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.

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.

Garra is a kind of small- to medium-sized fish that is widely distributed from southern Eurasia to central Africa. As one of the most diverse genera of Cyprinidae, investigating the phylogeny and biogeography of Garra remains challenging. In this study, we combined sequences of Garra samples collected from Myanmar with sequences downloaded from GenBank to investigate the phylogeny, diversification, and biogeography of Garra on a global scale, with an emphasis on Southeast Asia. Species delimitation results indicated that there are at least 22 potential species, including eight undescribed species in Myanmar, suggesting that the diversity of Garra in this region have been largely underestimated. Diversification analysis suggested a relatively high diversification rate in the early branches of Garra. Ancestral distribution reconstruction results revealed that Garra originated from the Southeast Asia in the late Eocene, approximately 34 million years ago, with subsequent dispersals across different drainages influenced by the uplift of the Qinghai-Tibet Plateau. Our study provided a new insight into the evolutionary history of Garra and the basis for further research on this genus.

Our understanding of sexual selection is advancing with new technologies that tag individuals or their sperm, revealing how females use post-copulatory processes to discriminate between competing mates. Many tagging methods have been devised primarily for model insect organisms like Drosophila or Gryllidae. Developing such novel methods, however, is expensive and requires intensive investment. In this experiment, we trial the use of Rhodamine B and Rhodamine 110 in a small arachnid, the bulb mite Rhizoglyphus echinopus, for pre and post copulatory observations as it is a relatively inexpensive and simple way to tag individuals and their ejaculate proteins. First, we tested whether Rhodamine B and Rhodamine 110 applied to food can be used as a tagging method to track and distinguish between individuals. Second, we explored whether Rhodamine applied in this way can be used to track sperm transfer. We found that both tagging probes worked well in tagging individuals and that we were able to distinguish between individuals using both LED and fluorescent microscopy. We also found that Rhodamine degraded rapidly in the animals, likely due to their fast metabolism. Due to the rapid degradation, we observed variable results in the sperm transfer trials. We suggest multiple uses for Rhodamine and highlight other invertebrates where this method may come into use for the study of sexual selection.

Global climate change has led to a shift in rainfall patterns. And as water is an essential ingredient for plant photosynthesis, shifts in rainfall patterns will inevitably affect plant growth. In this study, the response of leaf traits and photosynthetic fluorescence properties of Fraxinus malacophylla seedlings to rainfall patterns during the dry and rainy seasons was investigated using a natural rainfall duration of 5 d (T) and an extended rainfall duration of 10 d (T+) as rainfall intervals; and a monthly average rainfall as control (W), with the corresponding rainfall treatments of a 40% increase in rainfall (W+) and a 40% decrease in rainfall (W-). The results showed that Pn, Gs, and Tr basically all tended to increase and then decrease with increasing rainfall in the dry season, and generally reached the highest under the W treatment; and Pn, Gs, Ci, and Tr mostly remained high at 5d relative to 10d; PI was overall higher under the W treatment throughout the dry season. Extending the rainfall interval at the beginning of the rainy season significantly reduced Fm; throughout the rainy season, Gs, Ci, and Tr basically showed a decreasing trend with increasing rainfall, reaching the highest under the W-treatment, and mostly higher at 5d than at 10d. These results suggest that natural rainfall intervals and natural rainfall amounts are more favorable to the growth of Fraxinus malacophylla seedlings in the dry season; reduced rainfall and multiple rainfalls in the rainy season tend to promote photosynthesis in Fraxinus malacophylla. This study reflects the different survival strategies of Fraxinus malacophylla under different rainfall patterns, as well as providing a theoretical basis for understanding how Fraxinus malacophylla can grow better under rainfall variability and for future management.

