Outlier loci highlight the direction of introgression in oaks

Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Quercus petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and nonoutlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q. petraea (a late‐successional species) than in Q. robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with nonoutlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q. petraea caused by the species' contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized.     

Distinct male reproductive strategies in two closely related oak species

Reproductive strategies of closely related species distributed along successional gradients should differ as a consequence of the trade‐off between competition and colonization abilities. We compared male reproductive strategies of Quercus robur and Q. petraea, two partly interfertile European oak species with different successional status. In the studied even‐aged stand, trees of the late‐successional species (Q. petraea) grew faster and suffered less from intertree competition than trees of the early‐successional species (Q. robur). A large‐scale paternity study and a spatially explicit individual‐based mating model were used to estimate parameters of pollen production and dispersal as well as sexual barriers between species. Male fecundity was found to be dependent both on a tree's circumference and on its environment, particularly so for Q. petraea. Pollen dispersal was greater and more isotropic in Q. robur than in Q. petraea. Premating barriers to hybridization were strong in both species, but more so in Q. petraea than in Q. robur. Hence, predictions based on the competition–colonization trade‐off are well supported, whereas the sexual barriers themselves seem to be shaped by colonization dynamics.     

Prediction of biodiversity hotspots in the Anthropocene: The case of veteran oaks

Over the past centuries, humans have transformed large parts of the biosphere, and there is a growing need to understand and predict the distribution of biodiversity hotspots influenced by the presence of humans. Our basic hypothesis is that human influence in the Anthropocene is ubiquitous, and we predict that biodiversity hot spot modeling can be improved by addressing three challenges raised by the increasing ecological influence of humans: (i) anthropogenically modified responses to individual ecological factors, (ii) fundamentally different processes and predictors in landscape types shaped by different land use histories and (iii) a multitude and complexity of natural and anthropogenic processes that may require many predictors and even multiple models in different landscape types. We modeled the occurrence of veteran oaks in Norway, and found, in accordance with our basic hypothesis and predictions, that humans influence the distribution of veteran oaks throughout its range, but in different ways in forests and open landscapes. In forests, geographical and topographic variables related to the oak niche are still important, but the occurrence of veteran oaks is shifted toward steeper slopes, where logging is difficult. In open landscapes, land cover variables are more important, and veteran oaks are more common toward the north than expected from the fundamental oak niche. In both landscape types, multiple predictor variables representing ecological and human‐influenced processes were needed to build a good model, and several models performed almost equally well. Models accounting for the different anthropogenic influences on landscape structure and processes consistently performed better than models based exclusively on natural biogeographical and ecological predictors. Thus, our results for veteran oaks clearly illustrate the challenges to distribution modeling raised by the ubiquitous influence of humans, even in a moderately populated region, but also show that predictions can be improved by explicitly addressing these anthropogenic complexities.     

Fine‐scale genetic structure and flowering output of the seagrass Enhalus acoroides undergoing disturbance

Seagrass are under great stress in the tropical coast of Asia, where Enhalus acoroides is frequently the dominant species with a large food web. Here, we investigate the question of the fine‐scale genetic structure of this ecologically important foundation species, subject to severe anthropogenic disturbance in China. The genetic structure will illuminate potential mechanisms for population dynamics and sustainability, which are critical for preservation of biodiversity and for decision‐making in management and restoration. We evaluated the fine‐scale spatial genetic structure (SGS) and flowering output of E. acoroides, and indirectly estimated the relative importance of sexual versus asexual reproduction for population persistence using spatial autocorrelation analysis. Results reveal high clonal diversity for this species, as predicted from its high sexual reproduction output. The stronger Sp statistic at the ramet‐level compared with genet‐level indicates that clonality increases the SGS pattern for E. acoroides. Significant SGS at the genet‐level may be explained by the aggregated dispersal of seed/pollen cohorts. The estimated gene dispersal variance suggests that dispersal mediated by sexual reproduction is more important than clonal growth in this study area. The ongoing anthropogenic disturbance will negatively affect the mating pattern and the SGS patterns in the future due to massive death of shoots, and less frequency of sexual reproduction.     

