The study of the spatial point patterns in ecology, such as the records of the observed locations of trees, shrubs, nests, burrows, or documented animal presence, relies on multivariate point process models. This study aims to compare the efficacy and applicability of two prominent multivariate point process models, the multivariate log Gaussian Cox process (MLGCP) and the Saturated Pairwise Interaction Gibbs Point Process model (SPIGPP) , highlighting their respective strengths and weaknesses in various scenarios. Using synthetic and real datasets, we assessed both models based on their predictive accuracy of the empirical K function. Our analysis revealed that both MLGCP and SPIGPP effectively identify and capture mild to moderate attractions and regulations. MLGCP struggles to capture repulsive associations as they intensify. In contrast, SPIGPP can well estimates both the direction and magnitude of interactions even when the model is miss-specified. Both models present unique advantages: MLGCP is particularly effective when there is a need to account for complex, unobserved heterogeneities that vary across space, while SPIGPP is suitable when interactions between points are the primary focus. The choice between these models should be guided by the specific needs of the research question and data characteristics.

A process-based understanding of community assembly at multiple scales can allow forecasting of community response to degradation and restoration practices. We draw attention to a distinct metacommunity arrangement characterised by multiple levels of assembly filters, and exemplified by freshwater habitat patches on islands. This type of metacommunity has complex spatial dynamics, and dispersal must occur across multiple intermediate habitat types. An interdisciplinary approach harnessing mathematical models and genetic tools such as eDNA and population genomics will allow us to unravel the fundamental processes acting over a large spatial and temporal scale influenced by the region's geography, historical events and species pool.

The hydrothermal springs (HTSs) are unique environments characterised by the emergence of geothermally heated groundwater that often releases large amounts of dissolved minerals. Despite interest in HTSs, the microbial composition of these sites remains largely under-explored, particularly concerning the interactions between marine invertebrates and microorganisms. As an example, the shallow HTSs of Trapani (West coast of Sicily, Italy) maintain a constant temperature of 31 °C throughout the year and two invertebrates and are inhabited by the nudibranch Peltodoris atromaculata (P. atromaculata) and the sponge Petrosia ficiformis (P. ficiformis). This study aimed to analyse the bacterial communities associated with the sponge P. ficiformis and the mantle and gut of P. atromaculata. Our results, based on Next-Generation sequencing of the bacterial marker gene (16S rDNA), revealed that the bacterial communities associated with the sponge P. ficiformis and the mantle of P. atromaculata are strikingly similar, suggesting a shared bacterial community, while also exhibiting distinct bacterial differences. However, signatures of bacterial families were found in the gut and mantle of P. atromaculata. These findings shed light on the bacterial composition of the nudibranch P. atromaculata and the sponge P. ficiformis, both considered bioindicators of environmental conditions and highlight the importance of investigating the microbial biodiversity in these peculiar environments to be preserved at every taxonomic level. Additionally, to date, we have provided a brief introduction to understanding the role of host-bacteria interactions in marine invertebrates and these unique environments in shaping entire communities.

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.

The microbiome plays a key role in animal health, and is an important aspect of any natural or farmed ecosystem. Here we present the first environmental microbiome study of Ostrea edulis, as well as the first of a natural wild spawning event of any oyster species. Larval abundance was hypothesised to be correlated with specific microbial signatures. Water samples were collected throughout a natural spawning event of O. edulis at Loch Ryan, Scotland, UK. Samples were collected on 4 different dates from June to September 2019, across 8 different sampling sites on the loch at mid, bottom and surface levels within the water column to remove effects of salinity and tidal fluctuations. Larval count data was obtained from these samples before full-length sequencing of the 16S rRNA gene using Oxford Nanopore Technologies. Significant microbial differences were only found between samples collected on different dates, and not at different sites or water column depths. Differences in the microbiome throughout the spawning season were driven by changes in the abundance of certain taxa, most notably those belonging to the Rhodobacteraceae family. Inverse abundance profiles of Rhodobacteraceae and Vibrio over time are also discussed. This study provides important microbial baseline data about the spawning environment of O. edulis.

