Roegneria yenchiana sp. nov. (Triticeae) is described as a new species collected from Shangri-la of Yunnan Province in China based on morphological, cytological, and molecular data. It is morphologically characterized by one spikelet per node, rectangular glums, awns flanked by two short mucros in lemmas, which is distinguished from other species of Roegneria. The genomic in situ hybridization results indicate that R. yenchiana is an allotetraploid, and its genomic constitution is StY. Phylogenetic analyses based on multiple loci suggested that R. yenchiana is closely related to Pseudoroegneria and Roegneria, and the Pseudoroegneria served as the maternal donors during its polyploid speciation.

Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB-LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries of Silphium integrifolium Michx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short-read (n=99) and PacBio long-read (n=10) approaches. We found a positive relationship between the mean effective annual precipitation of a plant’s source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non-model relatives of model organisms.

Understanding animal movement and behaviour can aid spatial planning and inform conservation management. However, it is difficult to directly observe behaviours in remote and hostile terrain such as the marine environment. Behaviours can be inferred from telemetry data using hidden Markov models (HMMs), but model predictions are not typically validated due to difficulty obtaining ‘ground truth’ behavioural information. We investigate the accuracy of HMM-inferred behaviours by considering a unique dataset provided by Joint Nature Conservation Committee. The data consist of simultaneous proxy movement tracks of the boat (defined as visual tracks as birds are followed by eye) and seabird behaviour obtained at the same time-frequency by observers on the boat. We use these data to assess whether (i) visual track is a good proxy for true bird locations in relation to HMM-inferred behaviours, and (ii) inferred behaviours from HMMs fitted to visual tracking data accurately represent true behaviours as identified by behavioural observations taken from the boat. We demonstrate that visual tracking data can be regarded as a good proxy for true movement data of birds in terms of similarity in inferred behaviours. Accuracy of HMMs ranging from 71% to 87% during chick-rearing and 54% to 70% during incubation was generally insensitive to model choice, even when AIC values varied substantially across different models. Finally, we show that for foraging, a state of primary interest for conservation purposes, identified missed foraging bouts lasted for only a few seconds. We conclude that HMMs fitted to tracking data can accurately identify important conservation-relevant behaviours, demonstrated using visual tracking data. Therefore, confidence in using HMMs for behavioural inference should increase even when validation data are unavailable. This has important implications for animal conservation, where the size and location of protected areas are often informed by behaviours identified using HMMs fitted to movement data.

1. Recognition of favourable environmental conditions for seed germination and seedling survival in different types of forest sites is crucial both for effective regeneration of introduced tree and for control of its spontaneous spread. Studies on the encroachment of North American northern red oak Quercus rubra into European Scots pine forests revealed high abundances of seedlings and saplings under shrubs, with lower abundances in open areas or in clumps of bilberry Vaccinium myrtillus. It was unclear, does burying acorns by seed-hoarders in moss or soil in different microhabitats impact survival of red oak seeds and seedlings, and does acorn size matter? 2. Results of previous (observational) studies were verified in a 3-year experimental study: a pool of 900 sown acorns was monitored in natural conditions. 3. Study revealed that ~80% of sown acorns were lost due to pilferage, lack of germination, fungal infection, and death of sprouting acorns and leafed-out seedlings. The fate of acorns and seedlings depended largely on acorn size and differed among microsite types. Viable seedlings were twice as likely to develop from large- and medium-sized, than from small acorns. Surviving seedlings grew mainly from acorns sown under moss cover within bilberry clumps or in open area, confirming a positive ‘burial effect’. Less than 10% of acorns sown under shrubs developed into viable seedlings, contradicting former conclusions on their ‘nurse effect’. 4. The occurrence of extensive bilberry clumps and small clusters of shrubs in pine forests favours Q. rubra regeneration, but severe fluctuations of the warming climate limit the viability of red oak seeds and seedlings. Prognosed range shifts of native tree species and expected dramatic loss of V. myrtillus climatic optima will impact Q. rubra distribution in European forests. Meanwhile, to prevent red oak spread (if necessary), it is recommended to remove shrubs from pine stand.

