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.

Aphids are observed on various plant species, with most aphids feeding downward on stems. In this study, I studied the variations in feeding postures of aphids and their mechanisms. My field observations revealed that the majority of individuals from most species fed facing downward, or more precisely, towards the roots. Exceptions included Indomegoura indica on the scapes of Hemerocallis spp., which were aligned with their head facing the sky. Next, I investigated how plant orientation affects three aphid species, Macrosiphoniella yomogifoliae, Megoura crassicauda, and I. indica with different body alignments on upright immature stems. On the stems of the inverted plants, the number of Ma. yomogifoliae and Me. crassicauda in the upward position (head facing the root of the plant) was significantly greater than that in the downward position (head facing the shoot apex of the plant). If their posture is affected by gravity or by certain advantages of the headstand posture, Ma. yomogifoliae and Me. crassicauda are expected to align in a consistent direction, regardless of the orientation of the plant. This suggests that plant cues influence their posture. In contrast, the majority of I. indica were aligned with the head facing the sky on the scape, regardless of Hemerocallis’s direction. This result indicates that the feeding posture of I. indica is affected by gravity and/or aphid’s intrinsic factors. Therefore, this study provides a new perspective on the factors influencing aphid feeding posture preferences.

Modification and deterioration of old-growth forests by industrial forestry have seriously threatened species diversity worldwide. The loss of natural habitats increases the concentration of circulating glucocorticoids and incurs chronic stress in animals, influencing the immune system, growth, survival, and lifespan of animals inhabiting such areas. In this study, we tested whether great tit (Parus major) nestlings grown in old-growth unmanaged coniferous forests have longer telomeres than great tit nestlings developing in young managed coniferous forests. This study showed that the patches of young managed coniferous forests had lower larval biomass than old-growth forests. Since insect larvae are the preferred food for great tit nestlings, the shortage of food may divert energy resources away from growth, which can show up as physiological stress, often raising the heterophil/lymphocyte (H/L) ratio. The H/L ratio revealed a significant difference in stress levels, being the highest in great tit nestlings developing in young-managed pine forests. We also found that the development of great tit nestlings in young managed forests had significantly shorter telomeres than in old-growth forests. Although nestling survival did not differ between the habitats, nestlings growing up in old-growth forests had greater telomere lengths, which can positively affect their lifespan. Our results suggest that the forest habitats affected by industrial forestry may represent ecological traps as the development of young birds in deteriorated environments can affect the age structure of populations.

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.

A document by Daniel Estevez-Barcia. Click on the document to view its contents.

The black piranha (Serrasalmus rhombeus), a widely spread species in the rivers of the Amazon basin, plays a vital role as both key predator and important prey. Despite its essential contribution to ecosystem stability, there is a lack of information regarding its genetic diversity and population dynamics in the central Amazon region. As the Amazon continues to undergo environmental changes in the context of growing anthropogenic threats, such knowledge is fundamental for assist in the conservation of this species. This study is the first to analyze the genetic diversity and population structure of S. rhombeus in the central Amazon region using high-resolution genomic data. We employed a Genotyping-by-Sequencing approach with 248 samples across 14 study sites from various tributaries, encompassing diverse water types (black, white and clear water) and characterized by 34 physiochemical parameters. The data reveals low diversity accompanied by pronounced signs of inbreeding in half of the sites and robust genetic differentiation and variation among sites and within-sites. Surprisingly, we also found evidence of higher dispersal capacity than previously recognized. Our analysis exposed a complex and high population structure with genetic groups exclusive to some sites. Gene flow was low and some groups presented ambiguous genealogical divergence index (gdi) signals, suggesting the occurrence of potential cryptic species. Moreover, our results suggest that the the population structure of black piranha appears more influenced by historical events than contemporary factors. These results underscore the need to give greater attention to this keystone species, for which no regulatory framework or conservation strategies is presently in effect.

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.

Killer whales (Orcinus orca) have been documented to prey on white sharks (Carcharodon carcharias), in some cases causing localised shark displacement and triggering ecological cascades. Notably, a series of such predation events have been reported from South Africa over the last decade, with killer whales specifically targeting shark’s liver. However, observations of these interactions are rare and knowledge of their frequency across the world’s oceans remain limited. In October 2023, a 4.7 m (total length) white shark carcass washed ashore in south-eastern Australia, coinciding with reports from citizen scientists of killer whales hunting a large, unidentified prey item in the area. Visual inspection of the carcass revealed that the liver, digestive and reproductive organs were missing, and the presence of four distinctive bite wounds, one of which was characteristic of killer whale liver extraction as seen in South Africa. Genomic analyses performed on swabs taken from the bite wounds confirmed the presence of killer whale DNA in the major bite area, while the other bites were embedded with genetic material from the scavenging broadnose sevengill shark (Notorynchus cepedianus). These results provide confirmed evidence of killer whale predation on white sharks in Australia, and the likely selective consumption of the liver, suggesting predations of this nature are more globally prevalent than currently assumed.

The Yarlung Zangbo River (YLZB), as the highest plateau river in the world, has a particularly fragile ecological environment and is easily impacted by global climate change. Studying the changes in its habitat quality and the driving mechanisms behind them is crucial for the ecological protection and sustainable development of the YLZB. Based on land use data from 2000 to 2020, using a habitat quality model, optimal parameter geographical detector, and partial least squares structural equation model (PLS-SEM), we conducted a quantitative study on the spatiotemporal changes and driving mechanisms of habitat quality in the YLZB from 2000 to 2020. The results show that: (1) Forests, grasslands, and unused land account for 94.14% of the basin area. The areas of unused land, forest land, and water bodies have continuously increased, while the areas of grasslands, permanent glaciers, and snowfields have continuously decreased. The decline was most pronounced from 2005 to 2010. The habitat quality in the study area is higher in the southeast and lower in the west. The area of degraded habitats is significantly larger than that of improved habitats. (3) NDVI, elevation, and annual average temperature are key factors affecting changes in habitat quality. Elevation indirectly affects NDVI by influencing climate conditions, leading to a decline in habitat quality. Our research findings help to better understand the ecological dynamics within the basin and provide scientific insights for sustainable management and conservation efforts.

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.