Seagrasses provide critical ecosystem services such as carbon sequestration, sediment stabilisation and nursery habitat for juvenile fish. Zostera muelleri is ubiquitous within Australian and New Zealand estuaries however as a species is relatively understudied. We sourced seeds from a thermally-affected east Australian estuary and investigated if germination rates differed between ambient and thermally affected seeds over a variety of temperatures (16°C, - 28°C) to determine how seagrass systems might react in a warming climate. Germination for the experiment was low and totalled 5% of all seeds however similar numbers are typical in seed germination studies. Germination was highest at 16°C and was enhanced through the simulation of a 48-hour freshwater pulse. Thermally affected sites germinated faster and had greater mean maximum germination when compared to control sites regardless of experimental temperature. These findings indicate that Zostera muelleri in this system may be exhibiting transgenerational plasticity due to the thermal stress the parent experiences. This result provides an alternate viewpoint to current literature by suggesting that unknown transgenerational effects may provide Z. muelleri with greater germination plasticity against temperatures expected under predicted climate change scenarios than previously expected.

1. Tree growth–survival relationships link two demographic processes that dictate the com-position, structure and functioning of forest ecosystems. While these relationships have been shown to vary intra-specifically, it remains unclear how this reflects environmental variation and disturbance. We examined the influence of a 700-m elevation gradient and an Mw = 6.7 earthquake in 1994 on intra-specific variability in growth–survival relationships. We expected that survival models that incorporated recent growth would be better sup-ported than those using other factors known to influence tree survival. 2. We used a permanent plot network that representatively sampled a monodominant Nothofagus forest in New Zealand’s Southern Alps in 1974 and that was remeasured seven times through to 2009. The relationships were assessed using pre-earthquake growth and survival, pre-earthquake growth and post-earthquake survival (0–5 years post-earthquake), and post-earthquake growth and survival (5+ years post-earthquake). Sur-vival was related to growth of 4504 trees on 216 plots using Bayesian modelling. We hy-pothesised there would be a positive, logistic relationship between growth and survival. 3. Pre-earthquake, we found a positive, logarithmic growth–survival relationship at all eleva-tions. At higher elevations, trees grew more slowly but had higher survival, supporting our hypothesised demographic trade-off with elevation. As we expected, the earthquake al-tered the pre-earthquake growth–survival relationships and 0–5 years post-earthquake survival held little relationship with growth. Less expected was a strong, logarithmic growth–survival relationship that developed 5+ years post-earthquake because of en-hanced survival of fast-growing trees yet low survival of slow-growing trees. 4. Synthesis. Our findings demonstrate there can be trends in growth–survival relationships along an elevation gradient. If we assume a gradual climate warming is the equivalent of a forest stand shifting to a lower elevation, then data from our pre-earthquake period sug-gests that tree growth–survival relationships at any elevation could adjust to faster growth and lower survival. We also show how these novel growth–survival relationships could be altered by periodic disturbance.

The effects of climate change on coastal biodiversity are a major concern because altered community compositions may change associated rates of ecosystem functioning and services. While responses of single species or taxa have been studied extensively, it remains challenging to estimate responses to climate change across different levels of biological organisation. Studies that consider the effects of moderate realistic near-future levels of ocean warming and acidification are needed to identify scope for adaptation and evolution. Also, studies including different levels of biological complexity may reveal opportunities for amelioration or facilitation under changing environmental conditions. To test experimentally for independent and combined effects of predicted near-future warming and acidification on key benthic species, we manipulated three levels of temperature (ambient, +0.8 °C, +2 °C) and two levels of pCO2 (ambient at 450 ppm, elevated at 645 ppm) and quantified their effects on mussels and algae growing separately or together (to also test for inter-specific interactions). Warming increased mussel clearance and mortality rates simultaneously, which meant that total biomass peaked at + 0.8 °C. Surprisingly, however, no effects of elevated pCO2 were identified on mussels or algae. Moreover, when kept together, mussels and algae had mutually positive effects on each other’s performance (i.e. mussel survival and condition index, mussel and algal biomass, and proxies for algal productivity including relative maximum electron transport rate [rETRmax], saturating light intensity [Ik], and maximum quantum yield [Fv/Fm]), independent of warming and acidification. Our results show that even moderate warming affected the functioning of key benthic species, and we identified a level of resistance to predicted ocean acidification. Importantly, we show that the presence of a second functional group enhanced the functioning of both groups (mussels and algae), independent of changing environmental conditions, which highlights the ecological and potential economic benefits of conserving biodiversity in marine ecosystems.

