1. Cyanobacterial blooms in freshwater sources are a global concern, and gaining insight into their causes is crucial for effective resource management and control. 2. In this study, we present a computational framework for the causal analysis of cyanobacterial harmful algal blooms (cyanoHABs) in Lake Kinneret. Our framework integrates Convergence Cross Mapping (CCM) and Extended CCM (ECCM) causal networks with Bayesian Network (BN) models. 3. The constructed CCM - ECCM causal networks and BN models unveil significant interactions among factors influencing cyanoHAB formation. These interactions have been validated by domain experts and supported by evidence from peer-reviewed publications. Our findings suggest that M. flos-aquae levels are influenced not only by community structure but also by nitrate, nitrite, ammonium, phosphate, oxygen, and temperature levels in the weeks preceding bloom occurrences. 4. We have demonstrated a non-parametric computational framework for the causal analysis of a multivariate ecosystem. Our framework offers a more comprehensive understanding of the underlying mechanisms driving M. flos-aquae in Lake Kinneret. It captures complex interactions and provides an explainable prediction model. By considering causal relationships, temporal dynamics, and joint probabilities of environmental factors, the proposed framework enhances our understanding of cyanoHABs in Lake Kinneret.
1. The fixation index, FIS has been a staple measure to detect selection or departures from random mating in populations. However, current Next Generation Sequencing (NGS) cannot easily estimate Fis, in multi-locus gene families, which contain multiple loci having similar or identical arrays of variant sequences of ≥1 kilobase, which differ at multiple positions. In these families, high-quality short-read NGS data typically identify variants, but not the genomic location, which is required to calculate Fis (based on locus-specific observed and expected heterozygosity). Thus, to assess assortative mating, or selection on heterozygotes, from NGS of multi-locus gene families, we need a method that does not require knowledge of which variants are allelic at which locus in the genome. 2. We developed such a method. Like Fis, our novel measure, 1His, is based on the principle that positive assortative mating, or selection against heterozygotes, reduces within-individual variability relative to the population. 3. We demonstrate high accuracy of 1His on a wide-range of simulated scenarios, and two datasets from natural populations of penguins and dolphins. 4. 1His is important because multi-locus gene families are often involved in assortative mating, or selection on heterozygotes. 1His is particularly useful for multi-locus gene families such as toll-like receptors, the major-histocompatibility-complex in animals, homeobox genes in fungi and self-incompatibility genes in plants.
Arid and semi-arid vegetation is characterized by plant patches of different sizes, and plant cover is determined by patch size (PS) and number of patches (NP). However, it is still unclear how PS and NP contribute to the restoration of degraded grasslands through grazing exclusion (GE). Transect lines were sampled in six alpine steppe communities in Tibet in 2017 and 2018. Both PS and NP were assessed and compared between inside and outside grazing exclosures. Our results showed that grazing exclosures increased the mean size but decreased the total number of plant patches. This pattern of change was common to other species and could not be attributed to a shift in community composition. The results suggest that the recovery of the degraded alpine steppe is being driven by PS at the expense of NP. By promoting the expansion of the larger patches while excluding the smaller ones, GE led to an aggregating pattern with a higher proportion of bare ground, potentially reducing primary productivity.
Metabolic theories in ecology interpret ecological patterns at different levels through the lens of metabolism, typically applying allometric power scaling laws to describe rates of energy use. This requires a sound theory for metabolism at the individual level. Commonly used mechanistic growth models, such as von Bertalanffy, DEB and the ontogenetic growth model lack a number of potentially important aspects and fail to accurately capture a growth pattern often observed in insects. Recently, a new model (MGM – the Maintenance-Growth Model) was developed for ontogenetic and post-mature growth, based on an energy balance that expresses growth as the net result of assimilation and metabolic costs for maintenance and feeding. The most important contributions of MGM are: 1) the division of maintenance costs into a non-negotiable and a negotiable part, potentially resulting in non-linear allometric scaling of maintenance and lowered maintenance under food restriction; 2) differentiated energy allocation strategies between sexes and 3) inclusion of costs for finding and processing food. MGM may also account for effects of body composition and type of growth at the cellular level. The model was here calibrated and evaluated using empirical data from an experiment on house crickets growing under ad libitum conditions. The procedure involved parameter estimations from the literature and collected data, using statistical models to account for individual variation in parameter values. It was found that ingestion rates cannot be generally described by simple allometries, here requiring more complex descriptions after maturation. By the unusual assumption of super-linear scaling of maintenance with body mass, MGM could well capture the differentiated growth patterns of male and female crickets. Other mechanistic growth models have also been able to provide good predictions of insect growth during early ontogeny, but MGM seems to be unique in its ability to accurately describe the trajectory until terminated growth.
