Evolution & Development最新文献

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.

Developmental changes in animals reflect important behavioral, biological, and ecological shifts. Allometric adjustments in arthropods, specifically, are associated with changes in sexual maturity or alterations in life mode. Examining post-embryological allometry of the American horseshoe crab—Limulus polyphemus—here evidences early shifts in prosomal development, later changes in thoracetronic size, and possible modularity across exoskeletal sections. Modifications in prosomal allometry reflect transitions from living above the substrate to primarily burrowing. This change occurs at the 3–4 moult stage and is associated with a 70% mortality rate in both natural settings and under aquaculture conditions. Thoracetron allometry changes record the fusion of opisthosomal tergites into a plate, where tergal development drives shifts in thoracetron morphology. Allometric changes between main body sections present possible evidence for modularity within the horseshoe crab exoskeleton that manifest across moulting events. These allometric shifts reflect the complex evolutionary history of the group, especially changes from surface dwelling and enrollment to burrowing, likely in response to increased predation pressures.

Sulfidic caves are harsh and extreme environments characterized by limited oxygen, low pH, and the presence of hydrogen sulfide. Amazingly, animals can live in sulfidic caves, one such animal being Asellus infernus, a representative of the Asellus aquaticus species complex, originating from Movile Cave and from old wells that represent windows of access to a sulfidic groundwater ecosystem located in southeast Romania. Little previous work has been done on lab-reared populations of A. infernus as they have been historically difficult to raise in the lab. Here, we develop resources for A. infernus, examining questions of timing of morphological differences in cave versus surface individuals, whether the environment (lab-bred vs. wild-caught) influenced size characteristics, and the genes and pathways showing differential expression between cave and surface samples. We found that A. infernus did not develop pigmentation embryonically, and juveniles had increased body length and longer antenna II as compared to surface individuals. Furthermore, we found that some of these measures differed between wild-caught and lab-reared juveniles for a given population, indicating that environmental differences can also influence these size characteristics. In addition, differential expression between cave and surface samples and allele-specific expression studies within F1 hybrids identified multiple genes, including those involved in sulfide metabolism and phototransduction. Strikingly, molecular convergence of genes involved in sulfide detoxification was observed between A. infernus and previous work on a fish that lives in both cave and sulfidic environments, Poecilia mexicana. In sum, we were able to develop embryonic and genomic tools for A. infernus, a model for understanding cave adaptation and adaptation to sulfidic environments.

The biological processes underlying the wide phenotypic mammal diversity are still not thoroughly understood. In this study, we examined how major stages in the life history of the common hippopotamus (Hippopotamus Amphibius) influence its craniomandibular morphology throughout ontogeny. Using geometric morphometrics and life-history meta-analysis correlations, we characterized skulls from 198 individuals spanning 20 developmental stages. The most significant morphological changes were observed during early infancy (0–3 years), coinciding with lactation and weaning, and during puberty (10–15 years), coinciding with reproductive maturation. These findings align with growth patterns typical of social mammals exhibiting high sexual dimorphism. Notably, we identified a pattern previously undocumented in any other vertebrate: cranial morphology stabilizes earlier than the mandibular one. Specifically, late-stage (20–25 years) shape modification in the mandibles indicates progressive reconfiguration of masticatory biomechanics as well as a continuous change of dental occlusion throughout life. This pattern is common in both male and female individuals and may be related to shifts in diet rather than sexual selection. This study provides the most comprehensive ontogenetic dataset for a semi-aquatic, large semigraviportal mammal with a polygynous social structure, offering a valuable foundation for future evolutionary studies based on comparative analyses.

