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Insects use sex pheromones as a reproductive isolating mechanism to attract conspecifics and repel heterospecifics. Despite the profound knowledge of sex pheromones, little is known about the coevolutionary mechanisms and constraints on their production and detection. Using whole-genome sequences to infer the kinship among 99 drosophilids, we investigate how phylogenetic and chemical traits have interacted at a wide evolutionary timescale. Through a series of chemical syntheses and electrophysiological recordings, we identify 52 sex-specific compounds, many of which are detected via olfaction. Behavioral analyses reveal that many of the 43 male-specific compounds are transferred to the female during copulation and mediate female receptivity and/or male courtship inhibition. Measurement of phylogenetic signals demonstrates that sex pheromones and their cognate olfactory channels evolve rapidly and independently over evolutionary time to guarantee efficient intra- and inter-specific communication systems. Our results show how sexual isolation barriers between species can be reinforced by species-specific olfactory signals. Despite the profound knowledge of sex pheromones, little is known about the coevolutionary mechanisms and constraints on their production and detection. Whole-genome sequences from 99 drosophilids, with chemical and behavioural data, show that sex pheromones and their cognate olfactory channels evolve rapidly and independently.

Despite its role in homogenizing populations, hybridization has also been proposed as a means to generate new species. The conceptual basis for this idea is that hybridization can result in novel phenotypes through recombination between the parental genomes, allowing a hybrid population to occupy ecological niches unavailable to parental species. Here we present an alternative model of the evolution of reproductive isolation in hybrid populations that occurs as a simple consequence of selection against genetic incompatibilities. Unlike previous models of hybrid speciation, our model does not incorporate inbreeding, or assume that hybrids have an ecological or reproductive fitness advantage relative to parental populations. We show that reproductive isolation between hybrids and parental species can evolve frequently and rapidly under this model, even in the presence of substantial ongoing immigration from parental species and strong selection against hybrids. An interesting prediction of our model is that replicate hybrid populations formed from the same pair of parental species can evolve reproductive isolation from each other. This non-adaptive process can therefore generate patterns of species diversity and relatedness that resemble an adaptive radiation. Intriguingly, several known hybrid species exhibit patterns of reproductive isolation consistent with the predictions of our model.

The evolutionary forces shaping life history divergence within species are largely unknown. Turquoise killifish display differences in lifespan among wild populations, representing an ideal natural experiment in evolution and diversification of life history. By combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among wild turquoise killifish populations. We generate an improved reference genome assembly and identify genes under positive and purifying selection, as well as those evolving neutrally. Short-lived populations from the outer margin of the species range have small population size and accumulate deleterious mutations in genes significantly enriched in the WNT signaling pathway, neurodegeneration, cancer and the mTOR pathway. We propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by increasing the genome-wide mutation load, exacerbates the effects of mutation accumulation and cumulatively contribute to the short adult lifespan.

Hybridization is increasingly being recognized as a common process in both animal and plant species. Negative epistatic interactions between genes from different parental genomes decrease the fitness of hybrids and can limit gene flow between species. However, little is known about the number and genome-wide distribution of genetic incompatibilities separating species. To detect interacting genes, we perform a high-resolution genome scan for linkage disequilibrium between unlinked genomic regions in naturally occurring hybrid populations of swordtail fish. We estimate that hundreds of pairs of genomic regions contribute to reproductive isolation between these species, despite them being recently diverged. Many of these incompatibilities are likely the result of natural or sexual selection on hybrids, since intrinsic isolation is known to be weak. Patterns of genomic divergence at these regions imply that genetic incompatibilities play a significant role in limiting gene flow even in young species. In nature, closely related species often interbreed to produce hybrids. However, hybrids are often less fertile or unable to compete with parent species, making them less likely to thrive in the wild. When the genomes of two different species are mixed, versions of genes that are meant to work together can become separated, which means that these genes do not work as well as they should. This reduces the hybrids' chances of survival, and a poor survival rate of hybrids is one barrier that keeps different species distinct, even though the species can interbreed. Two species of swordtail fish live in the rivers in Mexico, and although they mostly live in different stretches of these rivers, the two species interbreed to produce hybrids in the regions where they overlap. These hybrids can outnumber the parental species in these ‘hybrid zones’, but the two species have remained separate in other parts of the rivers. Though some genetic incompatibilities that might keep the species distinct have previously been suggested, it is not known how many incompatibilities there are in these fish's genomes. Schumer et al. have searched the genomes of wild hybrids between these species and found hundreds of genetic incompatibilities. These were identified by looking for species-specific pairs of genes that are found together more often than would be expected if there were no selection against hybrids. It is likely that many of these incompatibilities reduce the evolutionary fitness of the hybrid fish and Schumer et al. suggest that many could be the result of environmental pressures and the fish's mating preferences. Furthermore, Schumer et al. demonstrate that genes close to identified incompatibilities are more different between species, on average, than genes that are further away. When there is on-going interbreeding between two the species (as is the case with the swordtails), this finding is expected only if these incompatibilities reduce the hybrids' chances of finding mates or surviving. The findings of Schumer et al. demonstrate how conflicts in the genomes of two species allow these species to remain distinct even when they live in overlapping environments and frequently interbreed. Future work will investigate how these genetic incompatibilities shape the hybrid populations that are found in the wild; and which incompatibilities are caused by poor survival of the hybrids or by the fish's mating preferences selecting against the hybrids.

