Quercus chungii is an endemic tree species in China, rare and endangered in subtropical areas of China. Understanding its population structure and temporal dynamics is crucial for conserving and restoring Q. chungii population and its associated ecosystems. However, large knowledge gaps remain about its population structure and temporal change, and its key demographic rates across size classes. In this study, we investigated the population structures of Q. chungii in 2013 and 2023 in a nature reserve specifically established to better conserve Q. chungii and its associated ecosystems. We found that Q. chungii increased in its overall abundance, frequency and tree size in the past decade, suggesting active regeneration and fast growth rate of this species and the effectiveness of past conservation efforts. The age structure in 2023 shows a pyramid shape, with a sharp decline in the numbers of individuals from germinated seeds to seedlings and from seedlings to saplings. These lead to the low numbers of seedlings and saplings and high age-specific death probabilities at the early developmental stages. These results indicate potential risks of future population decline. These risks may have already manifested over the past decade, as a high mortality rate during the seedling-to-sapling transition could be one of the primary reasons contributing to the decreased proportion of saplings in 2023 compared to 2013. We propose that future studies may benefit from in-depth studies on the regeneration processes of Q. chungii by considering seed predation and germination under changing climate. This study improves the prediction of population development of Q. chungii and provide theoretical guidance for the conservation of Q. chungii.

It is 100 years since the first paper described the multiannual cycles in Arctic rodents and lagomorphs. The mechanisms driving population cycles in animals like lemmings and voles are complex, often attributed to extrinsic factors, such as food availability and quality, pathogens, parasites and/or predators. While extrinsic factors provide insights into population cycles, none fully explain the phenomenon. We propose an underlying innate, intrinsic mechanism, based on epigenetic regulation, that drives population cycles under harsh arctic conditions. We propose that epigenetically driven phenotypic changes associated with sexual development, growth, and behaviour accumulate over time in offspring, eventually producing a phase change from rising population density to eventual population collapse. Under this hypothesis, and unlike previous hypotheses, extrinsic factors would modify population cycles but would not be primary drivers. The interaction between our intrinsic cycle and extrinsic factors explains established phenomena like delayed-density dependence, whereby population growth is controlled by time-dependent negative feedback. We advocate for integrating a century of field research with the latest epigenetic analysis to better understand the drivers of population cycles.

During an intensive study of the urban population of the Blackbird Turdus merula in Szczecin (1997-2023), four cases of surrogate copulation were observed in the Blackbird and three in the Fieldfare Turdus pilaris. In three cases birds (Blackbirds twice and Fieldfare once) try to copulate with fledglings of their own species, in all other cases the birds try to copulate with moss and sticks. In three cases copulation attempts were done by adult birds (two blackbirds and one fieldfare), in four cases it was a fledgling.

On the flanks of >6000 m Andean volcanoes that tower over the Atacama Desert, leaf-eared mice (Phyllotis vaccarum) live at extreme elevations that surpass known vegetation limits. What the mice eat in these barren, hyperarid environments has been the subject of much speculation. According to the arthropod fallout hypothesis, sustenance is provided by windblown insects that accumulate in snowdrifts (‘aolian deposits’). It is also possible that mice feed on saxicolous lichen or forms of cryptic vegetation that have yet to be discovered at such high elevations. We tested hypotheses about the diet of mice living at extreme elevations on Atacama volcanoes by combining metagenomic and DNA metabarcoding analyses of gut contents with stable-isotope analyses of mouse tissues. Genomic analyses of contents of the gastrointestinal tract of a live-captured mouse from the 6739 m summit of Volcán Llullaillaco revealed evidence for an opportunistic but purely herbivorous diet, including lichens. Although we found no evidence of animal DNA in gut contents of the summit mouse, stable isotope data for a larger sample of mice indicate that mice native to elevations at or near vegetation limits (~5100 m) include a larger fraction of animal prey in their diet than mice from lower elevations. Some plants detected in the gut contents of the summit mouse are known to exist at lower elevations at the base of the volcano and in the surrounding Altiplano, suggesting that such species may occur at higher elevations beneath the snowpack or in other cryptic microhabitats.

1. Widely used methods to assess population genetic structure and differentiation rely on independence of marker loci. Following the assumption, the common metrics, for example FST, evaluate genetic structure by averaging across loci. Common metrics do not use information in the associations among loci at the individual level and are often criticized for failing to measure true differentiation even when loci segregate independently. 2. We introduce a new concept to measure β-variation (Effective Number of Different Populations, ENDP). It requires the following steps: (a) calculation of a proper dissimilarity between genetic profiles of all individuals; (b) calculation of suitable pairwise distances between the samples based on the dissimilarities between individuals; (c) calculation of diversity (in terms of Hill numbers) and dispersion of samples based on the pairwise distances between samples; (d) ENDP is then estimated as a combination of the diversity and dispersion. ENDP estimates β-variation independently of within-sample α-variation. This new concept differs from the existing standard where β-diversity is estimated based on the ‘partition of variation’ scheme (beta=gamma-alpha or beta=gamma/alpha). 3. Estimates of ENDP are obtained by evaluating information in the available genetic profiles of individuals including association of loci. Therefore, ENDP can be used even in an absence of panmixia. 4. We illustrate the use of this concept by analyzing the population genetic structure of a sexual species (a trematode parasite) occupying connected populations across a broad geographic area. Analysis is complicated by two coexisting cryptic sister clades and the potentially mixed-mating system of this hermaphroditic parasite.