Species-environment relationships have been extensively explored through species distribution models (SDM) and species abundance models (SAM), which have become key components to understand the spatial ecology and population dynamics directed at biodiversity conservation. Nonetheless, within the internal structure of species’ ranges, habitat suitability and species abundance do not always show similar patterns, and using information derived from either SDM or SAM could be incomplete and mislead conservation efforts. We gauged support for the abundance-suitability relationship and used the combined information to prioritize the conservation of South American dwarf caimans (Paleosuchus palpebrosus and P. trigonatus). We used 7 environmental predictor sets (surface water, human impact, topography, precipitation, temperature, dynamic habitat indices, soil temperature), 2 regressions methods (Generalized Linear Models - GLM, Generalized Additive Models - GAM), and 4 parametric distributions (Binomial, Poisson, Negative binomial, Gamma) to develop distribution and abundance models. We used the best predictive models to define 4 categories (low, medium, high, very high) to plan species conservation. The best distribution and abundance models for both Paleosuchus species included a combination of all predictor sets, except for the best abundance model for P. trigonatus which incorporated only temperature, precipitation, surface water, human impact, and topography. We found non-consistent and low explanatory power of environmental suitability to predict abundance which aligns with previous studies relating SDM-SAM. We extracted the most relevant information from each optimal SDM and SAM and created a consensus model (2,790,583 km2) that we categorized as low (39.6%), medium (42.7%), high (14.9%), and very high (2.8%) conservation priorities. We identified 279,338 km2 where conservation must be critically prioritized and only 29% of these areas are under protection. We concluded that optimal models from correlative methods can be used to provide a systematic prioritization scheme to promote conservation and as surrogates to generate insights for quantifying ecological patterns.

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.

1. Biodiversity and ecosystem multifunctionality are currently hot topics in ecological research. However, little is known about the role of multitrophic diversity in regulating various ecosystem functions, which limits our ability to predict the impact of biodiversity loss on human well–being and ecosystem multifunctionality. 2. In this study, multitrophic diversity was divided into three categories: plant, animal, and microbial communities (i.e., plant diversity, rodent diversity, bacterial and fungal diversity). Also, 15 ecosystem functions were divided into four categories–water conservation, soil fertility, nutrient cycling and transformation, and community production–to evaluate the significance of biotic and abiotic variables in maintaining ecosystem multifunctionality. 3. Results indicated that species diversity at multiple trophic levels had a greater positive impact on ecosystem multifunctionality than species diversity at a single trophic level. Notably, the specific nature of this relationship depended on the niche breadths of plants, indicating that plants were key indicators linking above and below ground trophic levels. Abiotic factors such as altitude and pH directly acted on ecosystem multifunctionality and could explain changes in ecosystem functions. 4. Overall, our study offers valuable insights into the critical role of multitrophic species diversity in preserving ecosystem multifunctionality within alpine grassland communities, as well as strong support for the importance of biodiversity protection.

The mechanisms underlying plant species distribution and abundance have been long studied in ecology. However, the role of heterospecific pollen interference in shaping these patterns needs more attention. Species distribution and abundance are important factors determining whether a species is endangered or not, thus understanding the impact of heterospecific pollen interference on rare species could help to inform conservation strategies aimed at preserving plant communities. In this study, we conducted a multispecies experiment using eight co-occurring and co-flowering plant species with varying rarity levels in Switzerland. We performed hand-pollination experiments between all species pairs and measured seed set (whether a flower produces seed) and seed number (number of seeds per flower) as outcomes. We looked at the effects of rarity status, self-compatibility and recipient-donor relatedness on heterospecific pollen interference. Contrary to expectations, neither seed set nor seed number were affected by heterospecific pollen deposition. Self-compatible species had a higher seed set probability, but this was independent from species rarity. In our study setting, heterospecific pollen interference seems to have only minor effects on seed set and seed number, and consequently on recruitment. Thus, heterospecific pollen interference seems to play only a minor role in shaping plant species distribution and abundance. Nevertheless, the higher impact of heterospecific pollen deposition on rare and closely related species, as well as the importance of conspecific pollen loss, might need further investigation for both in-situ and ex-situ conservation strategies.

