Molecular Ecology最新文献

The global scale of biodiversity loss and land degradation has prompted the establishment of ambitious international restoration agreements, with the goal of returning biodiverse and functional ecosystems. Restoration interventions are often vegetation focused, and while they yield positive, measurable outcomes, they do not always lead to whole ecosystem recovery. Although soil microbiota such as fungi are integral ecosystem components (e.g., as symbionts, decomposers and drivers of nutrient cycling), they are largely absent from restoration planning and monitoring. Therefore, how fungi respond to ecosystem restoration, especially over longer time scales, is largely unknown. Here, we show trends of reduced dominance of soil fungal pathotrophs across a restoration chronosequence 6 years after initial sampling. This decline in soil fungal pathotrophs is consistent with continued functional recovery, despite little evidence of additional whole-community fungal recovery. Fungal community composition was also strongly associated with soil properties, particularly phosphorus, consistent with persistent land-use legacies constraining further recovery. The observed change in fungal functional composition is consistent with previous studies reporting higher relative abundance of pathotrophic fungi in ecologically degraded sites. Our study provides valuable insights into how soil fungal communities respond to restoration plantings and highlights the importance of repeated sampling. Our findings also demonstrate the value of considering both taxonomic and functional indicators when assessing ecosystem recovery.

Regulatory variation is increasingly recognized as a major driver of adaptive evolution, yet its role in natural populations remains largely unresolved. By integrating ATAC-seq chromatin profiles with population genomic outlier scans and RNA-seq gene expression data, we characterize the functional impact of regulatory elements and identify candidate loci where selection signatures coincide with tissue-specific chromatin and transcriptional shifts. We mapped genome-wide chromatin accessibility in three tissues (eye, liver and spleen) of wild European perch (Perca fluviatilis) inhabiting contrasting humic- (dark-water) and clear-water lakes. We identified over 76,000 accessible chromatin regions spanning 36.1 Mb of the genome, which were enriched for gene functions related to vision, metabolism and immune response. Chromatin landscapes were strongly tissue-specific, while only a subset of regions (0.32%, n = 161) showed differential accessibility between environments, suggesting that the regulatory architecture is dominated by tissue identity rather than environmental context. Integrating population genomic outlier scans with chromatin profiles revealed significant enrichment of adaptive SNPs within common open chromatin regions (1.5-fold) and transcription start sites (1.7-fold), directly implicating cis-regulatory elements as frequent targets of natural selection. This study demonstrates that humic adaptation in perch targets specific regulatory regions readily identified by the ATAC-seq approach, highlighting the value of functional chromatin maps in evolutionary genomics. Together, our results provide one of the first genome-wide regulatory maps for a wild vertebrate and establish a functional framework for connecting natural selection to regulatory mechanisms in the wild.

Genomic mechanisms explaining why some hybrid zones remain stable while others collapse into hybrid swarms are poorly understood. In Montana's Kootenai River Basin, native interior redband trout (Oncorhynchus mykiss gairdneri; IRT) and westslope cutthroat trout (O. lewisi; WCT) are naturally sympatric and historically exhibited limited hybridization. However, the introduction of allopatric coastal rainbow trout (O. m. ssp.; CRT) has coincided with hybrid swarm formation. Using novel IRT linkage maps and 3489 individuals genotyped at 189,984 SNPs, we characterized the role of genome structure in hybridization among native and invasive taxa. Native IRT were fixed for the derived arrangement of a double inversion complex on chromosome 5 (Chr05), whereas introduced CRT and intraspecific hybrids retained the ancestral polymorphism associated with migratory behaviour. Widespread hybridization was primarily driven by intraspecific admixture among rainbow trout (RBT) taxa, rather than with other species, likely mediated by genomic structural variants introduced into IRT populations via CRT admixture. Specifically, Chr05 genotypes exhibited strong habitat stratification; migratory-associated haplotypes occurred primarily in migration-associated habitats, implicating dispersal as a key mechanism promoting introgression. We found evidence of selection against interspecific hybrids, possibly tied to interspecific inversions. Notably, WCT carried a distinct form of Chr05 that is colinear with the ancestral RBT form. Interspecific hybrids carrying both the WCT and ancestral RBT forms (WCT_A/RBT_A), despite being structurally homozygous, were rare (1.59%), suggesting selection or stronger genomic incompatibility. Ultimately, introduced intraspecific variation may facilitate introgression via dispersal while distinct interspecific structural arrangements maintain genomic barriers, restricting gene flow.

Host–parasite interactions represent an evolutionary arms race, with parasites evolving strategies to exploit host resources, and hosts deploying mechanisms to resist or tolerate infection. Unlike vertebrates, which possess a sophisticated immune system, invertebrates rely entirely on innate immunity to combat pathogens. Yet, the molecular underpinnings and life-history consequences of immune activation remain little understood in non-insect invertebrates. Here, we combine life-history trait analysis with transcriptomics to investigate immune responses in an aquatic invertebrate exposed to a natural yeast parasite. By comparing infected, exposed-uninfected, and unexposed individuals, we identified candidate genes potentially involved in haemocyte recruitment and the reinforcement of the gut epithelium. These patterns highlight candidate mechanisms that may contribute to resistance following pathogen exposure. Exposed-uninfected individuals also showed delayed reproductive maturation, though lifetime reproductive output was ultimately maintained. Therefore, this suggests that successful exposure and immunity changes may be associated with a transient shift in reproductive allocation rather than a persistent reduction in reproductive output. In contrast, infected hosts exhibited stronger changes in metabolic and protein biosynthesis processes, consistent with a resource depletion hypothesis. These metabolic shifts align with reduced investment in reproduction, as infection appears to affect the number of offspring produced in the first brood. Our findings provide novel insights into the molecular and life-history responses associated with pathogen exposure and established infection and suggest candidate mechanisms through which host responses may shape life-history strategies in non-insect invertebrates, with broad implications for understanding host–parasite coevolution.

