BMC Biology最新文献

Background: Human-induced habitat changes threaten biodiversity, prompting large-scale restoration initiatives. Revegetation through direct seeding is common in agricultural and infrastructure construction projects, yet the provenance of seed material and its genetic impacts on natural populations remain underexplored. Introducing foreign ecotypes can lead to unintended consequences, as they may be adapted to different environmental conditions or represent distinct evolutionary lineages. In Switzerland, direct seeding is widely used to promote dry meadows, often using seeds of the Carthusian pink (Dianthus carthusianorum).

Results: To assess the extent and genetic effects of direct seeding and infer seed provenances, we combined genomic data from 446 samples collected in independent, smaller-scale studies. We assembled a chromosome-level reference genome to map reads and developed a panel of 48,299 representative single nucleotide polymorphisms (SNPs). We identified six evolutionary significant units (ESUs) within the European distribution range of D. carthusianorum. As biodiversity promotion efforts are often coordinated nationally, we focused on populations in Switzerland, where we found five ESUs: four occur naturally, and one was introduced from Eastern Europe. Our combined genomic data revealed that 15 of 31 randomly sampled populations across Switzerland (48.4%) originated from direct seeding. Allochthonous seed material was detected in eight populations (25.8%), with six of these showing admixture involving two to three ESUs.

Conclusions: Our results demonstrate the effectiveness of genomic approaches for identifying direct seeding and clarifying seed provenance, thereby supporting decision-making in national revegetation projects and emphasising the importance of using autochthonous seed sources.

Background: Both endophytes, microorganisms that reside within plants, and methylotrophs, which grow using methanol produced from plant leaves, play key roles in protecting plants against biotic and abiotic stresses. However, the source of endophytes and the mechanisms of their selection in plants are poorly understood. Therefore, experiments were carried out to identify wheat seed methylotrophic endophytes and evaluate their partitioning in root, stem and leaf of aseptic-controlled plants cultivated from surface-sterilized seeds.

Results: The counts of endophytic methanol utilizers were higher in leaf tissue than in stem, root and seed, as estimated using viable counts and qPCR targeting rrn gene. The methanol dehydrogenase subunit mxaF gene was PCR-detected in all pink-coloured isolates that grew using methanol or succinate. These pink-pigmented facultative methylotrophs (PPFM) were dominant in shoot tissue. Using mass spectrometry for alkaloid content analysis, peganine was detected as a peak 16.6% higher in root than shoot. Root extracts and peganine alone inhibited the growth of PPFM.

Conclusions: PPFM transmitted from seed are more abundant in shoot than root. How plant compounds such as peganine are involved in the methylotrophic endo-phytomicrobiome dynamics remains to be better characterized.

Background: Mimicry is an adaptive strategy widespread in modern ecosystems, yet its deep-time origins and evolution remain poorly understood due to the scarcity of unequivocal fossil evidence. Leaf mimicry has independently evolved in multiple insect lineages, reliable fossil evidence remains exceedingly rare and is primarily known from the Mesozoic and Cenozoic.

Results: We report a highly specialised cicadomorphan forewing from the Guadalupian Yinping Formation of China (ca. 260 Ma) that exhibits a striking morphological resemblance to Sphenophyllum Brongniart, 1828, a groundcover widely distributed in late Paleozoic floras. An integrated assessment of wing morphology, geometric morphometric analysis, and the ecological association between the insect and the plant supports the hypothesis of mimicry.

Conclusions: This finding enriches the Paleozoic record of leaf mimicry in insects, broadens our understanding of its evolutionary history in Hemiptera, and provides a rare perspective on insect-plant ecological associations in the South China Block before the end-Permian mass extinction.

Background: Cyanophages, viruses that infect cyanobacteria, are diverse and ubiquitous in the marine environment and play important roles in regulating the host community's structure, dynamics, and metabolism. Isolation is an efficient method to explore the genetic diversity of cyanophages and their interactions with hosts. However, our understanding of these interactions is still limited, and further in-depth research is needed to address this gap.

Results: In this study, we report a novel marine T4-like cyanophage, S-SCSM2R, that is able to cross-infect eight picocyanobacterial phylogenetic clades, including three Prochlorococcus clades of both high-light and low-light ecotypes and eight Synechococcus subclades across all five Synechococcus clades of 5.1, 5.2, 5.3, Subalpine II and Bornholm Sea. S-SCSM2R contains novel auxiliary metabolic genes involved in photosynthesis, alleviation of oxidative stress, cell wall synthesis and modification, and antibiotic synthesis. Alongside the receptor-binding protein gene, a set of counter-defense genes related to DNA methylation and NAD⁺ synthesis provide clues about the broad cross-infectivity of S-SCSM2R.

Conclusions: S-SCSM2R has an extremely broad host range and novel genetic features related to phage-host interactions. The discovery and characterization of S-SCSM2R broaden our knowledge of cyanophage cross-infectivity and reveal new ways in which cyanophages manipulate host metabolism in marine ecosystems.

Background: Stipules are specialized appendages borne at the base of a leaf petiole and may perform a variety of functions including sheltering delicate growing tissues from environmental exposure, facilitating vegetative propagation and dispersal, and providing climbing hooks or protective spines. While stipules are widespread in extant angiosperms and a few fern groups, their origins in geological history remain poorly understood. This study critically reconsiders the absence of stipules in the ancestry of Marattiales.

