Molecular Ecology最新文献

Rocky reefs may shift between two distinct stable states: productive algal forests, characterised by high abundance and biodiversity of macrofauna, and impoverished barrens, dominated by overgrazing sea urchins. Barren states may persist despite the recovery of adult sea urchin predators, suggesting additional stabilising mechanisms. Sea urchin settlers equally colonise forests and barrens in large numbers, but in forests only a few of them reach adult size, suggesting that post-settlement predation might play a crucial role in determining sea urchin population density. Visual assessment of predation events in the field is unfeasible due to the microscopic scale of both predators and prey and the complexity of the arena. In this study, we designed and tested specific primers for the detection of mtDNA of settlers of the Mediterranean sympatric sea urchin species Paracentrotus lividus and Arbacia lixula in the stomach content of macroinvertebrates. By testing 360 invertebrates collected in algal forests during an urchin settling event at five mtDNA loci, we identified 60 (17%) samples positive for P. lividus DNA. Presence of urchin DNA was confirmed by sequencing and NGS metabarcoding analyses. Our results suggest that predation by macroinvertebrates may represent an important process in controlling sea urchin population density and maintaining the forest state in temperate rocky reefs.

The temporal sequence and mechanistic interplay between life-history and mating-system transitions in plants remain poorly understood. Here, we combine crossing experiments with population genomic analyses to investigate these processes in the Incarvillea sinensis complex (Bignoniaceae), which contains annual selfing and perennial outcrossing populations. Crossing experiments revealed complete post-zygotic isolation between annuals and perennials. Genomic data derived from de novo assemblies of annual and perennial individuals, along with SNP and chloroplast sequencing of 126 individuals from 30 populations, demonstrated strong genetic divergence between life histories, with no evidence of contemporary gene flow between them. Compared to perennials, annuals exhibited significantly reduced genetic diversity, elevated differentiation and a greater number of chromosomal rearrangements-particularly translocations. Divergence time estimates indicated that annual and perennial lineages split during the early Pleistocene (ca. 2.22 Mya), whereas the shift to selfing from outcrossing within the annual lineage was a more recent event, occurring during the late Pleistocene (~0.03 Mya). These results indicate that the mating-system shift was not the initial driver of divergence, and we infer that the life-history transition likely occurred earlier, although its precise timing could not be directly determined. Our findings support a two-stage model of divergence in which adaptation to seasonally arid environments first drove the evolution of annuality, initiating speciation through ecological isolation and genetic divergence. The subsequent evolution of selfing then likely further promoted reproductive isolation via both pre- and post-zygotic mechanisms, potentially accelerating rapid genomic differentiation and effectively completing the speciation process.

Weedy rice is a close relative of cultivated rice (Oryza sativa) that infests rice fields worldwide and drastically reduces yields. To combat this agricultural pest, rice farmers in the southern US began to grow herbicide-resistant (HR) rice cultivars in the early 2000s, which permitted the application of herbicides that selectively targeted weedy rice without harming the crop. The widespread adoption of HR rice coincided with increased reliance on hybrid rice cultivars in place of traditional inbred varieties. Although both cultivated and weedy rice are predominantly self-fertilising, the combined introductions of HR and hybrid rice dramatically altered the opportunities and selective pressure for crop-weed hybridization and adaptive introgression. In this study, we generated genotyping-by-sequencing data for 178 weedy rice samples collected from across the rice growing region of the southern US; these were analysed together with previously published rice and weedy rice genome sequences to determine the recent genomic and population genetic consequences of adaptive introgression and selection for herbicide resistance in US weedy rice populations. We find a reshaped geographical structure of southern US weedy rice as well as purging of crop-derived alleles in some weed strains of crop-weed hybrid origin. Furthermore, we uncover evidence that related weedy rice strains have made use of different genetic mechanisms to respond to selection. Lastly, we identify widespread presence of HR alleles in both hybrid-derived and nonadmixed samples, which further supports an overall picture of weedy rice evolution and adaptation through diverse genetic mechanisms.