Abstract Aim Goldenseal (Hydrastis canadensis L.) is a perennial herbaceous plant native to eastern North America. Commercial harvesting for the medicinal plant trade and habitat loss have led to international conservation concerns. This study aimed to gain an understanding of habitat predilections for the purpose of guiding in situ conservation efforts. Location This study was conducted in Pennsylvania, within natural range of the species in the northeastern U.S. The state’s variation in geology and biogeographic location an opportunity to examine the influences of edaphic, topographic, and climatic factors on goldenseal habitat suitability here. Methods GIS-based Maximum Entropy (Maxent) modeling using known occurrence points (n=51) was combined with field plot data (n=28) to identify potential factors governing goldenseal’s distribution in PA and identify vegetative indicators of supportive habitat. Results Bedrock type and winter temperature were the best predictors of habitat suitability. Suitable bedrock types were base-rich; a trait confirmed in the field by soil test results showing high calcium and pH levels. However, the influence of bedrock is complicated by overlapping land use legacy. Suitability increased with average winter temperature, peaking at 1.0°C toward upper end of winter temperatures in PA. Community analysis identified 159 woody and herbaceous associates, including indicators of the following supportive rich mesic forest types: “Tuliptree-Beech-Maple,” “Red Oak-Mixed hardwood,” and “Central Appalachian Rich Cove”. Main Conclusions Model and field results can be used in tandem to assess site suitability, which was found to be greatest within forestlands with slightly acidic to neutral loamy soils underlain by base-rich bedrock types on moist, lower slope positions. Vegetative “indicator” species of these rich-mesic forests including Liriodendron tulipifera, Acer saccharum, Lindera benzoin, Arisaema triphyllum, and Botrypus virginianus appeared to be useful field indicators of supportive habitat for in situ conservation efforts.

Fragmentation of landscapes is a common impairment of habitats highlighting the need to increase connectivity to support wildlife populations. This study focuses on the Eastern green lizard (Lacerta viridis) and investigates the effectiveness of a species-specific corridor network in a vineyard landscape. Using a non-invasive photographic capture-recapture approach, individual movements were tracked to assess sex-specific patterns and distances covered in adult lizards. The study also provided insight into population parameters such as sex ratio and spatial distribution of the resident green lizard population. Results showed a surplus of male individuals and clustered distributions along the habitats. Both, male and female green lizards use the habitat network, with males covering larger distances. The connectivity structures facilitated the movement of males between habitat sections with some individuals covering distances exceeding 250 m. Hereby, male movement distances correlated with female abundance, which emphasizes the importance of connectivity structures in maintaining population stability. Two parameters correlated to female abundance showed significance in the models. First, the fewer females were detected in a male’s core area, the higher the probability that it migrated a long distance. Secondly, a positive correlation existed between males’ covered distance and female abundance in its entire activity range. Overall, this research highlights the importance of habitat connectivity measures for natural population dynamics through supporting male lizards to migrate in search of females.

Pangolins are under severe threat from illegal trade and habitat loss. Despite their conservation significance, these elusive creatures remain poorly understood, particularly in the context of phylogeography and genetic diversity. In this study DNA was isolated from two types of pangolin scat (faeces) samples (whole scat and swabs) which had been stored frozen for up to 3 years between the time of collection and our analyses. A mitochondrial sequence for the cytochrome b gene (424 bp) region was reliably generated from both sample types, for scats which appeared in ‘good’ or ‘poor’ condition at the time of collection. Sanger sequencing revealed four new cytochrome b haplotypes for pangolin, with variations in distinct sampling regions in Nepal (central and east). Comparison to reference sequences for pangolin originating from China, Taiwan and Thailand, indicated a distinct variant of Chinese pangolin in Nepal (15-19 base pair difference). Genetic differentiation of Chinese pangolin in Nepal has broader conservation significance for this species. Methods described here are robust and could be applied to broader genetic studies of pangolin populations across Nepal, allowing for genetic mapping of pangolin variations to assist in identifying populations of significance, evaluation of conservation interventions, and forensic applications supporting the fight against illegal poaching.

Entomopathogenic fungi can cause infectious diseases within host insect populations, while insects may counteract disease transmission through the strategy of isolating infected individuals. This study develops a system of differential equations to model the temporal dynamics of susceptible and infected individuals, as well as the concentration of fungal spores in the environment, to investigate the complex dynamics of disease transmission. The study focuses on three critical parameters: infection probability, population size, and isolation rate. The results show that infection probability is a key determinant of disease spread; as infection probability increases, the basic reproduction number (R_0) rises, potentially leading to periodic oscillations in disease incidence, highlighting the nonlinear response of disease transmission to changes in virulence. This underscores the importance of managing environmental factors such as temperature and humidity, which influence infection probability, to control disease spread. Furthermore, the analysis reveals that larger populations, due to higher contact frequency, exhibit more pronounced and persistent disease dynamics, suggesting that population density control is an effective strategy for managing disease outbreaks. The study also identifies isolation behavior as crucial for disease control, where moderate increases in isolation rates can lead to complete eradication under certain conditions. The timing of spore production relative to host death is also identified as a key variable affecting the efficacy of isolation. In conclusion, this study elucidates the complex interplay between infection probability, population size, and isolation behavior, providing a theoretical basis for optimizing biological control strategies using entomopathogenic fungi and managing high-density insect populations.