Although seed size is one of the most important agronomic traits in plants, the genetic and molecular mechanisms that set the final size of seeds are largely unknown. We previously identified the ubiquitin receptor DA1 as a negative regulator of seed size, and the Arabidopsis thaliana da1-1 mutant produces larger seeds than the wild type. Here, we describe a B3 domain transcriptional repressor NGATHA-like protein (NGAL2), encoded by the suppressor of da1-1 (SOD7), which acts maternally to regulate seed size by restricting cell proliferation in the integuments of ovules and developing seeds. Overexpression of SOD7 significantly decreases seed size of wild-type plants, while the simultaneous disruption of SOD7 and its closest homolog DEVELOPMENT-RELATED PcG TARGET IN THE APEX4 (DPA4/NGAL3) increases seed size. Genetic analyses indicate that SOD7 and DPA4 act in a common pathway with the seed size regulator KLU to regulate seed growth, but do so independently of DA1. Further results show that SOD7 directly binds to the promoter of KLUH (KLU) in vitro and in vivo and represses the expression of KLU. Therefore, our findings reveal the genetic and molecular mechanisms of SOD7, DPA4, and KLU in seed size regulation and suggest that they are promising targets for seed size improvement in crops.

Over the last three decades, microglia have been recognized as essential components of central nervous system (CNS) development, homeostasis, immune surveillance, and neurodegenerative pathogenesis. Historically, microglia were regarded as exclusive to the CNS, based on the absence of cells bearing microglial morphology, transcriptional identity, and ontogeny in tissues outside the CNS in standard mouse and rat models. However, recent studies, including those from our group, have identified cells in peripheral tissues of humans and other vertebrates that share the transcriptomic signature and yolk sac-derived ontogeny characteristic of CNS microglia. These findings suggest that the microglial lineage represents a broader spectrum of tissue-resident macrophages with specialized roles across organs. Microglia constitute one of the most evolutionarily ancient macrophage subtypes, with IBA1-positive cells already identifiable in the brain of the annelid Hirudo medicinalis. Wu et al's recent identification of microglial cells in the peripheral nervous system (PNS) provides compelling evidence supporting the notion that homologous cell types may evolve independently in distinct anatomical niches. In evolutionary biology, homology denotes descent from a common ancestor, irrespective of phenotypic similarity. Conventionally, cell type homology within and between species has primarily been inferred from shared anatomical location, phenotype, or function.

The emergence of new species is driven by the establishment of mechanisms that limit gene flow between populations. A major challenge is reconciling the theoretical and empirical importance of assortative mating in speciation with the ease with which it can fail. Swordtail fish have an evolutionary history of hybridization and fragile prezygotic isolating mechanisms. Hybridization between two swordtail species likely arose via pollution-mediated breakdown of assortative mating in the 1990s. Here we track unusual genetic patterns in one hybrid population over the past decade using whole-genome sequencing. Hybrids in this population formed separate genetic clusters by 2003, and maintained near-perfect isolation over 25 generations through strong ancestry-assortative mating. However, we also find that assortative mating was plastic, varying in strength over time and disappearing under manipulated conditions. In addition, a nearby population did not show evidence of assortative mating. Thus, our findings suggest that assortative mating may constitute an intermittent and unpredictable barrier to gene flow, but that variation in its strength can have a major effect on how hybrid populations evolve. Understanding how reproductive isolation varies across populations and through time is critical to understanding speciation and hybridization, as well as their dependence on disturbance.

