Environmental DNA (eDNA) analysis has become a popular conservation tool for detecting rare and elusive species. eDNA assays typically target mitochondrial DNA (mtDNA) due to its high copy number per cell and its ability to persist in the environment longer than nuclear DNA. Consequently, the development of eDNA assays has relied on mitochondrial reference sequences available in online databases, or in cases where such data are unavailable, de novo DNA extraction and sequencing of mtDNA. In this study, we designed eDNA primers for the critically endangered Bellinger River turtle (Myuchelys georgesi) using a bioinformatically assembled mitochondrial genome (mitogenome) derived from a reference genome. We confirmed the accuracy of this assembled mitogenome by comparing it to a Sanger-sequenced mitogenome of the same species, and no base pair mismatches were detected. Using the bioinformatically extracted mitogenome, we designed two 20 bp primers that target a 152-base-pair-long fragment of the cytochrome oxidase 1 (CO1) gene and a 186-base-pair-long fragment of the cytochrome B (CytB) gene. Both primers were successfully validated in silico, in vitro, and in situ.

not-yet-known not-yet-known not-yet-known unknown Ecosystem size and spatial resource flows are key factors driving species diversity and ecosystem function. However, the question of whether and how these drivers interact has been largely overlooked. Here, we investigated how ecosystem size asymmetry affects species diversity and function of two-patch meta-ecosystems connected through flows of non-living resources. We conducted a microcosm experiment, mimicking resource flows between ecosystems of different sizes yet otherwise identical properties or between ecosystems of the same size. Meta-ecosystems with asymmetric ecosystem sizes displayed higher α- diversity but lower β-diversity and ecosystem function (total biomass) than their unconnected counterparts. At the same time, such an effect was not found for meta-ecosystems of identical patch sizes. Our work demonstrates how the size of ecosystems, interconnected via resource flows, can modulate cross-ecosystem dynamics, having implications for species diversity and function across scales.

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.

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.

Facultative scavenging can be observed across a large range of carnivorous mammals, but is an uncommon behavioural trait in cheetahs (Acinonyx jubatus). Very few incidents of cheetahs scavenging have been reported, with no explanation given as to why it may occur. In this paper we provide three more observations of cheetahs scavenging between 2019 and 2023 in three different protected areas in South Africa and Malawi. We suggest a common factor between these observations, namely that all adult individuals involved were temporarily housed in holding enclosures (bomas) during relocation processes and were provisioned with carrion as supplemental feed. The observed scavenging events could also have been influenced by the easy access of food in a situation where food acquisition was potentially difficult (i.e. old age, loss of hunting partner, mother with cubs). We hypothesise that these contributing factors, combined with the prior exposure of the adult individuals to eating carrion, could be a potential explanation for our observations of cheetahs scavenging. These observations provide a basis for further research into cheetah scavenging behaviour and the potential impacts of translocations that require prolonged holding periods on wildlife behaviour post-release. Understanding these behavioural shifts is crucial for cheetah conservation, as successful reintroduction efforts depend on the ability of cheetahs to adapt to new environments and food acquisition strategies.

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.

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.

Aim The genus Camellia is widely distributed, primarily in East Asia. Camellia japonica is located at the northern limit of this genus distribution, and elucidating its distribution changes is crucial for understanding the evolution of plants in this region, as well as their relationship with geological history and climate change. Also, the classification of sect. Camellia in Japan has not been clarified. Therefore, the aim of this study is to understand the evolutionary history of Japanese sect. Camellia. Location Japan, Korea, Taiwan, and the coastal area of China Taxon Camella (Theaceae). Methods The genetic population structure was analyzed by SNP data using MIG-seq. The relationship between Japanese sect. Camellia including the related species in China was further inferred from the phylogeny generated by RA x ML, SplitsTree and PCA. Population genetic structure was inferred using a Bayesian clustering method (ADMIXTURE). We then employed approximate Bayesian computation to explore the changes in population, asking which events best explain the phylogeographical signature. Ecological niche modeling was combined with genetic analyses to compare current and past distributions. Results The analyses consistently showed that C. japonica and C. rusticana are distinct, having diverged from each other between approximately 5.4 and 12 million years ago. Furthermore, C. japonica differentiated into four major populations (North, South, Ryukyu-Taiwan, and Continent). Main Conclusion Japanese sect. Camellia underwent speciation during archipelago formation, reflecting its ancient evolutionary history compared with other native Japanese plants. The conventional hypothesis that C. rusticana diverged from C. japonica in snow-rich environments under Quaternary period was rejected. Our results suggest that both species have been independent since ancient times, and that ancestral populations of C. japonica have persisted in northern regions. Furthermore, it is estimated that C. japonica population on the continent experienced a back-dispersal event from southern Japan during the late Pleistocene glaciation.