Birds and ants co-occur in most terrestrial ecosystems and engage in a range of interactions. Competition, mutualism and predation are prominent examples of these interactions, but there are possibly many others that remain to be identified and characterized. This study provides quantitative estimates of the frequency of toe amputations resulting from ant bites in a population of migratory red-necked nightjars (Caprimulgus ruficollis) monitored for 15 years (2009-2023) in S Spain and identifies the attacker(s) based on taxonomic analyses of ant-mandible remains found on injured toes. Less than 1% of examined adults (N = 369) missed one or more toes. The analysis of ant remains identified African army ants (Dorylus sp.) as the primary cause of toe amputations in nightjars and revealed that body parts of the attacker may remain attached to the birds even after intercontinental migration. No cases of severe damage were observed in juveniles (N = 269), apart from the mandible of a Messor barbarus –a local ant species– attached to one of the teeth of the characteristic comb of the medial toe of nightjars. The incidence of ant-bite damage may appear unimportant for nightjar populations, but this might not be true if only birds that manage to survive their injuries and potential complications (e.g. severe bleeding and sepsis from opportunistic infections) return from the tropics. More field studies, ideally in tropical areas, that incorporate routine examination of ant-induced injuries into their protocols are needed to understand the true incidence and eco-evolutionary implications of antagonistic ant-bird interactions.

Reference conditions are difficult to find in the Anthropocene but essential for effective conservation of biodiversity. Aquatic ecosystems in the Andes-Amazon transition zone of Colombia are now at high risk due to expanded human activities after peace agreements in 2016 ended armed conflict. Expanding human land use may reduce fish diversity across the altitudinal gradient but especially in premontane streams (i.e., <500 m a.s.l.) because lands are more amenable to human use than at greater altitudes. We evaluated natural fish diversity in twelve sites over eight years bracketing the end of armed conflict. Strong differences in community structure (measured as species richness, total abundance, and effective species number, and multivariate analyses) occurred as a function of altitude, as measured by. Our results provide a baseline to identify short-term and long-term changes due to impending human land use at a critical moment for the conservation of tropical fish diversity.

Olive baboons (Papio anubis) use fixed, secure and naturally-occurring sleeping sites such as tall trees and rocky cliffs, as protection from predators. Although these sleeping sites are safe, they can be limited in availability. We documented olive baboons’ use of 45m tall high-tension electrical pylons (towers) as sleeping sites in Laikipia, Kenya. These observations suggest that olive baboons may use anthropic infrastructure for sleeping sites in areas where naturally occurring cliffs and tall trees are limited.

Bitterling fishes evolve an idiosyncratic symbiosis with freshwater mussels, in which they are obligated to spawn in the gills of mussels for reproduction. In recent years, freshwater mussel populations have been drastically diminishing, due to accelerating anthropogenic impacts, which can be large threats to the risk of bitterling’s extinction cascade (i.e. ‘coextinction’). The host mussel size may be an important factor driving the adaptation and evolution of bitterling’s reproductive phenotypes. Here we examined the host size preference and morphological adaptation of female bitterling to the host size from 17 localities at the Han River in Korea. Using our developed molecular-based species identification for bitterling’s eggs/larvae inside the mussels, we further determined the spawning patterns of seven bitterling species. Mean length of spawned mussels (N=453) was significantly larger than that of unspawned mussels (N=1,814), suggesting that bitterling prefers to use larger hosts as a spawning ground. Spawning probability was clearly greater as mussel size increases. Results of our reciprocal transplant experiments do provide some evidence supporting the ‘bitterling’s larger host preference’ hypothesis. Interspecific competition appeared to be intense as two fish species often spawned eggs in the same mussel individuals simultaneously. Longer ovipositor and more elongated egg may evolve in females of Tanakia signifier in response to larger host environments. The observed bitterling’s spawning preference for large-sized mussels may evolve perhaps because of the fitness advantage in relation to the offspring survival. Our findings further inform on the development of effective conservation and management strategy for the endangered bitterling fishes.