Mate choice can play a pivotal role in the nature and extent of reproductive isolation between species. Mating preferences are often dependent on an individual's social experience with adult phenotypes throughout development. We show that olfactory preference in a swordtail fish (Xiphophorus malinche) is affected by previous experience with adult olfactory signals. We compare transcriptome-wide gene expression levels of pooled sensory and brain tissues between three treatment groups that differ by social experience: females with no adult exposure, females exposed to conspecifics and females exposed to heterospecifics. We identify potential functionally relevant genes and biological pathways differentially expressed not only between control and exposure groups, but also between groups exposed to conspecifics and heterospecifics. Based on our results, we speculate that vomeronasal receptor type 2 paralogs may detect species-specific pheromone components and thus play an important role in reproductive isolation between species.

Background In the field of ornamental horticulture, phenotypic mutations, particularly in leaf color, are of great interest due to their potential in developing new plant varieties. The introduction of variegated leaf traits in plants like Heliopsis helianthoides , a perennial herbaceous species with ecological adaptability, provides a rich resource for molecular breeding and research on pigment metabolism and photosynthesis. We aimed to explore the mechanism of leaf variegation of Heliopsis helianthoides (using HY2021F1-0915 variegated mutant named HY, and green-leaf control check named CK in 2020 April, May and June) by analyzing the transcriptome and metabolome. Results Leaf color and physiological parameters were found to be significantly different between HY and CK types. Chlorophyll content of HY was lower than that of CK samples. Combined with the result of Weighted Gene Co-expression Network Analysis (WGCNA), 26 consistently downregulated differentially expressed genes (DEGs) were screened in HY compared to CK subtypes. Among the DEGs, 9 genes were verified to be downregulated in HY than CK by qRT-PCR. The reduction of chlorophyll content in HY might be due to the downregulation of FSD2. Low expression level of PFE2, annotated as ferritin-4, might also contribute to the interveinal chlorosis of HY. Based on metabolome data, differential metabolites (DEMs) between HY and CK samples were significantly enriched on ABC transporters in three months. By integrating DEGs and DEMs, they were enriched on carotenoids pathway. Downregulation of four carotenoid pigments might be one of the reasons for HY’s light color. Conclusion FSD2 and PFE2 (ferritin-4) were identified as key genes which likely contribute to the reduced chlorophyll content and interveinal chlorosis observed in HY. The differential metabolites were significantly enriched in ABC transporters. Carotenoid biosynthesis pathway was highlighted with decreased pigments in HY individuals. These findings not only enhance our understanding of leaf variegation mechanisms but also offer valuable insights for future plant breeding strategies aimed at preserving and enhancing variegated-leaf traits in ornamental plants.

The starter diet for Japanese eel ( Anguilla japonica ) has always been a difficult problem for the realization of total artificial reproduction. Therefore, this research analyzed the nutritional composition of artificially fertilized eggs, and transcriptome of samples from early hatchlings of fry to better understand nutrients requirements. The composition of crude lipid and crude protein in fertilized eggs was 7.24% ± 0.32% and 10.56% ± 0.41%, respectively. Seven kinds of essential amino acids (EAA) were detected but took a comparable lower content (3.19%) than other marine fish eggs. We randomly assembled 265.74 million clean reads and identified 1751 differentially expressed genes (DEGs) ( P < 0.01) from pre-leptocephalus larvae. A total of 23 KEGG pathways related to the digestive and metabolic system were detected. Genes related to the secretion pathway of saliva, pancreatic juice and other digestive juices were significantly changed. Transcriptome analysis showed that as larvae aged, glycolytic metabolism and the transcription level of hexokinase (HK) increased significantly (day 0 to 12). This study will facilitate future studies on the nutrition of A. japonica larvae and other biological traits to reproductive research.