Understanding how agriculturally important species respond to environmental change is critical for maintaining productivity, mitigating agroecosystem threats and sustaining resilience. While crops have traditionally been the focus in agroecosystems, agricultural weeds are integral components that often face even stronger selective pressures, making them powerful models for investigating ecological and evolutionary responses to climatic and human-mediated challenges. Insights from how weeds adapt rapidly under these pressures can inform strategies to improve agricultural outcomes, since both pests and crops evolve under the same multivariate selective pressures. Here, we integrate two centuries of distribution records with whole-genome sequencing from natural populations of the most damaging weed in Europe—Alopecurus myosuroides (blackgrass) – to examine its ecological and evolutionary responses in agroecosystems. Blackgrass largely maintained its historical climatic niche, expanding its range primarily by tracking environments analogous to those it historically occupied. Genome-wide analyses revealed a polygenic basis of environmental responses, with most loci linked to single environmental variables and a subset showing limited environmental pleiotropy, indicating modular adaptation to the complex selective pressures of managed agricultural landscapes. Coupling these genomic-environment relationships with projected climate change and genomic offset analyses indicated that most blackgrass populations will remain well aligned with future conditions. Our findings show that ecological niche tracking and polygenic adaptation allow agricultural weeds like blackgrass to persist under rapid environmental change, offering insights relevant not only for weed management but also for designing resilient cropping systems under future climates.

International trade of shark fins remains difficult to monitor because products are rarely labelled to species and are often highly processed, resulting in severely degraded DNA. For several shark species listed under Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), this limits external verification of source populations supplying global trade hubs. Here, we assess whether nuclear genomic approaches can be applied to market-derived bull shark (Carcharhinus leucas) fins to determine their population of origin. We analysed dried fin trimmings collected from retail vendors in Hong Kong SAR, one of the world's largest dried shark fin trade hubs, using a targeted DArTcap single nucleotide polymorphism (SNP) panel, originally developed for population genomic studies of this species. Despite substantial DNA degradation, genomic libraries were successfully obtained for most samples, yielding sufficient SNP data to perform robust provenance and sex assignment. Using a Bayesian mixed-stock analysis, most fin samples were assigned to the Indo–West Pacific (71.4%), with smaller contributions from the western Atlantic (22.6%) and eastern Pacific (3.0%). Genetic sex assignment revealed twice as many males as females, although results indicated a conservative bias towards male assignment due to the limited number of X-linked markers available in degraded samples. Our results demonstrate that genome-wide targeted approaches can be effectively applied to highly processed shark fin products to infer population sources and sex composition. This study provides proof-of-concept for integrating genomics into shark trade monitoring, highlighting its potential to improve traceability, support CITES implementation and inform conservation and fisheries management, particularly for species with well-resolved population structure.

Crawford Lake has an exceptional stratigraphic record that began recording biannual (varved) sedimentation in the lake basin ~750 years ago, preserving evidence of shifting cultural zones and agricultural practices, from Late Woodland Period Indigenous agriculturalists to the impacts of industrialization during the late 19th century. It was selected as the candidate site for the proposed ‘Anthropocene’ epoch in 2023—a proposal ultimately rejected in 2024—but the lake's significance extends beyond a formal stratigraphic boundary. Its sediments preserve a long record of human-ecosystem entanglement that captures the cumulative, reverberating nature of local human impacts and global change. While many proxies have been studied at the site, the lake's sedimentary ancient DNA (sedaDNA) record has yet to be investigated. Here, we report on sedaDNA preserved at Crawford Lake over the last ~1300 years. Sedentism and agriculture clearly impacted the entire lake ecosystem, with corresponding shifts observable in the sedaDNA of plants, animals, algae, fungi and bacteria. Canada goose (Branta canadensis) roosting on the lake—likely drawn by foraging opportunities in fields cleared for Three/Four Sisters agriculture and sedentism—contributed to repeated eutrophications and algal blooms that permanently shifted the lake's ecological structure. Subsequent impacts during the Euro-Canadian zone furthered anthropogenic succession, although local impacts have been minimal since closure of the sawmill in 1900 ce, allowing for sensitivity to global change. Beyond the molecular ecological history of the lake, we also evaluate the effectiveness of an Arctic/Subarctic bait-set for palaeoecological reconstructions of the Eastern Woodlands, and the preservation of lake sedaDNA.

In populations with low genetic diversity, the capacity to adapt to environmental change is limited. While epigenetic mechanisms can generate phenotypic plasticity, their role in mediating adaptive life-history transitions in the wild is largely unknown. Here, we show that in adult Namibian cheetahs (Acinonyx jubatus jubatus), a species with remarkably low genetic diversity, the transition from a floater to a male holding a territory is associated with widespread DNA methylation changes, with a predominance of hypermethylation in territorial males. Using paired blood samples collected from the same individuals before and after becoming territorial, we identified differentially methylated genes which function in pathways related to anatomical and head development, brain development and neurodevelopment, cAMP biosynthesis and ion channel transport, consistent with the observed phenotypic shifts in morphology, spatial movement and aggressive behaviour. These findings suggest that DNA methylation mediates this life-history transition at the molecular level. More broadly, they provide rare evidence that epigenetic regulation is relevant in phenotypic diversity within species with low genetic diversity, potentially supporting adaptive potential at the population level.