Pathogen genomic epidemiology has the potential to provide a deep understanding of population dynamics, facilitating strategic planning of interventions, monitoring their impact, and enabling timely responses, and thereby supporting control and elimination efforts of parasitic tropical diseases. Plasmodium vivax, responsible for most malaria cases outside Africa, shows high genetic diversity at the population level, driven by factors like sub-patent infections, a hidden reservoir of hypnozoites, and early transmission to mosquitoes. While Latin America has made significant progress in controlling Plasmodium falciparum, it faces challenges with residual P. vivax. To characterize genetic diversity and population structure and dynamics, we have analysed the largest collection of P. vivax genomes to date, including 1474 high-quality genomes from 31 countries across Asia, Africa, Oceania, and America. While P. vivax shows high genetic diversity globally, Latin American isolates form a distinctive population, which is further divided in sub-populations and occasional clonal pockets. Genetic diversity within the continent was associated with the intensity of transmission. Population differentiation exists between Central America and the North Coast of South America, vs. the Amazon Basin, with significant gene flow within the Amazon Basin, but limited connectivity between the Northwest Coast and the Amazon Basin. Shared genomic regions in these parasite populations indicate adaptive evolution, particularly in genes related to DNA replication, RNA processing, invasion, and motility -- crucial for the parasite's survival in diverse environments. Understanding these population-level adaptations is crucial for effective control efforts, offering insights into potential mechanisms behind drug resistance, immune evasion, and transmission dynamics.

Parentage analyses via molecular markers have revealed multiple paternity within the broods of polytocous species, reshaping our understanding of animal behavior, ecology, and evolution. In a meta-analysis of multiple paternity in bird and mammal species, we conducted a literature search and found 138 bird and 64 mammal populations with microsatellite DNA paternity results. Bird populations averaged 19.5% multiple paternity and mammals more than twice that level (46.1%). We used a Bayesian approach to construct a null model for how multiple paternity should behave at random among species, under the assumption that all mated males have equal likelihood of siring success, given mean brood size and mean number of sires. We compared the differences between the null model and actual probabilities of multiple paternity. While a few bird populations fell close to the null model, most did not, averaging 34.0-percentage points below null model predictions; mammals had an average probability of multiple paternity 13.6-percentage points below the null model. Differences between bird and mammal species were also subjected to comparative phylogenetic analyses that generally confirmed our analyses that did not adjust for estimated historical relationships. Birds exhibited extremely low probabilities of multiple paternity, not only compared to mammals, but relative to other major animal taxa. The generally low probability of multiple paternity in birds might be produced by a variety of factors, including behaviors that reflect sexual selection (extreme mate guarding or unifocal female choice) and sperm competition (e.g., precedence effects favoring fertilization by early or late matings).

Anthropogenic pressures on nature have been causing population declines for centuries. Intensified persecution of apex predators, like the golden eagle, resulted in population bottlenecks during the 19th-20th centuries. To study population genetics and demographic history of the golden eagle throughout its distribution, we collected museum samples from previously underrepresented regions, such as Russia and Central Asia. We used 12 microsatellite loci and a fragment of the mitochondrial DNA control region to re-evaluate phylogeography of Eurasian golden eagles and study the impacts of the population bottleneck. Our results revealed a north-south genetic gradient, expressed by the difference of Mediterranean and Holarctic lineages, as well as genetically distinct Northern Europe and Central Asia and Caucasus regions. Furthermore, Northern Europe exhibited the lowest, whereas Central Asia and Caucasus had the highest genetic diversity. Although golden eagles maintained relatively high genetic diversity, we detected genetic signatures of the recent bottleneck, including reduced genetic diversity and a decline in the effective female population size around the year 1975. Our study improves the knowledge of the genetic composition of Eurasian golden eagles and highlights the importance of understanding their historical population dynamics in the face of ongoing and future conservation efforts.

Quantitative evidence on tree space segregation among avian assemblages in temperate primeval forests is currently lacking. Therefore, our study aimed to determine the species composition of birds across different parts of trees. We investigated whether species richness differs between positions on a tree and how these positions influence the probability of occurrence of specific bird species. To achieve this, we observed birds within permanent plots in Białowieża National Park (BNP) and analyzed the distribution patterns of birds within six vertical and three horizontal sectors of trees. The compositional dissimilarity between tree sectors was assessed using detrended correspondence analysis. We employed generalized linear mixed-effects models to examine differences in species richness and the probability of occurrence for ten of the most frequently observed species across tree sectors. The majority of the BNP bird community was associated with the branches, while other birds occupied the tree crown trunks and the understory trunks. Species richness was the highest on branches in the crown part of trees, followed by lower species richness on trunks associated with crowns, and the lowest richness was observed on branches and trunks in the understory. These results indicate that branches in the middle and lower parts of the crown serve as avian diversity hotspots on trees, likely due to the abundance of various food sources. The differing patterns of tree usage by specific bird species may suggest the avoidance of interspecific competition for resources. Importantly, our study provides a pristine state for future investigations.

