Evolution & Development

The highly conserved body plan of nematodes makes members of this phylum excellent models to study cell type evolution. Early branching nematode lineages, mostly occupying aquatic habitats, usually contain caudal glands deployed for underwater attachment to a substrate, but have been thought to lack phasmid sensory organs, resulting in their historical classification as "Aphasmidia". With the transition to a terrestrial environment, nematodes lost caudal glands and gained phasmid sensory neurons. The supposed mutually exclusive existence of caudal glands and phasmids has led to the suggestion that phasmid neurons may have evolved from caudal glands. Here, we rule out this possibility through light and electron microscopical analysis of Mononchus aquaticus, a member of the early branching Dorylaimia lineage, showing that phasmid sensory neurons and caudal glands do coexist. This observation not only argues against a proposed cell type evolution scenario accompanying aquatic-to-terrestrial transitions but also indicates that the presence of phasmid sensory organs may have been an ancestral trait of the nematode phylum.

Tessellated calcified cartilage (TCC) is a hallmark of the chondrichthyan skeleton, yet its development early in ontogeny across the four major groups (batoids, galeomorphs, squalomorphs, and holocephalans) remains poorly understood. Specialised traits of TCC, such as multi-layered TCC and internal mineralised trabeculae, typically develop in response to feeding mechanics. In this study, we evaluated TCC morphology in the jaws of 12 representative taxa to observe its structure at an early ontogenetic stage to determine whether these specialised features had yet developed. Batoids consistently exhibited well-developed, homogeneous, polygonal tesserae early in ontogeny regardless of jaw morphology or feeding habit. In contrast, galeomorphs displayed high morphological heterogeneity. Notably, we document the first report of an extensive internal trabecular network in a non-batoid elasmobranch, observed in Ginglymostoma cirratum, which may serve to resist the mechanical pressures of specialised suction feeding. Furthermore, we identified voussoir tesserae in galeomorphs for the first time, extending their documented presence across all elasmobranch groups, where they display an inverted aspect ratio (wider than tall) compared to mature forms. The durophagous Mustelus mustelus exhibited surprisingly poor TCC development despite being a durophagous feeder, pointing to a pronounced ontogenetic lag. In Squatina oculata, TCC was characterised by large and thick tesserae and extensive fused tesseral regions which may relate to its explosive ambush predation mode, whereas the holocephalan Chimaera exhibited a poorly mineralized, mesh-like structure without resolvable discrete tesserae or trabeculae-matching findings from previous studies. Across all specimens, multi-layered TCC was absent, confirming that multi-layering develops later in ontogeny. These results demonstrate that generalised models of TCC development based on one group or a few taxa fail to capture the broader diversity of TCC morphology. It also opens up many exciting avenues for further study, and forms the basis for comparisons with fossil chondrichthyans, to investigate the evolution of TCC.

An animal's musculature must support its specific biomechanical needs, so muscle morphology and volume allocation may adapt when locomotor strategies diversify. We examined muscle size and morphology in two sister families of bombycoid moths, wild silkmoths (Saturniidae) and hawkmoths (Sphingidae), that have diverged in wingbeat frequency, wing morphology, and behavior. Although both families rely on the same muscles to power and steer flight, they may distribute muscle volume differently to prioritize distinct functions. We hypothesized that flight power muscle proportions are larger in hawkmoths and increase with wingbeat frequency, helping meet inertial power demands of high-frequency maneuverable flight. We also hypothesized that some individual muscles diverge in proportional volume and area to support distinct wing control strategies. To test our hypotheses, we took CT scans of twenty bombycoid species and quantified volumes and geometries of six flight muscle pairs. As expected, flight power muscle proportions positively correlate with wingbeat frequency and are generally greater in hawkmoths. Two of three steering muscles diverge substantially in relative volume and area between families. Most muscles exhibit greater length in silkmoths and greater cross-sectional area in hawkmoths. Finally, the dorsal oblique(DO) muscle diverges exceptionally in size and morphology, being highly developed in hawkmoths and smaller or absent in silkmoths. This unexpected difference supports the DO having an underappreciated role in flight control, possibly via shaping indirect strain propagation in the elastic thorax. We show that muscle volume distribution parallels bombycoids' divergent flight strategies, demonstrating how muscle allocation can adapt for specialized functional goals.