Partial migration is a phenomenon where migratory and resident individuals of the same species co-exist within a population, and has been linked to both intrinsic (e.g., genetic) as well as environmental factors. Here we investigated the genomic architecture of partial migration in the Common blackbird, a songbird that comprises resident populations in the southern distribution range, partial migratory populations in central Europe and exclusively migratory populations in northern and eastern Europe. We generated whole-genome sequencing data for 60 individuals across the species’ distribution range, including resident populations (Spain and France), obligate migrants (Russia), and a partial migratory population with equal numbers of migratory and resident individuals in Germany. We estimated genetic differentiation (FST) of single-nucleotide variants (SNVs) in 2.5 kb windows between all possible population and migratory phenotype combinations, and focused our characterization on birds from the partial migratory population in Germany that have been individually phenotyped with radio-telemetry tracking. Despite overall low differentiation within the partial migratory German population, we identified several outlier regions with elevated differentiation on four distinct chromosomes. The region with the highest relative and absolute differentiation was located on chromosome 9, overlapping PER2, which has previously been shown to be involved in the control of the circadian rhythm across vertebrates. While this region showed high levels of differentiation, no fixed variant could be identified, supporting the notion that a complex phenotype such as migratory behavior is likely controlled by a large number of genetic loci.

Factors affecting breeding success in seabirds result in indices that can be useful for predicting population reproductive output, without the need for invasive and intensive monitoring. Such factors include environmental conditions that affect prey availability and distribution, leading to variation in behaviours related to foraging effort, such as foraging trip duration. Further, social factors, such as divorce, may offer an opportunity for birds to seek a more suitable partner to enhance long-term reproductive success, but may negatively impact success in the short term. The relative importance of environmental, behavioural and social predictors on reproductive output is unclear, as these factors have seldom been examined in tandem. In this study, we investigated environmental factors at differing scales, alongside foraging trip duration and divorce rate, to examine the consequences on reproductive success over 13 breeding seasons in an inshore foraging seabird, the little penguin (Eudyptula minor). Population divorce rate proved to be the most useful predictor of reproductive success, with years of lower divorce associated with higher hatching and fledging success. Shorter foraging trip durations were associated with higher fledging success, but longer trips led to more successful hatching rates. After controlling for the effect of divorce, marine environmental conditions were not a strong predictor of breeding success in this study. Therefore, we propose that the divorce rate can be a powerful index and a valuable tool for predicting population level reproductive success for seabirds facing similar environmental and foraging pressures as little penguins.

Offspring and kin care are common in nature, while non-kin societies are unusual due to their susceptibility to cheaters. Here, we investigated the kinship of mast-building amphipods, Dyopedos bispinis (Gurjanova, 1930). Our goal was to determine if all mast inhabitants are descendants of a single founder female or if they represent a more complex social structure. We sequenced and assembled the complete mitochondrial genome of D. bispinis along with 59 partial genomes from four masts. One of the studied masts contained several adult females with embryos, all of which had identical partial mitochondrial genome sequences. This shows that masts can be inhabited by individuals from different generations. Mitochondrial genome sequences of ten mother-embryo pairs confirm maternal mtDNA inheritance in D. bispinis. However, another mast contained several groups of female individuals exhibiting pronounced (~0.7 substitutions per 1000 b.p.) distance between the groups. The genetic distance between groups from the same mast was not less than the genetic distance from specimens of other masts. This suggests collective usage of the mast by non-related families. Given that adult female D. bispinis individuals invest resources into mast maintenance, this case implies non-kin cooperation among amphipods. Overall, our study provides an insight into the family structures of mast-inhabiting amphipods and presents a new model for studying the cooperation of non-related individuals.