Fine‐scale belowground species associations in temperate grassland

Evaluating how belowground processes contribute to plant community dynamics is hampered by limited information on the spatial structure of root communities at the scale that plants interact belowground. In this study, roots were mapped to the nearest one mm and molecularly identified by species on vertical (0–15 cm deep) surfaces of soil blocks excavated from dry and mesic grasslands in Yellowstone National Park (YNP) to examine the spatial relationships among species at the scale that roots interact. Our results indicated that average interspecific root – root distances for the majority of species were within a distance (3 mm) that roots have been shown to compete for resources. Most species placed their roots at random, although low root numbers for many species probably led to overestimating the occurrence of random patterns. According to theory, we expected that most of the remaining species would segregate their root systems to avoid competition. Instead we found that more species aggregated than segregated from others. Based on previous investigations, we hypothesize that species aggregate to increase uptake of water, nitrogen and/or phosphorus made available by neighbouring roots, or as a consequence of a reduction in the pathogenicity of soil biota growing in multispecies mixtures. Our results indicate that YNP grassland root communities are organized as closely interdigitating networks of species that potentially can support strong interactions among many species combinations. Future root research should address the prevalence and functional consequences of species aggregation across plant communities.     

Fine‐scale spatial differences in humpback whale diet composition near Kodiak,Alaska

On the North Pacific feeding grounds, humpback whales (Megaptera novaeangliae) are recovering from commercial whaling at a rapid rate (6.8%). The potential effect that this recovery will have on trophic dynamics involving these predators is currently unknown. To better elucidate complex trophic dynamics, variability in diet composition of apex predators on their respective feeding grounds needs to be understood. Thus, we explored the diet composition of two defined subaggregations of humpback whales of the Kodiak Archipelago population (“North,” “South”) using stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope ratios of humpback whale skin and regional prey samples in Bayesian dietary mixing models. Humpback whales in the “North” region consumed proportionally more fish, dominated by capelin (Mallotus villosus), whereas, whales in the “South” region consumed predominantly krill. The difference in diet composition appears to reflect regional differences in prey availability. Thus, regional variability in diet composition by humpback whales may have disproportionate impacts on prey resources of sympatric predators depending on available prey biomass. As a result, we suggest fine‐scale studies of apex predator diets are needed to better model trophic dynamics with accuracy.     

Fine‐scale habitat selection by sympatric Canada lynx and bobcat

The Canada lynx (Lynx canadensis) and the bobcat (Lynx rufus) are closely related species with overlap at their range peripheries, but the factors that limit each species and the interactions between them are not well understood. Habitat selection is a hierarchical process, in which selection at higher orders (geographic range, home range) may constrain selection at lower orders (within the home range). Habitat selection at a very fine scale within the home range has been less studied for both lynx and bobcat compared to selection at broader spatiotemporal scales. To compare this fourth‐order habitat selection by the two species in an area of sympatry, we tracked lynx and bobcat during the winters of 2017 and 2018 on the north shore of Lake Huron, Ontario. We found that both lynx and bobcat selected shallower snow, higher snowshoe hare abundance, and higher amounts of coniferous forest at the fourth order. However, the two species were spatially segregated at the second order, and lynx were found in areas with deeper snow, more snowshoe hare, and more coniferous forest. Taken together, our findings demonstrate that the lynx and bobcat select different resources at the second order, assorting along an environmental gradient in the study area, and that competition is unlikely to be occurring between the two species at finer scales.     