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. In oviparous vertebrates, maternal androgens can alter offspring immune function, particularly early in development, but the potential for negative health effects of maternal androgens in mammals remains unclear. 2. We investigated the relation between maternal androgens, particularly in late gestation, and offspring health in the meerkat (Suricata suricatta) by comparing offspring from (a) normative dominant and subordinate matrilines, whose dams naturally express high versus lower circulating androgen concentrations, respectively, and (b) normative dominant and antiandrogen-treated dominant matrilines, whose dams’ androgen function was intact versus blocked owing to experimental antagonism of the latter’s androgen receptors (using Flutamide©). Foetal offspring thus experienced three different endocrine environments (‘high,’ ‘lower,’ ‘blocked’ androgens) late in prenatal development. We assessed parasitism, immune function, steroid concentrations and survivorship in these three offspring groups, both during juvenility and early adulthood. 3. The juvenile offspring of subordinate control and dominant treated dams generally had lower intensities of parasite infections and greater immune function than did their peers from dominant control dams – patterns not found in adult offspring, nor in relation to the offspring’s concurrent hormone concentrations. Survivorship to adulthood was greatest in the progeny of treated dams. 4. Descendants of dominant female meerkats – those in the ‘high’ prenatal androgen category – suffered increased parasitism and decreased immunocompetence as juveniles, as well as reduced survivorship relative to antiandrogen-exposed peers, providing evidence in mammals that maternal androgens can negatively impact offspring health and survival. These intergenerational, androgen-mediated, health effects represent early costs imposed by female intrasexual competition and its associated selection pressures.

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.

Shrub encroachment can alter the structure and function of grassland ecosystems, leading to their degradation. Therefore, population regeneration dynamics after shrub encroachment on the influence of grassland should not be ignored. H. rhamnoides, as a pioneer species, has significantly encroached with large areas onto the Qinghai-Tibetan Plateau (QTP) due to climate change and over-grazing. However, few studies have focused on the dynamics of population regeneration following successful encroachment. Therefore, we studied H. rhamnoides natural population in the alpine grasslands, investigating population regeneration pattern, seed, bud production and storage, and limitation imposed by microhabitats (soil, light and feeding). Our aim was to explore population regeneration strategies and identify key limiting factors for population regeneration after successful encroachment. Our findings revealed several key points: (i) H. rhamnoides entered the alpine grassland by relying on seeds, it would seize resources by low-cost clonal reproduction, then increase sexual reproduction to improve genetic diversity. (ii) The production and storage of seeds and buds was sufficient, seed vigor was high, seed emergence rate was higher duo to mechanical restriction of hard seed coat was weakened by the water transport channels in the palisade layer, and formation of seedlings was less restricted. (iii) H. rhamnoides population regeneration was mainly limited by microhabitats light and feeding. However, light and feeding significantly affected seedlings photosynthesis and carbon storage, their interaction significantly reduced the seedlings survival, and further restricted population regeneration. The results can provide theoretical basis for the restoration and management of alpine grassland degradation caused by shrub encroachment.

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.

Hawk tea (Litsea coreana var. sinensis), derived from the tender shoots or leaves, rich in flavonoids that can promote healthcare for humans. The primary flavonoid are kaempferol-3-O-β-D-glucoside, kaempferol-3-O-β-D-galactoside, quercetin-3-O-β-D-glucoside, and quercetin-3-O-β-D-galactoside. Is there an association between leaf phenotype and flavonoid content? And the mechanisms of flavonoid biosynthesis are not fully understood. In this study, 109 samples were analyzed to determine the correlation and genetic variability in leaf phenotype and flavonoid content. Furthermore, a transcriptome-wide association study identified candidate loci implicated in the biosynthesis of four key flavonoids. The study revealed that genetic variability in leaf traits and flavonoid concentrations is predominantly attributed to inter-population differences. Flavonoid accumulation may correlate with tree diameter at breast height (DBH), indicative of age-related traits. Transcriptome-wide association analysis identified 84 significant SNPs associated with flavonoid content, with only 13 located within gene regions. The majority of these genes are implicated in metabolic processes and secondary metabolite biosynthesis. Notably, structural genes within these regions are directly involved in pathways known to regulate flavonoid metabolism, exerting a pivotal influence on flavonoid biosynthesis. These results lay a solid theoretical groundwork for subsequent explorations into the genetic determinants influencing flavonoid accumulation of hawk tea.