Results: Based on extraordinary collections from the early Permian Wuda Tuff Flora, we report, for the first time, aphlebia fossils organically attached to psaroniaceous petioles. The psaroniaceous aphlebiae are homologous to marattiaceous stipules, as evidenced by numerous shared characteristics. Functionally, psaroniaceous stipules appear to shelter juvenile fronds and the stem apex, with a continued role in mature fronds. Furthermore, their continued and potentially indeterminate growth, along with their fully laminated structure, suggests a possible role in vegetative propagation after detachment from the parent frond. However, no direct fossil evidence of stipules acting as vegetative propagules is currently available.

Conclusions: Our discovery provides unprecedented view of stipules in psaroniaceous tree ferns. The discovery of psaroniaceous stipules is significant, as it represents the earliest known stipule in the plant kingdom and underscores their multifunctional roles in plant development.

Background: As populations age, the number of people with age-related chronic diseases increases, causing significant social, economic and health problems. Natural variation in lifespan depends on multiple interacting genes and environmental exposures. Its short generation time and many resources make Drosophila melanogaster an advantageous model to uncover the genetic architecture that underlies variation in lifespan.

Results: We performed whole genome sequencing on young and old flies, sexes separately, in an outbred advanced intercross population (AIP) derived from inbred, sequenced lines from the Drosophila Genetic Reference Panel (DGRP). We identified mostly sex-specific variants (extreme Quantitative Trait Loci; xQTLs) at 1,107 genes associated with increased lifespan. We used the same AIP for RNA sequencing of heads, bodies and reproductive tissues for males and females weekly to 10 weeks of age. We identified 2,613 genes with age-related changes, of which 186 had xQTLs. Over half of the significant effects of gene expression with age included sex- and/or tissue-specific context-dependent effects, many of which were antagonistic, indicating complex trade-offs in gene regulation in the context of lifespan. We mapped genes whose expression changes with age onto known gene-gene and protein-protein interactions to construct interaction networks anchored by xQTLs. These networks were enriched for evolutionarily conserved mitochondrial, metabolic, neuronal, immune and developmental genes. Human orthologs of Drosophila genes associated with senescence and lifespan were prevalent indicating the translational potential of results from Drosophila to human populations.

Conclusions: Natural genetic variation in Drosophila identifies sex- and/or tissue-specific genetic variation and networks enriched for evolutionarily conserved genes.

Background: Nutrition during early life often has lasting consequences for adult physiology. However, it remains unclear how developmental diet shapes both the initial energetic state and subsequent change of energy stores. To address this, we systematically varied yeast and sugar concentrations in the developmental diet of Drosophila melanogaster and quantified energy reserves (in joules, derived from fat, glycogen, trehalose, and glucose) at eclosion and after 10 days of adulthood on a standardized diet. Comparing these time points allowed estimation of net change in energy reserves. Additionally, we examined how these effects depend on sex, population, and reproductive status.

Results: Developmental diet strongly influenced initial energy reserves. Higher sugar concentrations increased energy stores at eclosion. However, the subsequent net change in energy was inversely related to these starting conditions. Flies reared on high-sugar larval diets, which emerged with the most energy, exhibited the smallest net change during early adulthood. In contrast, flies from low-sugar diets emerged leaner and subsequently showed the largest net increase. These patterns were modulated by sex and reproductive status. In males, energy stores more closely reflected the larval nutritional background, whereas in females this relationship was weaker-likely due to the energetic demands of oogenesis. Mating was generally associated with lower energy reserves across groups.

Conclusions: Early-life diet affects both the starting point and early-adult change in energy reserves in Drosophila. These findings outline a framework in which developmental history and adult conditions jointly shape energetic trajectories.

Nictation is a dispersal behavior in nematodes, aiding movement and host-finding under stress. This review explores its diversity, genetic and neuronal basis, regulation, and ecological relevance. Nictation involves sensory integration, plasticity, and inter-organismal communication. Though its neural circuitry and molecular pathways remain partly understood, recent findings highlight roles for dauer signaling, neurotransmitters, and neuropeptides. Advances in scoring methods and genetic tools, including of parasitic species, now enable deeper study of its environmental triggers, evolutionary context, and impact on nematode virulence, with key knowledge gaps identified for future research.

Background: The black soldier fly (BSF, Hermetia illucens) is widely used for waste bioconversion and sustainable protein production. However, domestication and prolonged captive rearing can rapidly alter genetic diversity and population structure. This study investigated how selective breeding, genetic drift, and relaxed selection have shaped genomic variation and effective population size in multiple BSF populations. Using genome-wide restriction site-associated DNA sequencing, we analysed population structure, heterozygosity, and selection signatures across 11 BSF populations, including 1 long-term domesticated line, 5 selectively bred lines (Line A to Line E), 3 wild-derived populations, and 2 commercial strains.

Results: Despite shared origins, lines LA to LE diverged rapidly within 6 years. Principal component analysis and ADMIXTURE clustering (K = 11) revealed that LC to LE retained close genetic affinity, while LA and LB diverged markedly from each other and LC-LE. Demographic reconstructions using Stairway Plot showed that effective population sizes increased during the initial homogenized selective breeding phase (2018-2019) but declined after 2022, consistent with bottlenecks and relaxed selection. Wild-derived populations maintained higher heterozygosity and lower inbreeding coefficients than domesticated lines. Finally, genome-wide analyses identified 133 candidate genes under selection, including signatures of balancing selection and selective sweeps, reflecting divergent evolution under domestication.

Conclusions: These findings demonstrate that genetic differentiation occurs rapidly in BSF populations under domestication, driven by artificial selection, relaxation, genetic drift, and environmental adaptation. These results highlight the need for genetic monitoring in breeding programmes, including maintenance of large founder populations, periodic genetic assessment, and genetic rescue to preserve adaptive potential and reduce inbreeding risks.