Fine‐scale spatial distribution of murundus structures in the semi‐arid region of Brazil

Murundus are earth mounds widespread in most landscapes in the semi‐arid region of Brazil. Evidence obtained from predictive modelling has suggested a termite origin for these structures, opening up new opportunities for further research. Distribution of densely packed murundus at larger spatial scales is most related to climatic regime and soil nutrient availability. However, factors and processes underlying their distribution and density at smaller spatial scales are not yet fully understood. In this study, we adopted an approach based on mapping point data using high‐resolution satellite imagery, multi‐scale second‐order analysis and general linear models to examine the fine‐scale spatial distribution and density of murundus. Our results suggest that the distribution of those structures within densely packed areas is regulated by more than one process acting or interacting across multiple spatial scales. All densely packed murundus showed a significant regular distribution at the distance scale of up to 50 m radially and a completely random distribution across all other upper distance scales. We interpret the regular pattern as a result of competition for foraging territories between different termite colonies during the process formation of densely packed murundus. The random pattern at larger distance scales (above 50 m radially) can be attributed to habitat selection preferences by termite species builders of murundus mediated by local environmental resources and conditions (i.e. availability of food resources and nesting and open habitat), which would be randomly distributed in space. Thus, at finer spatial scales murundus distributions are associated with biotic interactions acting on an abiotic template. On the basis of significant linear correlations, we suggest that the density of murundus is strongly related to local temperature regime with soil‐type influencing its effect on the murundus densities. Our findings provide novel evidences that mound‐building termites are involved in the formation of murundus in the semi‐arid region of Brazil.     

Fine‐scale selection by ovipositing females increases egg survival

One of the most important defenses for the eggs of ovipositing female organisms is to avoid being laid in the same habitat as their predators. However, for most organisms, completely avoiding an offspring's predators is not possible. One mechanism that has been largely overlooked is for females to partition an oviposition site into microhabitats that differ in quality for offspring survival. We conducted a series of experiments to examine whether female newts avoid microhabitats utilized by their offspring's primary predator, caddisfly larvae. Female newts avoided laying eggs near predatory caddisflies and shifted egg laying upward in the water column when provided with a vertical dimension. Caddisflies were attracted to chemical stimuli from female newts and their eggs, yet primarily used benthic areas in experimental chambers. Finally, results from a field experiment indicate that the behavioral strategy employed by female newts increases offspring survival. This subset of non‐genetic maternal effects, micro‐oviposition avoidance, is likely an important yet underexplored mechanism by which females increase offspring survival.     

Clonal Diversity and Fine‐scale Genetic Structure in a High Andean Treeline Population

Clonal propagation becomes more abundant with increasing altitudes as environmental conditions worsen. To date, little attention has been paid to the way in which clonal propagation affects genetic diversity and the fine‐scale spatial genetic structure (FSGS) of clonal alpine trees. An AFLP study was undertaken to quantify the clonal and genetic diversity and FSGS of the vulnerable treeline species Polylepis reticulata in Ecuador. We successfully genotyped 32 and 75 ramets within 4 m × 100 m (coarse scale) and 4 m × 4 m (fine scale) transects of one population, respectively. Higher genotypic diversity was detected at the coarse scale than at the fine scale, while lower genetic diversity was detected for P. reticulata than other Polylepis spp. at both scales. Significantly stronger FSGS was detected at the ramet level than the genet level for P. reticulata within a spatial distance of 3 m. The studied P. reticulata population showed pronounced FSGS (Sp = 0.012 at the genet level, a statistic reflecting declining pairwise kinship with distance) revealed restricted gene dispersal, which implies restricted seed dispersal for this population, assuming pollen flow is as extensive as that described for other wind‐pollinated tree species. Our results revealed that clonal diversity is a function of both sample size and the spatial scale of the sampling area. The findings highlights that clonal propagation has affected FSGS within a spatial distance of 3 m for this species.     