The human bony labyrinth has attracted increasing interest because of its taxonomic, evolutionary, and functional significance. Although sexual dimorphism has been reported in several aspects of the temporal bone, the extent to which sex, age, size, and allometry contribute to labyrinth shape variation remains poorly understood. Here, we investigated patterns of sexual shape variation in the human bony labyrinth using three-dimensional geometric morphometrics in a sample of 98 archaeological individuals from South America with known genomic sex. Centroid size and allometric effects were assessed in a subset of 90 individuals with comparable metric scaling. In addition to analysing the complete labyrinth, the cochlea and semicircular canals were examined separately to evaluate region-specific patterns of sexual shape variation. Principal Component Analysis showed extensive overlap between females and males, and overall labyrinth shape did not differ significantly between sexes. Males exhibited significantly larger labyrinths than females, and centroid size explained a small but significant proportion of overall shape variation. Regional analyses showed no evidence of significant sexual shape differences in the cochlea or in any individual semicircular canal when analysed separately. In contrast, the combined semicircular canal system exhibited subtle but significant sexual shape variation independent of centroid size, whereas morphological disparity did not differ between sexes. The geometric comparison of the female and male consensus configurations further showed that sexual shape variation was regionally heterogeneous. Whereas the cochlea exhibited a pattern of localized changes with low directional coherence, the semicircular canals displayed more coordinated regional shape changes. The male consensus also exhibited slightly higher canal circularity across all three semicircular canals, particularly the posterior canal, while differences in canal-plane orientation remained minimal. These findings demonstrate that sexual shape variation in the human bony labyrinth is subtle and anatomically partitioned among its components. Although significant sex differences in centroid size were detected across most anatomical regions, overall labyrinth shape and cochlear morphology were primarily influenced by allometry, whereas significant sex-related shape differences were detected only when the semicircular canals were considered as an integrated anatomical system. These findings demonstrate that sexual dimorphism in the human bony labyrinth is subtle but regionally heterogeneous, with the cochlea and semicircular canals exhibiting distinct patterns of shape variation, suggesting that these structures are influenced by different developmental, functional, and evolutionary processes.

The evolutionary patterns of trait diversification provide insights into the function of the trait. Early burst of trait evolution is often associated with adaptive radiation, rapidly diversifying the trait in response to vacant niches followed by the slowdown of the diversification with niche filling, whereas late burst is more likely to be associated with sexual selection, possibly contributing to reproductive barriers between closely related species. Here, we studied the diversification of tail fork depth through time in hirundines to infer its function, which remains unclear due to the competing two alternative hypotheses: the sexual selection hypothesis, which is a classic explanation of deeply forked tails, proposed that this trait has evolved via sexual selection, which was then challenged by the viability selection hypothesis, which proposed that deeply forked tails have mainly evolved via viability selection for enhancing aerodynamic performance during aerial foraging on large prey. We found a late burst of tail fork depth, but not of bill length, i.e., an index of prey size. The observed pattern is consistent with the sexual selection hypothesis but not with the viability selection hypothesis.

Parental qualities can influence the development and fitness of their offspring via genetic and non-genetic effects. Although these effects are often linked to parental phenotypes, the effect of parental genetic variation linked with relevant phenotypes is less well understood. We performed full factorial crosses based on parental genotypes for an age-at-maturity-related gene, vgll3, to investigate how the parental genotypes influence Atlantic salmon (Salmo salar) offspring survival, growth, and development in their early life. Beyond the connection with age at maturity, the additional association between vgll3 and body condition in Atlantic salmon offers a potential pathway by which the maternal vgll3 genotype could influence offspring early life fitness. Combined with measurements of maternal phenotype and egg characteristics, the crossing design therefore allowed us to disentangle the maternal and paternal genetic and non-genetic contributions to variation in offspring survival and phenotypic traits. The phenotypic traits measured were hatching length and yolk sac area, growth, and yolk sac consumption and conversion efficiency. Parental vgll3 genotype did not influence the majority of our measured egg traits or alevin traits except for a genetic effect of paternal vgll3 genotype on offspring survival, whereby the paternal late maturation allele was associated with higher survival. Maternal effects were strongest for survival and for traits associated with hatching and weaker for alevin growth and yolk sac usage. Paternal effects on the measured alevin traits were negligible. The results from our study demonstrate that both maternal and paternal effects have the potential to influence offspring early life fitness traits.

