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.
The management objectives of many protected areas must meet the dual mandates of protecting biodiversity while providing recreational opportunities. Balancing these mandates is made difficult by constraints on monitoring trends in the status of biodiversity and impacts of recreation. Using detections from 45 camera traps deployed between July 2019 and September 2021, we assessed the potential impacts of recreation on spatial and temporal habitat use for 8 medium- and large-bodied terrestrial mammals in an isolated alpine protected area: Cathedral Provincial Park, Canada. We hypothesized that some wildlife perceive a level of threat from people, such that they avoid ‘risky times’ or ‘risky places’ associated with human activity. Other species may benefit from associating with people, be it through access to anthropogenic resource subsidies or filtering of competitors/predators that are more human-averse (i.e., human shield hypothesis). Specifically, we predicted that large carnivores would show the greatest segregation from people while mesocarnivores and ungulates would associate spatially with people. We found spatial co-occurrence between ungulates and recreation, consistent with the human shield hypothesis, but did not see the predicted negative relationship between larger carnivores and humans, except for coyotes (Canis latrans). Temporally, all species other than cougars (Puma concolor) had activity patterns significantly different from that of recreationists, suggesting potential displacement in the temporal niche. Wolves (Canis lupus) and mountain goats (Oreamnos americanus) showed shifts in temporal activity away from people on recreation trails relative to off-trail areas, providing further evidence of potential displacement. Our results highlight the importance of monitoring spatial and temporal interactions between recreation activities and wildlife communities, in order to ensure the effectiveness of protected areas in an era of increasing human impacts.
Seed dispersal is one of the most important ecosystem services globally. It shapes plant populations, enhances forest succession, and has multiple, indirect benefits for humans, yet it is one of the most threatened processes in plant regeneration, worldwide. The restricted movement of local frugivores, through habitat fragmentation, is one of the main threats to seed dispersal. These restrictions alter the behaviour associated with movements before, during and after interacting with fruits and seeds. Consequently, there have been recent calls for animal movement and behaviour to be better integrated with seed dispersal studies to enable researchers to fully understand the processes that determine seed rain. To assess the current use of animal tracking in frugivory studies and to provide a baseline for future studies, we provide a comprehensive review and synthesis on the existing primary literature of global tracking studies that monitor movement of frugivorous animals. Specifically, we identify studies that estimate dispersal distances and how they vary with morphological and environmental traits. We show that over the last two decades there has been a large increase in frugivore tracking studies that determine seed dispersal distances. However, gaps across taxa and geographic distribution still exist. Furthermore, we found that certain morphological and environmental traits can be used to predict seed dispersal distances. We demonstrate that an increase in body mass significantly increases the estimated seed dispersal mean and maximum distances, as does species flight ability. Our results also suggest that protected areas have a positive effect on mean seed dispersal distances when compared to unprotected areas. We anticipate that this review act as a reference for future frugivore tracking studies to build upon, specifically to understand the drivers of movement, and to interpret how seed dispersal and other ecosystem services will be impacted by human disturbance and land use changes.
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.
The Neretva dwarf goby Orsinigobius croaticus (Gobiiformes, Gobionellidae) is an endemic fish native to the freshwaters of the Adriatic Basin in Croatia and Bosnia and Herzegovina. Due to its limited distribution range, specific karst habitat and endangered status, laboratory studies on reproductive biology are scarce. We investigated the sound production and acoustic behaviour of this species during reproductive intersexual laboratory encounters. We performed dissection and micro-computed tomography (μCT) scanning of the pectoral girdle to explore the anatomy of its putative sound producing mechanism. To study interspecific acoustic differences and determine whether acoustic features can discriminate among species, comparative analysis was conducted on sounds produced by closely related soniferous sand gobies. Our results indicate that males of the O. croaticus emit pulsatile sounds composed of a variable number of short (~ 15 ms) consecutive pulses when interacting with females, usually during the pre-spawning phase in the nest, but also during courtship outside the nest. Pulsatile sounds were low-frequency and short pulse trains (~ 140 Hz, < 1000 ms), and spectro-temporal parameters were correlated with physical traits and water temperature. Male visual behaviour rate was higher when co-occurring with sounds and females entered the male’s nest significantly more frequently when sounds were present. Male sound production was accompanied by movements such as head thrust and fin spreading. μCT scans and dissections suggest that O. croaticus shares certain anatomical similarities of the pectoral girdle (osseous elements and arrangement of levator pectoralis muscles) to previously studied sand gobies. Multivariate comparisons, using sounds produced by eight soniferous European sand gobies, effectively distinguished soniferous (and sympatric) species based on acoustic properties. Discrimination success decreased when temperature-dependent features (sound duration and pulse repetition rate) were excluded from analysis. Therefore, we suggest both spectral and temporal features are important for acoustic differentiation of sand gobies.