Increasing levels of UV-B radiation caused by the greenhouse effect has become an emerging threat to crop health and yield. The glutathione (GSH) metabolic pathway is generally involved in plant stress responses through scavenging accumulated reactive oxygen species, and is therefore believed to play an essential role in enhancing plant tolerance to UV-B stress. However, the complex evolutionary details of this pathway in polyploid plants, especially under UV-B stress, remain largely unknown. Here, using the important allotetraploid crop, Gossypium hirsutum, as an example, we comprehensively investigated the composition and phylogenetic relationships of genes encoding 12 key structural enzymes in this pathway, and compared the expression changes of all the relevant genes under UV-B stress (16 kJ m-2 d-1) based on six leaf transcriptomes. Consequently, we identified 205 structural genes by genome-wide searching and predicted 98 potential regulatory genes under multiple stress conditions by co-expression network analysis. Furthermore, we revealed that 19 structural genes including five homoeologous pairs and 96 regulatory genes possessing 25 homoeologous pairs were reticulately correlated without homoeologous selection preference under UV-B stress. This result suggests a complex rewiring and reassignment between structural genes and their regulatory networks in the duplicated metabolic pathways of polyploid cotton. This study extends our understanding of the molecular dynamics of the GSH metabolic pathway in response to UV-B stress in G. hirsutum and, more broadly, in polyploid plants.

Genome scans offer a comprehensive method to explore genome-wide variation associated with traits under study. However, connecting individual genes to broader functional groupings and pathways is often challenging, yet crucial for understanding the evolutionary mechanisms underlying these traits. This task is particularly relevant for multi-trait processes such as domestication, which are influenced by complex interactions between numerous genetic and non-genetic factors, including epigenetic regulation. As various traits within the broader spectrum of domestication are selected in concert over time, this process offers an opportunity to identify broader functional overlaps and understand the integrated genetic architecture underlying these traits. In this study, we analyzed approximately 600,000 SNPs from a Pool-Seq experiment comparing eight natural-origin and 12 farmed populations of European seabass in the Mediterranean Sea region. We implemented two genome scan approaches and focused on genomic regions supported by both methods, resulting in the identification of 96 candidate genes, including nine CpG islands, highlighting potential epigenetic influences. Many of these genes and CpG islands are in linkage groups previously associated with domestication-related traits. The most significantly overrepresented molecular function was ‘oxidoreductase activity’. Furthermore, a dense network of interactions was identified, connecting 22 of the candidate genes. Within this network, the most significantly enriched pathways and central genes were involved in ‘chromatin organization’, highlighting another potential epigenetic mechanism. Altogether, our findings underscore the utility of interactome-assisted pathway analysis in elucidating the genomic architecture of polygenic traits and suggest that epigenetic regulation may play a crucial role in the domestication of European seabass.

not-yet-known not-yet-known not-yet-known unknown The Arctic has warmed nearly four times faster than the global average since 1979, resulting in rapid glacier retreat and exposing new glacier forelands. These forelands offer unique experimental settings to explore how global warming impacts ecosystems, particularly for highly cli-mate-sensitive arthropods. Understanding these impacts can help anticipate future biodiversity and ecosystem changes under ongoing warming scenarios. In this study, we integrate data on arthropod diversity from DNA gut content analysis—offering insight into predator diets—with quantitative measures of arthropod activity-density at a Greenland glacier foreland using Structural Equation Modelling (SEM). Our SEM analysis reveals both bottom-up and top-down controlled food chains. Bottom-up control, linked to sit-and-wait predator behavior, was prominent for spider and harvestman populations, while top-down control, associated with active search behavior, was key for ground beetle populations. Bottom-up controlled dynamics predominated during the early stages of vegetation succession, while top-down mechanisms dominated in later successional stages further from the glacier, driven largely by increasing temperatures. In advanced successional stages, top-down cascades intensify intraguild predation (IGP) among arthropod predators. This is especially evident in the linyphiid spider Collinsia holmgreni, whose diet included other linyphiid and lycosid spiders, reflecting high IGP. The IGP ratio in C. holmgreni negatively correlated with the activity-density of ground-dwelling prey, likely con-tributing to the local decline and possible extinction of this cold-adapted species in warmer, late-succession habitats where lycosid spiders dominate. These findings suggest that sustained warming and associated shifts in food web dynamics could lead to the loss of cold-adapted species, while brief warm events may temporarily impact populations without lasting extinction effects.

The term “sixth mass extinction” has become synonymous with the current biodiversity crisis. However, despite a general agreement that current biodiversity declines are severe, no consensus has been reached on whether this constitutes a ‘mass extinction event’, and thus whether our current situation is comparable to the catastrophic extinction events of deep time. Here we suggest that our inability to gauge whether the current biodiversity crisis is a mass extinction event may lie less in quantifiable evidence and more in the language used to define such events. We highlight areas of linguistic contention, vagueness, and epistemic dispute, and discuss the role of post-hoc decision-making and language in shaping our understanding and communication of biodiversity loss. Our discussion raises larger questions about how we communicate science to the public, funders, and other scientists, and how we use language to both shape awareness and leverage action.