Tree mineral nutrition is deteriorating in Europe

The response of forest ecosystems to increased atmospheric CO₂ is constrained by nutrient availability. It is thus crucial to account for nutrient limitation when studying the forest response to climate change. The objectives of this study were to describe the nutritional status of the main European tree species, to identify growth‐limiting nutrients and to assess changes in tree nutrition during the past two decades. We analysed the foliar nutrition data collected during 1992–2009 on the intensive forest monitoring plots of the ICP Forests programme. Of the 22 significant temporal trends that were observed in foliar nutrient concentrations, 20 were decreasing and two were increasing. Some of these trends were alarming, among which the foliar P concentration in F. sylvatica, Q. Petraea and P. sylvestris that significantly deteriorated during 1992–2009. In Q. Petraea and P. sylvestris, the decrease in foliar P concentration was more pronounced on plots with low foliar P status, meaning that trees with latent P deficiency could become deficient in the near future. Increased tree productivity, possibly resulting from high N deposition and from the global increase in atmospheric CO₂, has led to higher nutrient demand by trees. As the soil nutrient supply was not always sufficient to meet the demands of faster growing trees, this could partly explain the deterioration of tree mineral nutrition. The results suggest that when evaluating forest carbon storage capacity and when planning to reduce CO₂ emissions by increasing use of wood biomass for bioenergy, it is crucial that nutrient limitations for forest growth are considered.     

High‐Throughput DNA sequencing of ancient wood

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management.     

Influence of canopy openness,ungulate exclosure,and low‐intensity fire for improved oak regeneration in temperate Europe

Failed oak regeneration is widely reported in temperate forests and has been linked in part to changed disturbance regimes and land‐use. We investigated if the North American fire–oak hypothesis could be applicable to temperate European oaks (Quercus robur, Quercus petraea) using a replicated field experiment with contrasting canopy openness, protection against ungulate browsing (fencing/no fencing), and low‐intensity surface fire (burn/no burn). Survival, relative height growth (RGR_H), browsing damage on naturally regenerated oaks (≤300 cm tall), and changes in competing woody vegetation were monitored over three years. Greater light availability in canopy gaps increased oak RGR_H (p = .034) and tended to increase survival (p = .092). There was also a trend that protection from browsing positively affected RGR_H (p = .058) and survival (p = .059). Burning reduced survival (p < .001), nonetheless, survival rates were relatively high across treatment combinations at the end of the experiment (54%–92%). Most oaks receiving fire were top‐killed and survived by producing new sprouts; therefore, RGR_H in burned plots became strongly negative the first year. Thereafter, RGR_H was greater in burned plots (p = .002). Burning altered the patterns of ungulate browsing frequency on oaks. Overall, browsing frequency was greater during winter; however, in recently burned plots summer browsing was prominent. Burning did not change relative density of oaks, but it had a clear effect on competing woody vegetation as it reduced the number of individuals (p < .001) and their heights (p < .001). Our results suggest that young, temperate European oaks may respond similarly to fire as their North American congeners. However, disturbance from a single low‐intensity fire may not be sufficient to ensure a persistent competitive advantage—multiple fires and canopy thinning to increase light availability may be needed. Further research investigating long‐term fire effects on oaks of various ages, species‐specific response of competitors and implications for biodiversity conservation is needed.     

Fine‐scale population structure of Collichtys lucidus populations inferred from microsatellite markers

The spinyhead croaker Collichthys lucidus (Richardson) is a small sciaenid species distributed along the inshore waters of northwestern Pacific Ocean, and now has been listed as Key Protected Commercial Sources of Aquatic Animals and Plants in China. To delineate stock boundaries and inform conservation policy for its management, samples were collected from eight locations across the Chinese coastal waters and analyzed at nine microsatellite loci. C. lucidus populations showed low genetic diversity (expected heterozygosity = 0.445–0.542; observed heterozygosity = 0.392–0.539; Polymorphism Information Content = 0.268–0.684). Strong genetic fdifferentiation (F_st = 0.065–0.510, all significant after Bonferroni correction) among all populations and high levels of self‐recruitment (89.2%–91.5%) were observed, which suggested limited genetic exchange for this species. Clustering results of discriminant analysis of principal components and STRUCTURE found strong support for obvious genetic clusters (populations FZ, XM and SZ vs. populations SH, YRE, ZS, WZ and ND). The results of the present study not only supported the phylogeographic pattern of north‐south differentiation, but also suggested that C. lucidus populations may be predominantly sustained by self‐replenishment rather than by recruitment from distant populations.     