The plants’ geographical distribution is affected by natural or human-induced climate change. Numerous studies at both the global and regional level currently focus on the potential changes in plant distribution areas. Ecological niche modeling can help predict the likely distribution of species according to environmental variables under different climate scenarios. In this study, we predicted the potential geographic distributions of Quercus ilex L. (holm oak), a keystone species of the Mediterranean ecosystem, for the Last Interglacial period (LIG: ~120 Ka), the Last Glacial Maximum (LGM: ~22 Ka), mid-Holocene (MH: ~6 Ka), and future climate scenarios (Representative Concentration Pathway (RCP) 4.5 and 8.5 scenarios) for years 2050-2070 obtained from CCSM4 and MIROC-ESM global climate scenarios respectively. The models were produced with algorithms from the R-package “biomod2” and assessed by AUC of the Receiver Operating Characteristic plot and True Skill Statistics. Apart from BIOCLIM (SRE), all model algorithms performed similarly and produced projections that are supported by good evaluation scores, although Random Forest (RF) slightly outperformed all the others. Additionally, distribution maps generated for the past period were validated through a comparison with pollen data acquired from the Neotoma Pollen Database. The results revealed that southern areas of the Mediterranean Basin, particularly coastal regions, served as long-term refugia for Q. ilex, which was supported by fossil pollen data. Furthermore, the models suggest long term refugia role for Anatolia and we argue that Anatolia may have served as a founding population for the species. Future climate scenarios indicated that Q. ilex distribution varied by region, with some areas experiencing range contractions and others range expands. This study provides significant insights into the vulnerability of the Q. ilex to future climate change in the Mediterranean ecosystem and highlights the crucial role of Anatolia in the species’ historical distribution.
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.
1. Grassy ecosystems cover ~40% of the global land surface and are an integral component of the global carbon cycle. Grass litter decomposes via a combination of ultraviolet radiation degradation (which returns carbon to the atmosphere rapidly) and biological decomposition (a slower carbon pathway). As such, decomposition and carbon storage in grasslands may vary with climate and exposure to solar radiation. We investigated rates of grass litter decomposition in Australian temperate grasslands along a climate gradient to uncouple the relative importance of UV radiation and climate on decomposition. 2. Litterbags containing two common native grass species were deployed at six grassland sites across a precipitation gradient (380-890 mm) in south-eastern Australia. Bags were retrieved over 39 weeks to measure mass loss from decomposition. We used shade treatments to partition UV degradation from biological decomposition. 3. The shade treatment consistently reduced the rate of decomposition relative to full-sun treatments at all sites; there was no significant difference in the effect size of the shade treatment among sites. The rate of decomposition was positively correlated with rainfall midway through the experiment, but there were no significant differences in total decomposition among sites after 39 weeks. In general, the shape of decomposition curves was more linear than has typically been observed in global decomposition studies. 4. Synthesis: We found that UV exposure was a strong contributor to litter decomposition in temperate Australian grasslands. This effect was not influenced by climatic variables and may be related to a period of photopriming prior to further biotic decomposition. This study highlights the importance of litter composition and UV exposure in our understanding of how decomposition patterns contribute to global carbon cycling.
C4 is one of three known photosynthetic processes of carbon fixation in flowering plants. It evolved independently more than 61 times in multiple angiosperm lineages and consists of a series of anatomical and biochemical modifications to the ancestral C3 pathway increasing plant productivity under warm and light-rich conditions. The C4 lineages of eudicots belong to seven orders and 15 families, are phylogenetically less clustered than those of monocots, and entail an enormous structural and ecological diversity. Eudicot C4 lineages likely evolved the C4 syndrome along different evolutionary paths. Therefore, a better understanding of this diversity is key to understanding the evolution of this complex trait as a whole. Compiling 1,207 recognized C4 eudicots species described in the literature and presenting trait data among these species, we identify global centres of species richness and of high phylogenetic diversity. Furthermore, we discuss climatic preferences in the context of plant functional traits. We identify two hotspots of C4 eudicot diversity: arid regions of Mexico/Southern United States and Australia, where several C4 eudicot lineages diversified independently. Further eudicot C4 hotspots with many different families and genera represented are in South Africa, West Africa, Patagonia, Central Asia and the Mediterranean. In general, C4 eudicots were abundant in deserts and xeric shrublands, tropical and subtropical grasslands, savannas and shrublands. We found C4 eudicots to occur in areas with less annual precipitation than C4 grasses which can be explained by frequently associated adaptations to drought stress such as among others succulence and salt tolerance. We conclude that in most eudicot lineages C4 evolved in ancestrally drought adapted clades and enabled these to further spread in these habitats and colonise even drier areas.