Uncovering mechanisms by which sensory systems evolve is critical for understanding how organisms adapt to a novel environment. Astyanax mexicanus is a species of fish with populations of surface fish, which inhabit rivers and streams, and cavefish, which have adapted to life within caves. Cavefish have evolved sensory system changes relative to their surface fish counterparts, providing an opportunity to investigate mechanisms underlying sensory system evolution. Here, we report the role of the gene retinal homeobox 3 (rx3) in cavefish eye evolution. We generated surface fish with putative loss-of-function mutations in the rx3 gene using CRISPR-Cas9 to determine the role of this gene in eye development in this species. These rx3 mutant surface fish fail to develop eyes, demonstrating that rx3 is required for surface fish eye development. Further, rx3 mutant surface fish exhibit altered behaviors relative to wild-type surface fish, suggesting that the loss of eyes impacts sensory-dependent behaviors. Finally, eye development is altered in cave-surface hybrid fish that inherit the mutant allele of rx3 from surface fish relative to siblings that inherit a wild-type surface fish rx3 allele, suggesting that cis-regulatory variation at the rx3 locus contributes to eye size evolution in cavefish. Together, these findings demonstrate that, as in other species, rx3 is required for eye development in A. mexicanus. Moreover, they suggest that variation at the rx3 locus plays a role in the evolved reduction of eye size in cavefish, shedding light on the genetic mechanisms underlying sensory system evolution in response to extreme environmental changes.

Two growth modes are recognized in colonial pterobranchs (Graptolithina): monopodial growth and sympodial growth. The earliest colonial Graptolithina likely developed through monopodial growth, a mode of colony formation well-documented in the extant graptolite Rhabdopleura normani. This growth involves a permanent terminal zooid and the sequential budding of additional zooids behind it, as the contractile stalk (gymnocaulus) of this terminal zooid elongates. This process is reflected in specific features of the secreted housing structure, the tubarium. Recently, monopodial growth was identified for the first time in a fossil taxon—the Cambrian dithecodendrid Tarnagraptus—based on tubarium characteristics, as no zooids were preserved. Monopodial growth also appears probable in other Cambrian taxa resembling Tarnagraptus, although evidence remains limited due to fragmentary materials. Sympodial growth, characterized by transient terminal zooids that are sequentially replaced as new buds form, is extensively documented in the fossil record of the Graptolithina. This growth mode characterizes the vast majority of Cambrian to Devonian Dendroidea and Graptoloidea. Phylogenetic evidence suggests sympodial growth evolved from monopodial growth in graptolithines, but the mechanisms underlying this evolutionary transition remain unclear.

Prey attraction is an integral component of the carnivorous syndrome, yet its molecular adaptations have remained largely unexplored. Our study utilized tissue-specific transcriptomic data from the South American marsh pitcher plant, Heliamphora tatei, to explore the molecular and developmental basis of prey attraction. Carnivorous plants often present specialized structures associated with prey attraction and in Heliamphora, that function is carried out by the nectar spoon, a colorful extension of the top of the pitcher that is densely covered in nectaries. Through comparisons of gene expression in the nectar spoon with the rest of the pitcher, we identified a suite of differentially expressed genes that likely contribute to prey attraction, including enzymes involved in volatile synthesis and sugar transporters. We found that one lineage of sugar transporters, the 14a clade of SWEETs (Sugars Will Eventually Be Exported Transporters), is highly upregulated in the nectar spoon and has evolved more rapidly in Sarraceniaceae, consistent with specialization for nectar transport as part of prey attraction. Among the genes related to volatile production, we found several enzymes best known for their role in floral scent. These results suggest that, similar to prey digestion, ancient genes are repurposed for novel functions during the transition to carnivory and may facilitate the repeated convergent origins of carnivory across angiosperms.

Variation in shape and size within a lineage, driven by developmental processes, plays a key role in diversification. Here, we explore the effects of allometry and heterochrony on the skull shape evolution during the post-metamorphic period of species within the Boana faber clade, which vary considerably in body size. We analyzed 61 skulls of specimens belonging to eight species of the Boana faber clade, in addition to two outgroups, through 2D geometric morphometric analyses taken from CT-Scan images. Our results demonstrated that skull shape is considerably impacted by the size, represented by centroid size, and this effect can be observed from ontogenetic and evolutionary perspectives. In this way, we accessed the ontogenetic trajectories of analysed species and, in light of the phylogenetic hypothesis of the clade, we discussed the observed variation based on the concept of heterochrony, suggesting that a peramorphic pattern has evolved in the group.