In forest ecosystems, litter decomposition is essential to sustaining productivity and nutrient cycling. Large herbivores are crucial in determining the processes of nutrient cycling. The temperate woods of Asia are growing more and more damaged and broken up by the widespread increase in human activity, including excessive livestock grazing. However, less research has been done on the impact of wild ungulates and cattle on the decomposition of forest litter. In this study, the effects of adding cattle and sika deer (Cervus nippon) feces to litter decomposition were examined using a litterbag experiment. Northeastern China was the study’s location from July 2022 to October 2023. We found that the addition of deer feces significantly reduced litter decomposition, but the addition of cattle feces greatly increased litter decomposition. The presence of cattle and deer excrement significantly accelerated the release of C after one year of litter decomposition. Compared with the results of the control group (no addition of feces), the addition of cattle and sika deer feces increased C release by 37.45% and 22.69%, respectively. Fecal addition increased the release of N; however, for the three treatment groups, the maximum accumulation of N occurred in the middle of litter decomposition, which may have been due to the initial chemical quality of the leaves and snow melt as well as nutrient limitations at the sites. Compared with the results of the control group, P release in the feces of cattle increased by 4.35%, but P release in the feces of deer decreased by 27.55%. Our findings demonstrate that broad-scale patterns of nitrogen cycling should be closely monitored for the consequences of fecal deposition by an excess of large livestock and ungulates in forests.

In recent decades, mangrove wetlands globally have suffered from human activities and climate change, leading to issues like area reduction, degraded ecological functions and declining biodiversity. Restoration efforts, primarily through mangrove afforestation (i.e. mangrove plantation in mudflats), have been widespread, yet they often overlook the significance of unvegetated mudflats. In addition, under the condition that the total area of suitable mudflats is limited, the problem of what is the threshold of mangrove forest and unvegetated mudflats to better protect mangrove biodiversity has not been solved. Therefore, this study conducted a field survey of molluscs in mangrove wetlands in Hainan Island in China, and explored the relative importance of mangrove and unvegetated mudflats through taxonomic alpha diversity and functional diversity. The results showed that: (1) Mollusc abundance of unvegetated mudflats were notably higher than this of mangrove forests, and the species richness, functional richness and functional vulnerability were significantly lower than those of mangrove forests; (2) The abundance and functional vulnerability of molluscs were mainly affected by sediment properties (pH, interstitial water salinity, median diameter, total nitrogen, C/N ratio) , while the species richness and functional richness of molluscs were primarily influenced by vegetation structure (plant density); (3) Retaining at least 20% of the unvegetated mudflat area could well protect the biodiversity of mangrove wetlands. To our knowledge, our study is the first to propose the proportion of mangrove forests and unvegetated mudflats on the basis of benthic biodiversity, providing theoretical support and decision-making reference for mangrove protection and restoration.

Animals with different life-history types vary in their stress-coping styles, which can affect their fitness and survival in changing environments. We studied how chronic exposure to manganese sulfate (MnSO4), a common aquatic pollutant, affects life-history traits, physiology, and behavior of zebrafish (Danio rerio) with two life-history types: fast (previously selected for fast juvenile growth, early maturation, and small adult body size) and slow life histories (selected for slow juvenile growth, late maturation, and large adult body size). We found that MnSO4 had negative effects on growth and condition factor, but the magnitude of these effects depended on the life-history type. Individuals with fast life histories were more susceptible to MnSO4 than fish with slow life histories as they had lower growth rate, condition factor and feeding probability in high MnSO4 concentrations. Our results demonstrate that MnSO4 can impair fish performance, and life-history variation can modulate the stress-coping ability of individuals.

