length.