Parasitic infections are ubiquitous in nature, but their consequences are often difficult to evaluate in wildlife. This is particularly the case for chronic infections for which fitness impacts can be subtle or confounded with other intrinsic and extrinsic factors. Infections by Babesia (Apicomplexa, Piroplasmidae) are widespread in wildlife, but little is known about their impacts on host health. Here, we evaluated the dynamics and possible fitness consequences of infection by Babesia sp. YLG, a recently described parasite infecting yellow-legged gulls (Larus michahellis). Using a qPCR assay developed for Babesia sp. YLG, we found that prevalence was much higher in chicks compared with adults. In chicks, infection depended on the colony and was tightly related to nest infestation by the tick vector Ornithodoros (Alectorobius) maritimus; this was not the case for adult birds. Infection intensities changed over time in chicks, increasing up to approximately 37 days old and then declining. Infection was associated with reduced body condition and fledging success for adults. In chicks, infection was significantly linked to reduced growth rates, even after accounting for the additive effect of ticks. However, no relationship was detected between infection and fledging date, migration strategy or flight distances measured on a subset of GPS-tagged juvenile birds. Through its subtle effects on fitness and reproductive success, infection by Babesia sp. YLG may have significant consequences for host demography and work focused on long-term dynamics is now called for to better understand how this parasite may shape the ecology and evolution of seabird populations.

Intraspecific genetic diversity (IGD) is a fundamental component of biodiversity, essential for understanding the evolutionary histories and demographic processes of species, and is key to effective conservation planning. However, ecologically important regions such as the Gran Chaco, South America's second-largest forested biome, remain largely underexplored. Encompassing diverse vegetation across climatic and altitudinal gradients, it harbours more than 3400 vascular plant species, 11% of which are endemic. Despite its ecological importance, genetic research in the region is limited and often biased. We reviewed IGD studies on vascular plants in the Gran Chaco from 1985 to 2024, identifying 85 studies covering 74 species. Coverage remains alarmingly low, with only 2.14% of species and 9.95% of the phylogenetic diversity represented. Research is skewed towards perennial (91%) and tree (46%) species, with limited representation of annuals and herbaceous taxa. Most studies relied on nuclear DNA (66%), fewer used chloroplast DNA (27%) and only 7% combined both genomes. Geographically, 33% of the Gran Chaco has no IGD data, and a further 22% includes data from a single species. Genetic sampling is concentrated in more accessible areas with higher road density and proximity to research institutions, particularly at higher altitudes. We found that in the Argentine Chaco ecoregions, 4.4 species have been genetically studied for every 100 species recorded, while in the Bolivia and Paraguay Chaco ecoregions, this proportion drops to 1.1 species for every 100 in each country. Future research on IGD in the Gran Chaco should broaden its taxonomic scope, diversify genomic tools and expand geographic coverage. Addressing these gaps will provide critical insights into the biogeographic history of the Gran Chaco and strengthen conservation strategies in this threatened and understudied biome.

Molluscs living in dynamic deep-sea cold seep environments have evolved distinct feeding strategies for survival. Here, we present the chromosome-level genomes of two sympatric mollusc species with distinct feeding strategies, a symbiosis-dependent mussel Gigantidas haimaensis and a predatory snail Phymorhynchus buccinoides. Comparative genomic analysis revealed gene family expansions related to the bacterial component degradation (e.g., b4GalTs) in G. haimaensis, suggesting an adaptation to symbiotic life. Conversely, P. buccinoides exhibited gene family expansions associated with appetite regulation (e.g., ox2r) and the digestive system (e.g., sult1 and chst), indicating genetic modifications for deep-sea predation. Furthermore, we conducted an in situ experiment mimicking a scenario in which ocean warming and sea-level rise resulted in a mass methane leakage in deep-sea cold seeps. Interestingly, G. haimaensis increased its metabolic rate and exhibited transcriptional responses. However, P. buccinoides suppressed energy production and responses at translational and posttranslational levels, which is compatible with their distinct feeding strategies. Collectively, our results provide insights on the evolutionary basis and resilience mechanisms related to energy management, which may facilitate methane tolerance of molluscs in the deep-sea cold seeps threatened by climate change.