Fish communities of streams and rivers might substantially be subsidized by terrestrial insects that fall into the water. Although such animal-mediated fluxes are increasingly recognized, little is known on how anthropogenic perturbations may influence the strength of such exchanges. Intense land-use, such as lignite mining may impact a river ecosystem due to the flocculation of iron (III) oxides, and thus altering food web dynamics. We compared sections of the Spree River in North-East Germany that were greatly influenced by iron oxides with sections located downstream of a dam where passive remediation technologies are applied. Compared to locations downstream of the dam, the abundance of benthic macroinvertebrates at locations of high iron concentrations upstream of the dam was significantly reduced. Similarly, catch per unit effort of all fishes was significantly higher in locations downstream of the dam compared to locations upstream of the dam and condition of juvenile and adult piscivorous pike Esox lucius were significantly lower in size in sections of high iron concentrations. Using an estimate of short-term (i.e., metabarcoding of the gut content) as well as longer-term (i.e., hydrogen stable isotopes) resource use, we could demonstrate that two of the three most abundant fish species, perch Perca fluviatilis, and bleak Alburnus alburnus, received higher contributions of terrestrial insects to their diet at locations of high iron concentration. In summary, lotic food webs upstream and downstream of the dam greatly differed in the overall structure with respect to the energy available for the highest tropic levels and the contribution of terrestrial insects to the diet of omnivorous fish. Therefore, human-induced environmental perturbation such as river damming and mining activities represent strong pressures that can alter the flow of energy between aquatic and terrestrial systems, indicating a broad impact on the landscape level.

Personality variation, defined as among-individual differences in behaviour that are repeatable across time and context, is widely reported across animal taxa. From an evolutionary perspective, characterising the amount and structure of this variation is useful since differences among individuals are the raw material for adaptive behavioural evolution. However, behavioural variation among-individuals also has implications for more applied areas of evolution and ecology – from invasion biology, to ecotoxicology, and selective breeding in captive systems. Here, we investigate the structure of personality variation in the red cherry shrimp, Neocaridina heteropoda, a popular ornamental species that is readily kept and bred under lab conditions and is emerging as a decapod crustacean model across these fields, but for which basic biological, ecological, and behavioural data is limited. Using two assays and a repeated measures approach, we quantify behaviours putatively indicative of shy-bold variation and test for sexual dimorphism and/or size-dependent behaviours (as predicted by some state-dependent models of personality). We find moderate to high behavioural repeatabilities across traits. Although strong individual-level correlations across behaviours are consistent with a major personality axis underlying these observed traits, the multivariate structure of personality variation does not fully match a priori expectations of a shy-bold axis. This may reflect our ecological naivety with respect to what really constitutes bolder, more risk prone, behaviour in this species. We find no evidence for sexual dimorphism and only weak support size-dependent behaviour. Our study contributes to the growing literature describing behavioural variation in aquatic invertebrates. Furthermore, it lays a foundation for further studies harnessing the potential of this emerging model system. In particular, this existing behavioural variation could be functionally linked to life-history traits, invasive success, and serve as target of artificial selection or bioassays. It thus holds significant promise in applied research across ecotoxicology, aquaculture, and invasion biology.

PREMISE OF THE STUDY Plant reproductive failure is a critical concern for conserving rare and endangered species that typically have low-density and sparse populations. One important factor contributing to reproductive failure is the spatial arrangement of plants within a population, which can lead to isolation and negatively affect seed output, particularly in obligate outcrossers. Additionally, this effect can be compounded by plant size. Here, we investigate how plants’ spatial distribution and size influence the reproductive success of Carica chilensis, a threatened papaya species. METHODS Using flower exclusion, we first examined whether C. chilensis can produce seeds via apomixis. We then used Spatial Point Pattern Analysis (SPPA) in three populations to examine the spatial arrangement of plants and, finally, we assess whether plant size and mate distance influence the reproductive success of this plant species. KEY RESULTS C. chilensis is a dioecious shrub unable to produce fruits through apomixis. The SPPA revealed significant clustering of female and male plants at different spatial scales, indicating a non-random distribution. Moreover, a significant attraction between the sexes suggested a preference for proximity. In two populations, closer proximity to male plants was linked to higher seed production. CONCLUSIONS Our study revealed that the absence of apomixis in C. chilensis makes it prone to experiencing distance-dependent reproductive failure. In particular, the seed set was compromised in female plants isolated from male neighbors. This link between isolation and seed production was especially significant in the driest site, and we discuss how environmental factors can exacerbate this effect.