Landscape structure plays a key role in mediating a variety of ecological processes affecting biodiversity patterns, however its precise effects and the mechanisms underpinning them remain unclear. While the effects of landscape structure have been extensively investigated both empirically, and theoretically from a metapopulation perspective, the effects of spatial structure at the landscape scale remain poorly explored from a metacommunity perspective. Here, we attempt to address this gap using a spatially explicit, individual-based metacommunity model to explore the effects of landscape compositional heterogeneity and per se spatial configuration on diversity at the landscape and patch level via their influence on long term community assembly processes. Our model simulates communities composed of lineages of annual, asexual organisms living, reproducing, dispersing, and competing within grid-based, fractal landscapes which vary in their magnitude of spatial environmental heterogeneity and in their degree of spatial environmental autocorrelation. Communities are additionally subject to temporal environmental fluctuation and external immigration, allowing for turnover in community composition. We found that compositional heterogeneity and spatial autocorrelation had differing effects on richness and diversity and the landscape and patch scales. We also note a slight negative effect of compositional heterogeneity on median total landscape population size. Landscape level diversity was driven by community dissimilarity at the patch level and increased with greater heterogeneity, while landscape richness was largely the result of short-term accumulation of immigrants and decreased with greater compositional heterogeneity. Both richness and diversity decreased in variance with greater compositional heterogeneity, indicating a reduction in community turnover over time. Patch-level richness and diversity patterns appeared to be driven by overall landscape richness and local mass effects, resulting in maximum patch level richness and diversity at moderate levels of compositional heterogeneity and high spatial autocorrelation.
1. Wetlands belong to the globally most threatened habitats, and organisms depending on them are of conservation concern. Wetland destruction and quality loss may affect negatively also boreal breeding ducks in which habitat selection often needs balancing between important determinants of habitat suitability. In Finland duck population trajectories are habitat-specific, while the reasons behind are not known. 2. In this research, the balance of nest predation risk and invertebrate food abundance in boreal breeding ducks was studied in Finland at 45 lakes and ponds in 2017 and 2018. Nest predation experiments were conducted with artificial nests followed by wildlife cameras during seven days. Invertebrates were sampled from the study water bodies using emergence and activity traps. Duck pairs and broods were also surveyed from these and 18 additional water bodies. 3. The wildlife camera results indicate that predation risk was higher in the water bodies surrounded by agricultural land than forestland. Ponds (seasonal, beaver and man-made) had lower nest predation risk and they were also more invertebrate-rich habitats than permanent lakes. In addition, artificial nests further away from water bodies had higher survival than shoreline nests. Habitat use of duck pairs (prior to nesting) was not associated with invertebrate food, but duck broods preferred habitats rich in food. 4. High nest predation pressure in shorelines of especially agricultural landscapes may contribute the declining population trends of ducks in Finland. Controlling predators would be an important conservation action to improve duck breeding success. This research underlines the benefits of the availability of different water body types for the breeding ducks. There is an urgent need to pay attention to protecting seasonal ponds, while the lack of flooded waters may be mitigated by favouring beavers or man-made ponds.
Understanding how ecological and environmental changes, anthropogenic activities, and climate have driven and will direct animals’ development and predicting their prospective distribution profiles in the Quaternary are essential to making a tangible conservation strategy. Macaques (Macaca) distributed in mainland East Asia provide an ideal research model for such an effort. We reconstruct macaques’ geographic distribution profiles during the Quaternary, from the last inter-glaciation (LIG, 120,000 - 140,000 years BP), the Last Glacial Maximum (LGM, 22,000 years BP), and the present (1970-2000) – based on which we deduce their perspective distribution in the 2050s. The results show their suitable habitats during LIG and LGM were mainly in Southwest, Central, and Coastal China. A noticeable distribution reduction started in LIG and persisted until the current (1970-2000). Their distribution centroid would shift northward to mountainous regions, mainly in Southwest China, where more migration corridors would be reserved for their future development. Also, the results indicate that China’s Protected Area currently does not cover more than 87% of macaques’ habitats, a dismal situation for their conservation. Finally, this study proclaims that the conservation priority of the macaques in the years to come should focus on Southwest China – their future refuge region in Quaternary.