Background: Chromosome-level genome assemblies are increasingly enabling tests of chromosome evolution, conserved synteny, and sex chromosome conservation across diverse animal lineages, including spiders. Results: Here, we present a chromosome-level genome assembly for the African hermit spider, Nephilingis cruentata, a species with extreme female-biased sexual size dimorphism and a cytogenetically inferred XX2 sex chromosome system. The final Hi-C-assisted assembly spans 1.72 Gbp, with 99.5% of bases assigned to 13 pseudochromosomes, a scaffold N50 of 131.6 Mbp, and a BUSCO completeness score of 98.8%. We annotated 20,021 protein-coding genes, and repetitive elements accounted for 42.7% of the genome. Sex-specific whole-genome resequencing identified Chr02 and Chr07 as candidate X chromosomes based on reduced male coverage, consistent with the expected XX2 system. Using comparative whole-genome alignments across existing chromosome-scale spider assemblies, we also show that sex-linked chromosomes retain broad homologous identity across sampled spider lineages but exhibit lower synteny conservation and greater chromosome-length divergence than autosomes. Conclusions: These results suggest that spider sex chromosomes are conserved in homologous identity but more labile in structure, providing a comparative framework for studying sex chromosome conservation and divergence across Araneae.

Alternative splicing (AS) can generate multiple RNA isoforms from a single gene and is thought to contribute to phenotypic divergence, including differences between the sexes. Studies in several organisms have documented sex differences in splicing, however these have been largely reliant on short-read RNA sequencing which requires complex algorithms to assemble full-length transcripts and may underestimate both isoform diversity and sex differences in splicing. We used long-read, single molecule RNA-Seq to build a more complete catalog of sex-biased splicing in Poecilia reticulata, a focal species for studies of sexual dimorphism. Pairing long-read sequencing with isoform-level analyses, we identified a sixfold higher proportion of sex-biased splicing genes (37%) compared with short and long-read event-level approaches (6%, 11%). AS was common (70% genes) but only 54% of isoforms produced unique open-reading frames (ORFs). We found that males exhibited greater isoform richness than females in both tail and gonad tissues but produced a smaller proportion of isoforms with unique ORFs, suggesting that much of the increased isoform variation is unlikely to expand proteomic complexity and may instead reflect stochasticity during splicing rather than intentional transcriptional products intended for translation. Despite widespread AS, we found only 2.3% of genes exhibited sex-biased isoform switching, and only 52% of these switches generated distinct sex-biased ORFs. Together, our long-read data suggest that although isoform diversity is more extensive than previously appreciated, most alternative isoforms are unlikely to generate novel proteins. Instead, a relatively small number of sex-biased isoforms may disproportionately contribute to proteomic divergence between the sexes.

Three new species of sun orchid (Thelymitra) endemic to Aotearoa New Zealand are here described. These are T. palustris, T. scabrifolia and T. semaphora. The morphological distinctiveness of these three species has been acknowledged for decades; however, their taxonomic status has remained unresolved. Evidence from existing karyological data, recently generated DNA sequence data (LFY and ycf1) and morphological studies from historical and fresh collections are used here to support their formal description. Both, T. palustris and T. semaphora are restricted to wet habitats north of Auckland (North Island). Thelymitra scabrifolia inhabits mostly scrub, and it has a similar northern North Island distribution, but is has been found also in Manawat[a]whi / Three Kings Islands and historically in Otago (South Island). All three species are polyploids and are of conservation concern.

Phenotypic differences among populations can arise through heritable genetic divergence, phenotypic plasticity, or both, making it difficult to determine whether trait-environment correlations observed in nature reflect adaptive evolution. Within threespine stickleback (Gasterosteus aculeatus) studies, numerous document morphological differences among allopatric-, parapatric-, and even sympatric populations. These phenotypic differences among populations are often correlated with diet and lake habitat (e.g., lake size), suggesting an adaptive value to the population differences. However, many studies of ecomorphological divergence in stickleback use wild-caught stickleback, which may differ due to evolution or plasticity. Although common garden experiments have confirmed that population differences can be heritable, such experiments typically entail small numbers of populations. Consequently, we still do not know to what extent well-known trait-environment correlations in stickleback are a result of evolution. To address this gap, we reared stickleback embryos from 27 lake populations on Vancouver Island, in a laboratory environment. Morphological differences among populations persist in common-garden fish, confirming a large role for divergent evolution. These heritable differences were associated with environmental variation among lakes, implying an adaptive value. However, some well-known trait-environment relationships in stickleback did not persist in common-garden fish and may be primarily plastic.