1. Graphs in research articles can increase the comprehension of statistical data but may mislead readers if poorly designed. Previous literature has found that the two most frequently used plot types - bar charts and dot and whisker plots - are a poor way to represent data because they only show the summary statistics of data, not their distribution, potentially hiding important information. 2. Calls have been made encouraging abandonment of bar charts and the use of more informative plot types, such as boxplots, violin plots, univariate scatter plots, and dot plots. We compare these plot types to assess their relative strengths and weaknesses to represent four different distributions of the data commonly observed in biological studies, finding that all the assessed plot types are either difficult to read at large sample sizes or misrepresent certain distributions of data. 3. We present an analysis of the plot types used in four ecology and conservation journals covering multiple areas of these research fields, finding widespread use of uninformative bar charts and dot and whisker plots (60 % of all plots showing one-dimensional data from multiple groups for the purpose of comparison). Some articles presented more informative figures by combining plot types, generally boxplots and a second layer such as a flat violin plot, to better display the data. This shows an appetite for more effective plot types within conservation and ecology, which may further increase if an accurate and user-friendly plot types were made available. 4. In response to this, we propose sea stack plots, which combine vertical histograms and summary statistics, and allow for an accurate representation of different data distributions, thereby largely overcoming the weaknesses associated with other alternatives to uninformative plots. We provide a tool to create sea stack plots with our R package ‘seastackplot’, available through GitHub.

Interactions among coexisting mesocarnivores can be influenced by different factors such as the presence of large carnivores, land-use, environmental productivity, or human disturbance. Disentangling the relative importance of bottom-up and top-down processes can be challenging, but it is important for biodiversity conservation and wildlife management. The aim of this study was to assess how the interactions among mesocarnivores (red fox Vulpes vulpes, badger Meles meles, and pine marten Martes martes) are affected by large carnivores (Eurasian lynx Lynx lynx and wolf Canis lupus), land cover variables (proportion of agricultural land and primary productivity), and human disturbance, as well as how these top-down and bottom-up mechanisms are influenced by season. We analyzed three years (2018-2020) of camera trapping data from Norway and used structural equation models to assess hypothesized networks of causal relationships. Our results show that land cover variables are stronger predictors of mesocarnivore activity than large carnivores in Norway. This might be caused by a combination of low density of large carnivores in an unproductive ecosystem with strong seasonality. Additionally, all mesocarnivores showed positive interactions among each other, which were stronger in winter. The prevalence of positive interactions among predators might indicate a tendency to use the same areas and resources combined with weak interference competition. Alternatively, it might indicate some kind of facilitative relationship among species. Human disturbance had contrasting effects for different species, benefiting the larger mesocarnivores (red fox and badger) probably through food subsidization, but negatively affecting apex predators (wolf and lynx) and smaller mesocarnivores (pine marten). In a human-dominated world, this highlights the importance of including anthropogenic influences in the study of species interactions.

Gene function conservation is crucial in molecular ecology, especially for key traits like growth and maturation in teleost fish. The vgll3 and six6 genes are known to influence age-at-maturity in Atlantic salmon, but their impact on other fish species is poorly understood. Here, we investigated the association of vgll3 and six6 in the domestication of gilthead seabream and European seabass, both undergoing selective breeding for growth-related traits in the Mediterranean. We analysed two different sets of samples using two different genotyping approaches. The first dataset comprised farmed and wild populations from Greece, genotyped for SNPs within the genomic range of the two genes (“gene-level genotyping”). The second dataset examined 300k to 600k SNPs located in the chromosomes of the two genes, derived from a meta-analysis of a Pool-Seq experiment involving farmed and wild populations distributed widely across the Mediterranean (“chromosome-level genotyping”). The gene-level analysis revealed a significant effect of domestication on both genes in each species. This finding was partially supported by the chromosome-level analysis, identifying highly differentiated regions associated with domestication at varying distances from the candidate genes. Noteworthy genomic features were found, such as a CpG island in gilthead seabream and novel candidate genes in European seabream, warranting further investigation. These findings support a putative role of vgll3 and six6 in the maturation and growth of gilthead seabream and European seabass, emphasizing the need for further research on their conserved function.