Aim High alpine regions are threatened but understudied ecosystems that harbor diverse endemic species, making them an important biome for testing the role of environmental factors in driving functional trait-mediated community assembly processes. We tested the hypothesis that plant-soil feedbacks along a climatic and elevation gradient influence plant community assembly through shifts in habitat suitability, which drive plant functional, phylogenetic, and spectral diversity. Location In a high mountain system (2400-3500 m) of Región Metropolitana in the Chilean Andes (33°S, 70°W). Methods We surveyed vegetation and spectroscopic reflectance (400-2400 nm) to quantify taxonomic, phylogenetic, functional, and spectral diversity at five sites from 2400 m to 3500 m elevation. We characterized soil attributes and processes by measuring water content, carbon and nitrogen, and net nitrogen mineralization rates. Results At high elevation, colder temperatures reduced available soil nitrogen, while at warmer, lower elevations, soil moisture was lower. Metrics of taxonomic, functional, and spectral alpha diversity peaked at mid-elevations, while phylogenetic species richness was highest at low elevation. Leaf nitrogen increased with elevation at the community level and within individual species, consistent with global patterns of increasing leaf nitrogen with colder temperatures. Main conclusions The increase in leaf nitrogen, coupled with shifts in taxonomic and functional diversity associated with turnover in lineages, indicate that the ability to acquire and retain nitrogen in colder temperatures may be important in plant community assembly in this range. Such environmental filters have important implications for forecasting shifts in alpine plant communities under a warming climate.
1. Fine root distribution influences the potential for resource acquisition in soil profiles, which defines how plants interact with local soil environments; however, a deep understanding of how fine root vertical distribution varies with soil structural variations and across plant ages is lacking. 2. We subjected four xerophytic species native to an arid valley of China, Artemisia vestita, Bauhinia brachycarpa, Sophora davidii, and Cotinus szechuanensis, to increasing rock fragment content (RFC) treatments (0%, 25%, 50%, and 75%, v v-1) in an arid environment and measured fine root vertical profiles over four years of growth. 3. Fine root depth and biomass of woody species increased with increasing RFC, but the extent of increase declined with plant age. Increasing RFC also increased the degree of interannual decreases in fine root diameter. The limited supply of soil resources in coarse soils explained the increases in rooting depth and variations in the pattern of fine root profiles across RFC. Fine root depth and biomass of the subshrub species (A. vestita) in soil profiles decreased with the increase in RFC and plant age, showing an opposite pattern from the other three woody species. 4. Within species, the annual increase in fine root biomass varied with RFC, which led to large interannual differences in the patterns of fine root profiles. Capacity of younger or subshrub plants to cope with soil environmental changes were greater than the older or shrub plants. These results provide insights into the limitations of soil resources in dry and rocky environments, and have management implications for degraded agroforest ecosystem.
In the Central Himalayas, where environmental conditions vary greatly, understanding the biophysical limitations on forest carbon is crucial for accurately determining the region’s forest carbon stocks. This study investigates the role of climate and disturbance on the spatial variation of two key forest carbon pools: aboveground carbon (AGC) and soil organic carbon (SOC). Using field-observed plot-level carbon pool estimates from Nepal’s national forest inventory and structural equation modeling, we explore the relationship between forest carbon stocks and proxies of environmental constraints. The forest AGC and SOC models explained 25 % and 59 % of the observed spatial variation in forest AGC and SOC, respectively. The climatic availability of water and energy in broad-scale gradients combined with the fine-scale gradients of terrain and disturbance intensity were found to influence forest carbon stocks, but the sign and strength of the statistical relationships differ for forest AGC and SOC. While AGC showed a negative relationship to disturbance, SOC was impacted by the availability of climatic energy. Disturbances such as selective logging and firewood collection result in immediate forest carbon loss, while soil carbon changes take longer to respond. The lower decomposition rates in the high-elevation region, due to lower temperatures, preserve organic matter and contribute to the high SOC stocks observed there. These results have important implications for forest carbon management and conservation in the Central Himalayas.
