The Daphnia carapace and other novel structures evolved via the cryptic persistence of serial homologs

Dissecting roles of pannier splice variants during pupal and adult morphogenesis in Henosepilachna vigintioctopunctata

The GATA transcription factor gene, pannier (pnr), has been extensively studied in Drosophila, revealing its crucial role in dorsal closure, heart development and the regulation of cuticular bristle patterns in adults. However, studies on the functions of pnr in the development of coleopteran insects are still scarce. Herein, we identified the pnr gene in Henosepilachna vigintioctopunctata and discovered two splicing variants named Hvpnr-α and Hvpnr-β respectively. Temporal expression analysis revealed that Hvpnr, Hvpnr-α and Hvpnr-β were expressed at various stages including egg, larval, pupal and adult stages. To investigate the developmental role of Hvpnr in H. vigintioctopunctata, RNA interference (RNAi) assays were conducted on third-instar larvae. Injection of dsHvpnr, dsHvpnr-α and dsHvpnr-β and co-injection of dsHvpnr-α and dsHvpnr-β (dsRNAs mix) all resulted in significant downregulation of the target transcripts. In pupae developed from dsHvpnr-treated larvae, the symmetric black spots on both sides of the mesothorax, metathorax and tergites approached and connected. Pupal morphometric analysis revealed that dsHvpnr, dsHvpnr-α and dsRNAs mix injections significantly narrowed the spacing of dorsal symmetric spots, contracted spiracle distances on tergite sides, diminished pronotum width and markedly reduced inter-compound eye spacing compared to controls. In addition, injections of dsHvpnr and dsRNAs mix significantly reduced the oviposition in female adults. Silencing of Hvpnr led to the disappearance of the scutellum in adults, preventing the elytra from closing and properly attaching to the dorsal side of the abdomen. It is noteworthy that dsHvpnr-α or dsRNA mix induced scutellum formation defects in adults, while knockdown of Hvpnr-β had no impact. Furthermore, in stark contrast to previous studies on ladybird species such as Harmonia axyridis and Coccinella septempunctata, silencing Hvpnr did not affect melanin synthesis in pupae and adults in H. vigintioctopunctata. These findings demonstrate that among the splice variants of Hvpnr, Hvpnr-α plays a dominant regulatory role in the post-embryonic morphogenesis of H. vigintioctopunctata. This study also shows that Hvpnr is not involved in melanin synthesis, indicating significant functional differentiation of pnr during the evolution of ladybirds.

The mosaicism of Cas-induced mutations and pleiotropic effects of scarlet gene in an emerging model system

The effective use of CRISPR technologies in emerging model organisms faces significant challenges in efficiently generating heritable mutations and in understanding the genomic consequences of induced DNA damages and the inheritance patterns of induced mutations. This study addresses these issues by 1) developing an efficient microinjection delivery method for gene editing in the microcrustacean Daphnia pulex; 2) assessing the editing dynamics of Cas9 and Cas12a nucleases in the scarlet knock-out mutants; and 3) investigating the transcriptomes of scarlet mutants to understand the pleiotropic effects of scarlet gene. Our reengineered microinjection method results in efficient biallelic editing with both nucleases. Our data suggest site-specific DNA cleavage mostly occurs in a stepwise fashion. Indels dominate the induced mutations. A few, unexpected on-site large deletions (>1 kb) are also observed. Notably, genome-wide analyses reveal no off-target mutations. Knock-in of a stop codon cassette to the scarlet locus was successful, despite complex induced mutations surrounding the target site. Moreover, extensive germline mosaicism exists in some mutants, which unexpectedly produce different phenotypes/genotypes in their asexual progeny. Lastly, our transcriptomic analyses unveil significant gene expression changes associated with scarlet knock-out and altered swimming behavior in mutants, including several genes involved in human neurodegenerative diseases.