Understanding how divergence in reproductive traits can promote speciation remains a fundamental question in evolutionary biology. Sperm morphology and kinematics diverge rapidly across species. However, the effect of hybridization between recently diverged species on sperm traits remains unclear, limiting our understanding of how reproductive isolation evolves. Here, we evaluated sperm morphology, kinematics, and trait integration in species of a young (~10,000 years), sympatric Cyprinodon pupfish radiation from San Salvador Island, Bahamas, as well as fertile advanced-generation hybrids between two of these species. We found significant divergence in flagellum length, midpiece area, and sperm velocity among species. In contrast, hybrids displayed transgressive kinematic profiles defined by high velocities, reduced path curvature, and distinct patterns of sperm kinematic integration. Our findings suggest that hybridization between recently diverged species may reorganize the underlying control of sperm locomotor mechanisms, generating novel phenotypes that could contribute to reproductive isolation in the early stages of speciation.

Transgenerational plasticity (TGP)- when parental environments influence offspring phenotypes - is ubiquitous across taxonomic groups and can have benefits for offspring beyond what is possible with developmental plasticity, particularly when selective pressures are high early in life. However, patterns of TGP vary widely across populations and species, and the evolutionary processes shaping this variation remain poorly understood. Here, we tested whether repeated evolutionary transitions result in parallel or population-specific evolutionary divergence in TGP relative to ancestral conditions. We examined sperm-mediated paternal effects across two ancestral marine and three derived freshwater populations of threespined stickleback fish (Gasterosteus aculeatus). We exposed fathers to dragonfly larvae (endemic to freshwater) or sculpin (endemic to all populations) predators and measured both paternal response to predators as well as antipredator behavior and growth in larval offspring. Fathers behaviorally responded to the presence of sculpin predators, but not dragonfly larvae. However, we found strong paternal effects in response to both predators in all populations. Further, the magnitude of TGP did not differ between marine and freshwater populations, suggesting that TGP does not become genetically accommodated as marine populations move into freshwater habitats. We found some evidence consistent with parallelism in both within and trans-generational plasticity: 1) personal exposure of larval stickleback to dragonfly larvae elicited strong antipredator responses in freshwater populations that were absent in marine populations, and 2) paternal predation exposure consistently increased offspring growth in marine populations while slowing growth in freshwater populations. In contrast, paternal effects altered offspring behavior in population-specific ways, with strong sex-specific effects of paternal exposure emerging in response to endemic predators. Adaptive evolution is a two-step process, in which heritable genotypic and phenotypic variation must first be present and then selected on. Therefore, high population-level variation in TGP suggests the capacity for rapid evolution of parental effects, while signatures of parallelism and sex-specific patterns suggest that TGP may evolve in targeted ways in response to ecological stressors.

Webspinners (Insecta: Embioptera) are an unusual insect order that are known for their subsocial behavior and prolific silk-production. Due to their unique foreleg silk glands, and spider-like ability to produce silk throughout their entire life cycle, webspinners are hypothesized to have evolved silk independently from other arthropod lineages. To date, there are no reference-quality genomes available for the order, preventing the study of their silk gene origination and diversification. Here, we assembled PacBio HiFi reference genomes and characterized the silk genes present in two webspinner species, Aposthonia ceylonica and Oligotoma nigra. The genomes reveal multiple full-length copies of the primary Embioptera silk gene, e-fibroin, that have undergone both ancestral and recent gene duplications within the group. For both species, all e-fibroin paralogs show the presence of complex repeat units consisting of multiple exons and introns that are remarkably homogenized across each gene. We also used CT-scanning of the internal silk glands to provide details concerning the localization of silk production in foreleg tarsi, and interspecific morphology. Article summaryThis study introduces the first high-quality genomes for webspinners, enabling new research on silk for evolutionary biologists and materials scientists alike. The authors sequenced two embiopteran species, Aposthonia ceylonica and Oligotoma nigra, to compare silk genes and gland structure using micro-computed tomography, an imaging method that shows internal anatomy in detail. They found multiple copies of the primary silk gene in both species that likely arose from multiple duplication events at different evolutionary times. These silk genes exhibit unusual gene structure with hierarchically organized repeat units that are highly homogenized within a gene. The findings show that silk genes have a complex evolutionary history in webspinners and provide a foundation for studying silk diversity within the order, and in the broader context of insect silk.