Migratory birds may either upregulate their immune system during migration as they might encounter novel pathogens or downregulate their immune system as a consequence of trade-offs with the resource costs of migration. Support for the latter comes not least from a study that reports a positive correlation in autumn migrating birds between fuel stores and parameters of innate and acquired immune function, i.e., energy exhausted migrants appear to have lowered immune function. However, to our knowledge, no study has tested whether this pattern exists in spring migrating birds, which may face other trade-offs than autumn migrants. Here, we investigate if in spring there is a relationship between fuel stores and microbial killing ability, a measure of innate immune function, and total immunoglobulin (IgY), a measure of acquired immune function, in four migrating bird species: Chaffinches (Fringilla coelebs), Dunnocks (Prunella modularis), Song thrushes (Turdus philomelos) and Northern wheatears (Oenanthe oenanthe). We found no correlation between fuel stores and bacterial killing ability or IgY levels in any of the species. However, there was a significant negative correlation between microbial killing ability and Julian date in Song thrushes and Northern wheatears, and between IgY levels and Julian date in Song thrushes. Sex did not affect immune function in any of the species. Our study suggests that the relationship between immune function and fuel stores may be different during spring migration compared to autumn migration. Differences in the speed of migration or pathogen pressure may result in different outcomes of the trade-off between investment in immune function and in migration among the seasons.
The consequences of biological invasions and habitat degradation for native biodiversity depend on how species cope with the individual and synergetic challenges these processes present. To assess the impact of anthropogenic land-use on the food web architecture of an invaded community, we examine the diets of nine native and two highly invasive mammal species at different trophic levels, inhabiting different land-uses across six biogeographic regions in Tasmania, Australia. We use two complementary methods, environmental DNA metabarcoding analysis (eDNA) of faeces and stable isotope analysis (SIA) of nitrogen (N) and carbon (C) in whole blood, to account for the high inter-individual and temporal variability in animal diets. eDNA showed regionalisation in the diet of smaller species, with land-use further defining dietary taxa within each region. SIA revealed that bioregion and land-use influence the δ13C values of all carnivore species and omnivores, whereas the δ15N values of these species are influenced only by land-use and not bioregion. Including multiple species showed that native rats are changing their diet in response to the presence of invasive rats, an impact that would have been otherwise attributed to land-use. Our findings demonstrate that human activities and invasive species are molding the diets of invaded communities raising questions about the potential impacts that dietary modifications will have on the life-history traits and the evolutionary consequences these modifications might have on the survival of native species. This highlights the urgency to include human activities in ecological studies and the importance of targeting multispecies assemblages to gain a better understanding of synergetic impacts on native biodiversity.
Evidence for spatially varying selection and adaptive variation can provide insight into a species’ ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect footprints of spatially varying selection in natural populations. Here we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Myodes/Clethrionomys glareolus) distributed across Europe. To identify the loci subject to spatially varying selection and associated with climate variation, we applied multiple genotype-environment association (GEA) methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate adaptive loci, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis (RDA), we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation in bank voles that are influenced by local climate.
Increasing studies have shown the importance of intraspecific trait variation (ITV) on the ecological process. However, the patterns and sources of ITV are still unclear, especially in the propagule of coastal vegetation. Here, we measured fresh weight (FW), fresh length (FL), maximum transverse diameter (TDmax), minimum transverse diameter (TDmin) and the ratio of TDmax to TDmin (RTD) of the hypocotyl (propagule) of Kandelia obovata for 66 genealogies across 26 sites. By combining multiple factors of climate, ocean and maternal tree to analyze their effects on the intraspecific trait variation of mangrove hypocotyl. The results showed that value of establishment traits (FW, FL, TDmax and TDmin which are related to mass) decreased along increasing latitudinal gradients and they were directly positively regulated by temperature. ITV of dispersal trait (RTD) was unstructured along latitudinal gradients, which was constrained by fitness tradeoff. Our findings indicate that establishment traits mainly varied between populations, whereas dispersal traits mainly varied between individuals. This study provides insights into the ITV of propagule in different functional dimensions on a broad scale and that may help integrate ITV into future analyses of mangrove protection.
1. Ice coverage duration on lakes and ponds is decreasing due to climate change, but experimentally testing the effects of decreased ice coverage on aquatic communities is challenging in field settings. 2. To assess whether we could simulate changes predicted to occur in aquatic habitats as climate change progresses including shorter ice duration, warmer temperatures, and thinner ice and associated water chemistry changes, we designed and constructed greenhouses to place over a set of ten experimental ponds, roughly 3x3m in area which slope to a maximum depth of 1m, dug into the ground at the Koffler Scientific Reserve (Ontario, Canada). Half of the wedge-shaped greenhouses were enclosed on all sides (n=5) while the other the other half were open on three sides, with only the top fitted with plastic sheeting (n=5). The open greenhouses provided a less-warmed treatment while controlling for precipitation reduction and light filtering caused by the sheeting. In November 2019 greenhouses were placed over the ponds. Snow was cleared from the greenhouses and water chemistry measures were taken once weekly through the 2019-2020 winter. 3. Ice was thinner across the winter and melted on average 10.6 days earlier in closed greenhouses compared to open greenhouses. Average winter water temperatures were also significantly higher in closed versus open greenhouses although these differences were not significant in all months. Similarly, maximum and minimum water temperatures were also higher in ponds with closed compared with open greenhouses. We successfully demonstrate a method for simulating expected changes in ice conditions as climate change progresses including decreasing ice coverage duration at levels similar to those observed in north temperate ecosystems (per century) and alpine ecosystems (per 36 years) and raising temperatures in a highly manipulatable experimental system.