The transition to flying insects: lessons from evo-devo and fossils

Insects are the only arthropod group to achieve powered flight, which facilitated their explosive radiation on land. It remains a significant challenge to understand the evolutionary transition from nonflying (apterygote) to flying (pterygote) insects due to the large gap in the fossil record. Under such a situation, ontogenic information has historically been used to compensate for fossil evidence. Recent evo-devo studies support and refine a paleontology-based classical hypothesis that an ancestral exite incorporated into the body wall contributed to the origin of insect wings. The modern hypothesis locates an ancestral precoxa leg segment with an exite within the hexapod lateral tergum, reframing the long-standing debate on the insect wing origin. A current focus is on the contributions of the incorporated exite homolog and surrounding tissues, such as the pleuron and the medial bona fide tergum, to wing evolution. In parallel, recent analyses of Paleozoic fossils have confirmed thoracic and abdominal lateral body outgrowths as transitional wing precursors and suggested their possible role as respiratory organs in aquatic or semiaquatic environments. These recent studies have revised our understanding of the transition to flying insects. This review highlights recent progress in both evo-devo and paleontology, and discusses future challenges, including the evolution of metamorphic development.

Comparative transcriptomics suggests a potential realizator gene for carapace expansion in longtail tadpole shrimp, Triops longicaudatus (Branchiopoda: Notostraca)

The origin of morphological innovation has been extensively studied within evolutionary developmental biology (evo-devo). Recent studies have demonstrated that the developmental module for double-layered epithelial outgrowths is conserved between the insect wings and branchiopod crustacean carapace, thereby introducing homology among these diverse structures. However, evo-devo studies on the branchiopod crustacean carapace have been primarily limited to a single species, the water flea Daphnia magna, leaving the gene regulatory network governing carapace development not comprehensively understood. Furthermore, realizator genes downstream of the character identity mechanism (ChIM) for bilayered epithelial development remain inadequately described. In this study, we analyzed tissue-specific transcriptional profiles in the developing longtail tadpole shrimp, Triops longicaudatus. We observed significant upregulation of papilin in the carapace-bearing head, along with its expression in both the carapace and the trunk limb lobes. Based on these results, we hypothesize that differential expression of papilin is involved in the disproportional growth of Triops carapace. Our findings will contribute to elucidating the diversification of double-layered epithelial outgrowths across distant arthropod lineages.

Parthenogenetic Stick Insects Exhibit Signatures of Preservation in the Molecular Architecture of Male Reproduction

After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (i) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (ii) that gene co-expression network architecture could constrain individual gene expression. Our testing ground has been the Bacillus stick insect species complex, which contains close relatives that are either bisexual or parthenogenetic. After the identification of genes expressed in male reproductive tissues in a bisexual species, we investigated their gene co-expression network structure in two parthenogenetic species. We found that gene co-expression within the male gonads was partially preserved in parthenogens. Furthermore, parthenogens did not show relaxed selection on genes upregulated in male gonads in the bisexual species. As these genes were mostly expressed in female gonads, this preservation could be driven by pleiotropic interactions and an ongoing role in female reproduction. Connectivity within the network also played a key role, with highly connected-and more pleiotropic-genes within male gonad also having a gonad-biased expression in parthenogens. Our findings provide novel insight into the mechanisms which could underlie the production of rare males in parthenogenetic lineages; more generally, they provide an example of the cryptic persistence of a lost trait molecular architecture, driven by gene pleiotropy on other traits and within their co-expression network.

Sox21b underlies the rapid diversification of a novel male genital structure between Drosophila species