Exaggerated sexually selected traits are known to be highly variable and their degree of expression is dependent on nutritional input. Yet the molecular mechanisms linking nutritional variation to phenotypic variation remain poorly understood. Here, we investigate how nutritional input shapes the development of male rear leg length, an exaggerated and highly variable trait in the water strider Microvelia longipes, using comparative transcriptomics and RNA interference gene knockdown experiments. We demonstrate that nutrition is the primary driver of gene expression variation, with male exaggerated rear legs exhibiting the highest number of nutrition-responsive genes. Moreover, the increase in morphological divergence between leg types or sex, which is systematically exacerbated by rich nutrition, is associated with increased number of leg-biased genes. These comparative analyses allowed us to identify BMP11 as specifically enriched in female and male rear legs. Knockdown of BMP11 abolishes nutritional plasticity in leg length only in males, positioning it as a key integrator of environmental, sex and developmental signals. Our findings reveal that transcriptional modulation provides a molecular interface between nutrition and trait exaggeration. This work advances our understanding of how environmental cues are translated into complex phenotypes and highlights the role of developmental plasticity as a substrate for evolutionary change.

Phenotypic plasticity, the ability of a single genotype to produce alternative phenotypes in response to environmental cues, is a key driver of evolutionary change. In the water strider Microvelia longipes, males display remarkable continuous variation in hindleg length, a sexually selected trait used as a weapon in male/male contests for access to females. To determine whether DNA methylation mediates this environmentally induced phenotypic variation, we used three inbred lines of M. longipes that differ in mean hindleg length, body size, and allometric coefficients. We performed whole-genome bisulfite sequencing on adult males and females from all lines, and tested the effect of nutritional treatment on DNA methylation patterns. Our analysis identified 12,684,876 CpG 12% of which were methylated. This global level of DNA methylation is among the highest reported in insects. DNA methylation was predominantly concentrated within or near gene bodies (77% of methylated CpGs), consistent with patterns observed in other insects. Unsupervised clustering and principal component analyses revealed that methylation patterns differed significantly between genetic lines but showed minimal differences between sexes, indicating a strong genetic influence. Most surprisingly, despite nutrition having a pronounced effect on leg length, we observed no significant changes in DNA methylation in response to dietary treatment. These results show that in M. longipes, DNA methylation patterns are largely stable across environmental conditions and primarily determined by genetic background. This challenges the common assumption that DNA methylation universally mediates environmentally induced phenotypic plasticity and suggests that other epigenetic mechanisms, such as histone modifications or non-coding RNAs, may play a more direct role in regulating continuous plastic traits. Our study underscores the complexity of epigenetic regulation and highlights the need for broader investigation of molecular pathways to fully understand the molecular basis of phenotypic variation in natural populations.

Sensory systems mediate the interaction between organisms and their environment, but how complex sensory pathways evolve and relate to variation in perception and behavior across ecological contexts, remains poorly understood, especially for terrestrial taxa. Here, we investigate whole-visual-system adaptation in Heliconius erato butterflies. Using continent-wide sampling, we demonstrate that within H. erato, facet count significantly decreased with increasing elevation. Common-garden rearing of low-elevation H. erato populations from Ecuador and their high-elevation sister species, H. himera, showed that eye and brain morphology are heritable, and comparisons to genomic measures of divergence indicates that this variation is due to divergent selection. Parallel comparisons from Colombia involving H. chestertonii (high elevation) and H. erato venus (low elevation) further revealed that eye and brain morphology can evolve as independent, decoupled traits. For both locations, differences in visual acuity correlated with variation in facet count. We also observed parallel evolution of spectral sensitivity, with independent high-elevation populations having fewer red-reflecting lateral filtering pigments. To experimentally link visual system morphology to behavior, we assessed visual acuity in second-generation H. erato cyrbia-H. himera hybrids. Overall, acuity was influenced by facet count, and when analyzed together with brain morphology, by a positive interaction between facet count and optic lobe volume, demonstrating that structural investment in the eye and neural expansion combine to maximize visual perception. This work shows that visual adaptation is a multi-layered process whereby sensory traits can evolve independently under localized ecological pressures, but evolution across the visual pathway contributes to refinements in behavioral performance.