The extended phenotype of helical burrowing behavior in animals has evolved independently many times since first appearing after the Cambrian explosion (~540 million years ago). A number of hypotheses have been proposed to explain the evolution of helical burrowing in certain taxa, but no study has searched for a general explanation encompassing all taxa. We reviewed helical burrowing in both extant and extinct animals and from the trace fossil record and compiled from the literature 10 possible hypotheses for why animals construct helical burrows, including our own ideas. Of these, six were post-construction hypotheses—-benefits to the creator or offspring, realized after burrow construction—-and four were construction hypotheses reflecting direct benefits to the creator during construction. We examined the fit of these hypotheses to a total of 21 extant taxa and ichnotaxa representing 59–184 spp. Only two hypotheses—-antipredator, biomechanical advantage—-could not be rejected for any species (possible in 100% of spp.), but six of the hypotheses could not be rejected for most species (possible in 86–100 % of spp.): microclimate buffer, reduced falling sediment (soil), anticrowding, vertical patch, and the above two hypotheses. Four of these six were construction hypotheses, raising the possibility that helical burrowing might have evolved without providing post-construction benefits. Our analysis showed that increased drainage, deposit feeding, microbial farming, and offspring escape could not explain helical burrowing behavior in the majority of taxa (5–48%). Overall, the evidence does not support a general explanation for the evolution of helical burrowing in animals. The function and evolution of the helix as an extended phenotype would seem, at least in some cases, to provide different advantages for different taxa. Although direct tests of many of the hypotheses would be difficult, we nevertheless offer ways to test some of the hypotheses for selected taxa.
1. Otoliths have been widely studied as natural recorders of the entire life cycle of aquatic teleosts. Trace elements and stable isotope rations in otoliths are well understood and used as proxies of migration histories, however few elements have shown the potential to reconstruct the migration history of oceanodromous fish. 2. This study reports the first use of radiocarbon in otolith to reconstruct the horizontal migration history of fish. We analyzed three different stocks of walleye pollock Gadus chalcogrammus around Hokkaido, Japan. 3. Radiocarbon concentration from the outermost edge of otoliths showed a general consistency with seawater radiocarbon concentration of the sampling region, validating the application of otolith radiocarbon concentration to fish migration studies. Pollocks of all three stocks generally inhabited the nearby sampling area throughout their life cycle, though some pollocks of the Okhotsk and Japan Sea stocks respectively showed a possibility of migration between different sea regions. 4. This study confirmed a novel method using radiocarbon concentrations to reconstruct the migration history of marine teleost. Using the high sensitivity of otolith radiocarbon concentration observed in this study, it may be possible to detect fish migration with higher spatial resolution than previous studies using conventional proxies.
Tidal flats can be found on most of the world's coastlines and are particularly vulnerable to anthropogenic disturbances. They are important transient ecosystems between terrestrial and marine ecosystems and their biodiversity provides important ecosystem services. Owed to their unique position between the terrestrial and the marine realm, strong environmental gradients of elevation, sediment composition but also food availability are prevailing. Here we investigate which environmental factors drive the spatial and temporal patterns in macrozoobenthos abundance, biomass, richness, diversity and species composition on back barrier tidal flats in the East-Frisian Wadden Sea. We found that with increasing mud content the total abundance of organisms in the sediment significantly increased, while biodiversity and biomass were not changing significantly with increasing mud content. Biomass of macrozoobenthos decreased with higher elevation towards the salt marsh. In contrast to expectations, increasing Chl a availability as a measure of primary productivity did not enhance biomass or abundance, but was associated with significantly reduced species richness. Species composition varied significantly among and within islands due to variation in sediment composition, resource availability and human-induced disturbance. In conclusion, macrozoobenthos biomass, abundance and biodiversity is interrelated in a complex way with the physical, abiotic and biotic processes in and above the sediment. Negative impacts of primary production on macrozoobenthos species richness demonstrate possible negative effects of nutrient inputs in tidal flat areas and the need for cross-boundary protection.