Aim: Here we report on a long-term transplant study of a serpentine endemic plant where individuals were transplanted into cooler macro- and microclimatic refugia (i.e. higher elevations and north-facing aspects) in locations outside of its current range. We asked: 1) Did transplanted populations persist outside of their current range in micro- (cooler aspects) or macro- (higher elevations) climatic refugia? and 2) Was population persistence in climatic refugia helped or hindered by soil microbial communities? Location: Siskiyou Mountains of southwestern Oregon (USA) Taxon: Horkelia sericata (Rosaceae), Angiosperms Mycota (Fungi) Monera (Bacteria) Methods: At each transplant site, we counted surviving individuals (noting reproductive status) and then collected soil from both the rhizosphere of transplanted individuals and from an equal number of areas of nearby bare soil with no plants. Soil bacterial and fungal communities were assessed using next generation sequencing of 16S and ITS-1 marker genes Results: Of the 15 initial transplant sites, one (high elevation) site displayed population persistence (i.e., ‘successful’ site), defined as having surviving individuals with reproductive success. Four sites had surviving individuals but no reproductive success (i.e., ‘unsuccessful’ sites); the remaining 10 sites had no surviving individuals and were excluded from microbial analyses. The successful site had distinct soil fungal and bacterial community composition and a higher mututalist:pathogen ratio than the unsuccessful sites. Additionally, the mututalist:pathogen ratio did not differ between Horkelia’s rhizosphere and bare ground at the successful site, suggesting that the persistence of this population was enhanced by soil mutualists that were already present at that site. Main conclusions: Taken together, these results highlight that the success of species range shifts into climatic refugia may be influenced by the presence of suitable soil mutualists, emphasizing the need to consider soil microbial communities in future ra

Understanding population demography of threatened species and how they vary in relation to natural and anthropogenic stressors is essential for effective conservation. We used a long-term photographic capture-recapture dataset (1993 – 2020) of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in the highly urbanised Adelaide Dolphin Sanctuary (ADS), South Australia, to estimate key demographic parameters and their variability over time. These parameters were analysed in relation to environmental variables used as indicators of local and large-scale climatic events. Our findings indicate that apparent survival was high (0.98-0.99) and did not vary seasonally. Estimates of abundance were not directly related to environmental variables but were linked to seasonal temporary emigration. Abundance peaked in summer with an average of 85.37 dolphins (SD = 30.23), and was lowest in winter, with 68.57 (SD = 24.70) individuals. Site fidelity at the population level was low, but lagged identification rates revealed a resident population of approximately 28 individuals. Trend analysis suggests high levels of dolphin abundance and persistence of the population over decades despite significant urbanisation, but numbers have declined in recent years. Further research is needed to understand the cumulative impacts leading to this population decline and to assess its future viability under different management scenarios. Conservation strategies aimed at increasing reproductive rates and promoting connectivity to adjacent waters are likely to be more effective in reversing population declines.

In the face of global climatic changes, exploring how plant adaptation and responses to drought vary among different regions is crucial to understand and predict its geographic distribution. In this study, to explore the drought adaptation and responses of the dominant species in the semi-arid Eurasian Steppes and their differences among the species distribution regions in terms of growth, physiology and RNA-seq transcriptome, Stipa krylovii was chosen as the study object and a seed source (3 regions: eastern, middle and western regions) × soil moisture treatment (3 treatments: control, light drought and heavy drought) two-factor experiment was conducted. (1) Four growth traits for individuals from the western region were significantly lower than those from the other two regions. By Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis on gene expressions of individuals from each treatment, unique enriched pathways were found mainly under heavy drought. (2) The decrease in the number of tillers with the increasing drought was much lower for individuals from the western region than those from the other two regions. By KEGG functional enrichment analysis on differentially expressed genes (DEGs) between heavy drought treatment vs control, enrichment pathways of individuals from the eastern and middle regions mainly regulated energy metabolism and metabolism of other amino acids; and those from the western region regulated biosynthesis of other secondary metabolites and carbohydrate metabolism. (3) Clustering analysis based on gene expressions separated the western region from the other two regions under the same soil moisture treatment. This study indicates that drought adaptation and response mechanisms of S. krylovii vary among different regions, especially between individuals from the western region and the other two regions. These findings are essential for us to understand the adaptive evolution of population and germplasm resource protection for this important species in semi-arid grasslands.

Environmental and individual experiences can result in immediate and persistent changes in behaviour. Often, such effects are also sex-dependent. Interspecific interactions can be one of the most important environments an individual faces. Such social interactions are expected to affect a suite of behavioural traits and their correlations. Here, we used Drosophila melanogaster and high-throughput automated behavioural phenotyping to determine how social environment (group mixed sex, group single sex, and social isolation) and sex interact to affect basic behaviours (exploration, movement within a y-maze, and habituation to a startle) that likely underlie more complex behaviours such as mate searching and foraging. We show that such behaviours and some behavioural correlations are indeed context- and sex-dependent. Males tended to show greater exploration, while females were more likely to show a habituation response to startle. Males and females from the mixed sex and isolated treatments showed opposite exploratory behaviour in the Y-maze, and social treatment interacted with sex to affect the rate of habituation to a startle. Females also tended to have slightly stronger trait correlations compared to males. These results show that social environment and sex can play a significant role in shaping behaviour in Drosophila melanogaster. Our study provides insights into how the type of social stimulation and sex can interact to affect behaviours that are important in forming critical behaviours related to foraging and mate searching.