Studies in evolution, ecology and conservation are increasingly based on genetic and genomic inferences. With increased focus on molecular approaches, ethical concerns about destructive or more invasive techniques need to be considered, with a push for minimally invasive sampling to be optimised. Buccal swabs have been increasingly used to collect DNA in a number of taxa, including amphibians. However, DNA yield and purity from swabs is often low, limiting its use. In this study we compare different types of swabs, preservation method and storage, and DNA extraction technique in three case studies to assess the optimal approach for recovering DNA in anurans. Out of the five different types of swab that we tested, Isohelix MS-02 and Rapidry swabs generated higher DNA yields than other swabs. When comparing storage buffers, ethanol is a better preservative than a non-alcoholic alternative. Dried samples resulted in similar or better final DNA yields than ethanol-fixed samples if kept cool. DNA extraction via a Qiagen™ DNeasy Blood and Tissue Kit and McHale’s salting out extraction method resulted in similar DNA yields but the Qiagen™ kit extracts contained less contamination. We also found that samples produce better DNA recovery if frozen as soon as possible after collection. We provide recommendations for sample collection and extraction under different conditions, including budgetary considerations, size of individual sampled, access to cold storage facilities, and DNA extraction methodology. Maximising efficacy of all of these factors for better DNA recovery will allow buccal swabs to be used for genetic and genomic studies in a range of vertebrates.

Aim: During the last decades mussels have shown a poleward shift in the distribution along the Atlantic coast conceivably driven by elevated sea-surface temperatures. We aimed to determine the baseline for the Northeast Atlantic (58 – 70° N) Mytilus species complex, and to compare the present distribution to surveys conducted 60 years ago. Location: Northeast Atlantic Methodology: Baseline was obtained by investigating a total of 509 stations in the intertidal zone, in four regions comprising the environmental gradient from head of fjord to coast, and distributed over the latitudinal gradient from 58 – 70° N. Results: The baseline shows a range in continuous abundance of mussels from 12 to 36 %, patchy abundance from 26 to 57 % and no or very limited mussel abundance from 26 to 46 % between the four regions. The presence of mussels in the southeast and west region was compared to previous surveys conducted 60 years ago. The data points to similar past and present presence of mussels in both regions, yet past major mussel fields in the inner section of region Southeast was not detected in this study. Main conclusions: The baseline of Mytilus spp. in the Northeast Atlantic (58 – 70° N) is now available for future reference. The baseline, compared to surveys conducted 60 years ago, points to awareness of the population situated in the southeast section of the investigated region. Continued monitoring and modelling are needed to clarify drivers of temporal and spatial variation in the mussel populations along the Northeastern Atlantic coast.

Geographical distribution and diversity patterns of bird species are influenced by climate change. The Rouget’s rail (Rougetius rougetii) is a ground-dwelling endemic bird species distributed in Ethiopia and Eritrea. It is a near-threatened species menaced by habitat loss, one of the main causes of population declines for bird species. The increasing effects of climate change may further threaten the species’ survival. So far, the spatial distribution of this species is not fully documented. With this study, we develop current potential suitable habitat and predict the future habitat shift of R. rougetii based on environmental data such as bioclimatic variables, population density, vegetation cover, and elevation using ten algorithms. We evaluated the importance of environmental factors in shaping the bird’s distribution and how it shifts under climate change scenarios. We used 182 records of R. rougetii from Ethiopia and nine bioclimatic, population density, vegetation cover, and elevation variables to run the 10 model algorithms. Among 10 algorithms, eight were selected for ensembling models according to their predictive abilities. The current suitable habitats for R. rougetii were predicted to cover an area of about 82,000 km² despite being highly fragmented. The model suggested that temperature seasonality (bio4), elevation, and mean daily air temperatures of the driest quarter (bio9) contributed the most to delimiting suitable areas for this species. R. rougetii is sensitive to climate change associated with elevation, leading to a large, shrinking distribution of suitable areas. The projected spatial and temporal pattern of habitat loss of R. rougetii suggests the importance of climate change mitigation and implementing long-term conservation and management strategies for this threatened endemic bird species.