The emergence and diversification of morphological novelties is a major feature of animal evolution.1,2,3,4,5,6,7,8,9 However, relatively little is known about the genetic basis of the evolution of novel structures and the mechanisms underlying their diversification. The epandrial posterior lobes of male genitalia are a novelty of particular Drosophila species.10,11,12,13 The lobes grasp the female ovipositor and insert between her abdominal tergites and, therefore, are important for copulation and species recognition.10,11,12,14,15,16,17 The posterior lobes likely evolved from co-option of a Hox-regulated gene network from the posterior spiracles10 and have since diversified in morphology in the D. simulans clade, in particular, over the last 240,000 years, driven by sexual selection.18,19,20,21 The genetic basis of this diversification is polygenic but, to the best of our knowledge, none of the causative genes have been identified.22,23,24,25,26,27,28,29,30 Identifying the genes underlying the diversification of these secondary sexual structures is essential to understanding the evolutionary impact on copulation and species recognition. Here, we show that Sox21b negatively regulates posterior lobe size. This is consistent with expanded Sox21b expression in D. mauritiana, which develops smaller posterior lobes than D. simulans. We tested this by generating reciprocal hemizygotes and confirmed that changes in Sox21b underlie posterior lobe evolution between these species. Furthermore, we found that posterior lobe size differences caused by the species-specific allele of Sox21b significantly affect copulation duration. Taken together, our study reveals the genetic basis for the sexual-selection-driven diversification of a novel morphological structure and its functional impact on copulatory behavior.

Efficient CRISPR genome editing and integrative genomic analyses reveal the mosaicism of Cas-induced mutations and pleiotropic effects of scarlet gene in an emerging model system

Despite the revolutionary impacts of CRISPR-Cas gene editing systems, the effective and widespread use of CRISPR technologies in emerging model organisms still faces significant challenges. These include the inefficiency in generating heritable mutations at the organismal level, limited knowledge about the genomic consequences of gene editing, and an inadequate understanding of the inheritance patterns of CRISPR-Cas-induced mutations. This study addresses these issues by 1) developing an efficient microinjection delivery method for CRISPR editing in the microcrustacean Daphnia pulex; 2) assessing the editing efficiency of Cas9 and Cas12a nucleases, examining mutation inheritance patterns, and analyzing the local and global mutation spectrum in the scarlet mutants; and 3) investigating the transcriptomes of scarlet mutants to understand the pleiotropic effects of scarlet underlying their swimming behavior changes. Our reengineered CRISPR microinjection method results in efficient biallelic editing with both nucleases. While indels are dominant in Cas-induced mutations, a few on-site large deletions (>1kb) are observed, most likely caused by microhomology-mediated end joining repair. Knock-in of a stop codon cassette to the scarlet locus was successful, despite complex induced mutations surrounding the target site. Moreover, extensive germline mosaicism exists in some mutants, which unexpectedly produce different phenotypes/genotypes in their asexual progenies. Lastly, our transcriptomic analyses unveil significant gene expression changes associated with scarlet knock-out and altered swimming behavior in mutants, including several genes (e.g., NMDA1, ABAT, CNTNAP2) involved in human neurodegenerative diseases. This study expands our understanding of the dynamics of gene editing in the tractable model organism Daphnia and highlights its promising potential as a neurological disease model.

Marine-montane transitions coupled with gill and genetic convergence in extant crustacean

Marine-terrestrial transition represents an important aspect of organismal evolution that requires numerous morphological and genetic innovations and has been hypothesized to be caused by geological changes. We used talitrid crustaceans with marine-coastal-montane extant species at a global scale to investigate the marine origination and terrestrial adaptation. Using genomic data, we demonstrated that marine ancestors repeatedly colonized montane terrestrial habitats during the Oligocene to Miocene. Biological transitions were well correlated with plate collisions or volcanic island formation, and top-down cladogenesis was observed on the basis of a positive relationship between ancestral habitat elevation and divergence time for montane lineages. We detected convergent variations of convoluted gills and convergent evolution of SMC3 associated with montane transitions. Moreover, using CRISPR-Cas9 mutagenesis, we proposed that SMC3 potentially regulates the development of exites, such as talitrid gills. Our results provide a living model for understanding biological innovations and related genetic regulatory mechanisms associated with marine-terrestrial transitions.

Evolution: Hidden homologies may underpin the diversity of arthropods

Arthropods are remarkable for the diversity of their exoskeletons. A new study shows that these structures, from crustacean carapaces to insect wings, may be homologous and derived from hidden developmental structures preserved through arthropod evolution.