Allochronic divergence is a key evolutionary mechanism that can frequently lead to incipient speciation. Although theoretical models suggest that such divergence is notably facilitated by small population size and genetic polymorphisms influencing reproductive timing, though constrained by genetic load, empirical validation remains limited. We investigated these predictions by re-analysing a case of allochronic differentiation between two sympatric populations of pine processionary moth (Thaumetopoea pityocampa) in Portugal, using whole genome resequencing (IndSeq and PoolSeq) of those two populations and eight allopatric ones. We inferred the demographic history of those populations, assessed their genetic load and searched for genomic regions associated with life cycle differences. Our analyses revealed a recent split between the sympatric allochronic populations, accompanied by a strong reduction in gene flow, bottlenecks, inbreeding and accumulation of deleterious variants. Genome scans identified several loci associated with life cycle variation, including genes putatively involved in circadian rhythm regulation, predominantly located on the Z chromosome. We discuss how these empirical genomic findings support theoretical expectations that assortative mating driven by differences in reproductive timing, underpinned by polymorphisms in circadian genes, along with genetic drift and purge of genetic load at high-impact sites, can promote the onset and persistence of allochronic divergence.

Conservation genomics has increasingly transitioned from a promising concept to a science that integrates a range of advanced analytical approaches, providing new insights into inbreeding, genetic load, demographic history and adaptive divergence in species of conservation concern. Yet, questions remain about how effectively these advances translate into practical conservation action. This Special Issue, Conservation Genomics—Making a Difference, brings together 37 papers that collectively assess how genomic data are contributing to conservation science and management. The contributions encompass empirical studies, reviews, and perspectives that together demonstrate how genomic tools are now used to identify management units, quantify inbreeding, analyse inbreeding depression, reveal adaptive variation, forecast genomic vulnerability under climate change, and guide genetic rescue and assisted migration. Several papers show direct integration of genomics into conservation planning, including fisheries management, guiding restoration of endangered or habitat-forming species, and monitoring of genetic indicators under the Convention on Biological Diversity. Others highlight emerging questions in conservation, such as the significance of structural variation, and the genomic basis of invasiveness. However, persistent challenges remain, notably in bridging the gap between research and policy, uneven global distribution of genomic resources, and translating complex analyses into practical management advice. Nevertheless, the advances presented in the 37 papers show that conservation genomics is moving beyond its early theoretical and technical focus towards real-world applications. The field is maturing and is increasingly fulfilling its promise to make a real difference for populations, species, and ecosystems.

Chemical communication during courtship is well documented in salamanders and newts, but its role in frogs is less understood. In some Neotropical poison frogs, males exhibit specialised mucous glands (SMGs) in the hand integument that express high levels of sodefrin precursor-like factors (SPFs), an amphibian pheromone. Some species also show integumentary swellings at the distal upper arm—known as the black arm gland (BAG)—of unclear function. We used histology and RNA sequencing to analyse the arm and finger integument of Hyloxalus nexipus and H. azureiventris to examine glandular composition, gene expression and potential pheromone production. We confirmed the co-occurrence of two sexually dimorphic macroglands—swollen fingers and BAG—in H. nexipus, a rare trait in dendrobatids. Both structures differentially expressed SPF, suggesting complementary roles in courtship. We also provide the first histological characterisation of the BAG in H. nexipus and the homologous region in H. azureiventris, revealing that both are composed of specialised serous glands (SSGs). Notably, SPF expression in the BAG of H. nexipus indicates that SSGs, previously not linked to this function, can also produce proteinaceous pheromones. In H. azureiventris, no differential SPF expression was found in the arm, making its reproductive role uncertain. Both species expressed SPF in their fingers; thus, we hypothesise that H. azureiventris may have specialised glands despite lacking visible swelling, based on other dendrobatids where SPF is upregulated in male fingers with SMGs linked to pheromone production. Our findings reveal a novel pheromone-producing gland and emphasise the complexity of chemical communication in dendrobatid reproduction.