Plants possess a remarkable capacity for regeneration, which involves the redeployment of developmental programs and diverse regulatory mechanisms. However, how related regulators with overlapping functions are differentially deployed during regeneration remains poorly understood. The model liverwort Marchantia polymorpha provides a powerful experimental system for studying regeneration because it readily regenerates apical meristems from basal thallus fragments after removal of the original meristem, even without exogenous plant hormones. Here, we identify the R2R3-MYB transcription factor GEMMA CUP-ASSOCIATED MYB1-LIKE (MpGC1L), the closest paralog of the clonal propagation regulator MpGCAM1, as a positive regulator of regeneration. MpGC1L was rapidly induced at the cut site following meristem removal. Ectopic overexpression of MpGC1L caused the proliferation of undifferentiated cells, whereas Mpgc1l mutants showed delayed regeneration and reduced S-phase entry. Loss of MpGCAM1 alone had little effect on regeneration but markedly enhanced the Mpgc1l phenotype, indicating partially redundant functions. Transcriptome analysis of the double mutant revealed reduced induction of genes associated with ribosome biogenesis and the cell cycle. We next examined the relationship between MpGC1L and the known jasmonate- and auxin- related regeneration regulators, MpERF15 and MpLAXR. MpGC1L induction was retained in Mperf15 and Mplaxr mutants and was unaffected by OPDA or auxin treatment, whereas MpERF15 and MpLAXR were still induced in Mpgc1l Mpgcam1 double mutants. Thus, these regulators are not arranged in a simple linear transcriptional pathway. Our findings reveal that the paralogous MYB transcription factors MpGC1L and MpGCAM1 promote cell proliferation in distinct developmental contexts, thereby linking clonal propagation and wound-induced regeneration.

Despite glutamates widespread role as the dominant excitatory transmitter in vertebrate brains, the early evolution of glutamate and its recruitment into neural signaling remain largely unknown. The major limitation is the lack of information on its distribution in early-branching basal metazoans, such as ctenophores (comb jellies). Here, using glutamate immunoreactivity (IR) in two ctenophore species with distinct ecologies (Pleurobrachia bachei and Beroe abyssicola), we show that glutamate IR is present in subpopulations of neurons within the subepithelial neural network and in small groups of mesogleal neuron-like cells, and that it differentially labels some muscle fibers. Remarkably, we also observed an enriched glutamate-ir signal within the nuclei of subepithelial neurons in Beroe. However, glutamate expression levels are species-specific, suggesting a tight coupling of glutamate recruitment for neural communication with energetic demands.

Amphibians develop both external and internal gills during ontogeny, offering an opportunity to investigate the developmental relationship between these positionally distinct respiratory organs. Although internal gills of vertebrates are widely accepted to arise from pharyngeal endoderm, external gills have long been regarded as purely ectodermal outgrowths, obscuring their relationship to other vertebrate gills. Here, we combine histological analysis with direct lineage tracing in the Mexican axolotl (Ambystoma mexicanum) and the African clawed frog (Xenopus laevis) to resolve the embryonic origin of amphibian gills. We show that the external gill develops as a continuous epithelial extension of the pharyngeal endoderm, which forms its basal epithelium and reaches the distal gill tip. In the frog, this extension remains continuous with the epithelium giving rise to the internal gills. Rather than representing separate epithelial structures, external and internal gills therefore arise from a shared epithelial domain of the pharyngeal endoderm. These findings resolve a longstanding question concerning the embryonic origin of amphibian gills and provide a developmental viewpoint for understanding how spatially diverse vertebrate gills can evolve through repeated modification of a conserved endodermal tissue.

Eph and ephrin genes encode receptor-ligand pairs that mediate contact-dependent cell signaling and are essential for nervous system development. However, less is known about the role of Ephrin signaling during adult tissue homeostasis and regeneration. Here, we investigated the role of Ephrin signaling in neural patterning in the planarian Schmidtea mediterranea. We discovered that RNAi against the Eph receptor EphR1 led to striking ectopic expression of the mechanosensory neuron markers pkd1L-2 and hmcn-1-L, without obvious disruption of the overall architecture of the central nervous system. To investigate the basis of this phenotype, we identified additional Eph receptor homologs and four putative ephrin ligands and assessed their function. An RNAi screen revealed that ephrin-1 phenocopies the defects of EphR1 RNAi. Temporal analyses of EphR1 and ephrin-1 inhibition revealed a progressive increase in pkd1L-2+ and hmcn-1-L+ cells, indicating an unappreciated role for Ephrin signaling in regulating neural patterning and cell number during adult tissue homeostasis. Together, these findings provide a framework for dissecting Ephrin-dependent mechanisms in adult tissue maintenance and regeneration.