Fine‐scale variation in natural nitrogen isotope ratios of ants

Stable isotopes provide a powerful means of elucidating the trophic ecology of organisms. Analyses of variation in the ratio of nitrogen isotopes (δ¹⁵N) can provide insights into the trophic position of species with broad diets and the ability to occupy multiple positions in food webs, such as ants. The most powerful studies compare subjects across various spatial scales, but to do so, local variation in δ¹⁵N baselines must be taken into account. To date, a wide variety of baseline calibration methods have been employed, leading some authors to suggest that a standard approach is needed, and that the reality of environmental variation necessitates that this should be at fine scales. In this study, we examine the fine‐scale variation in δ¹⁵N value of colonies of the ant Formica kozlovi Dlussky (Hymenoptera: Formicidae: Formicini) along a sloped transect in Mongolia, and compare these with values for associated soils in an effort to shed further light on this issue. We find variation in ant δ¹⁵N to the order of one trophic level (ca. 3‰), over a distance of only 1 km. Ant δ¹⁵N was highly correlated with soil δ¹⁵N, and variation in mineral soil δ¹⁵N explained ca. 81% of the variation in ant δ¹⁵N. This study underlines the importance of local‐scale baseline corrections for isotopic studies, particularly in environments where baseline variation might be expected. It further suggests that δ¹⁵N of mineral soils may provide a suitable baseline for ecological studies of terrestrial arthropods.     

Fine‐scale genetic structuring in a group‐living lizard,the gidgee skink (Egernia stokesii)

By constraining gene flow, group living and natal philopatry can result in fine‐scale genetic structure. Although the genetic structure of some group‐living lizards has been characterised, studies are few compared with those for group‐living bird and mammal species. The Egerniinae group of lizards exhibits a high diversity of social structures, making it a useful group for comparative studies of genetic structure across a broader range of social taxa. A well‐studied member of Egerniinae is Egernia stokesii, a lizard that forms long‐term pair bonds and stable social groups and exhibits natal philopatry and limited dispersal. Evidence exists for consistent E. stokesii social structure across seven close but disconnected rocky outcrops within a 40 × 10 km area. We used summary statistics, analysis of molecular variance, Bayesian clustering, and discriminant analysis of principal components to assess if E. stokesii exhibit a consistent pattern of fine‐scale genetic structure across the same seven outcrops. Due to E. stokesii social structure and constrained dispersal, we predicted significant genetic structuring – based on microsatellite markers – among outcrops. We found significant fine‐scale genetic structuring and evidence for two genetic clusters. We discuss features of E. stokesii biology and ecology that may explain our findings. Some rocky outcrops, and some social groups, contained lizards from both genetic clusters. An examination of the composition of mixed cluster social groups did not detect any notable patterns. Therefore, further work is necessary to identify how the observed patterns may have arisen. Future investigations in E. stokesii and other group‐living lizard species are likely to contribute greatly to our understanding of the genetic consequences of group living.     

Fine‐scale habitat heterogeneity influences browsing damage by elephant and giraffe

Effects of large mammalian herbivores on woody vegetation tend to be heterogeneous in space and time, but the factors that drive such heterogeneity are poorly understood. We examined the influence of fine‐scale habitat heterogeneity on the distribution and browsing effects of two of the largest African terrestrial mammals, the elephant and giraffe. We conducted this study within a 120‐ha (500 x 2,400 m) ForestGEO long‐term vegetation monitoring plot located at Mpala Research Center, Kenya. The plot traverses three distinct topographic habitats (“plateau,” “steep slopes,” and “valley”) with contrasting elevation, slope, soil properties, and vegetation composition. To quantify browsing damage, we focused on Acacia mellifera, a palatable tree species that occurs across the three habitat categories. Overall tree density, species richness, and diversity were highest on the steep slopes and lowest on the plateau. Acacia mellifera trees were tallest and had the lowest number of stems per tree on the steep slopes. Both elephant and giraffe avoided the steep slopes, and their activity was higher during the wet season than during the dry season. Browsing damage on Acacia mellifera was lowest on the steep slopes. Elephant browsing damage was highest in the valley, whereas giraffe browsing damage was highest on the plateau. Our findings suggest that fine‐scale habitat heterogeneity is an important factor in predicting the distribution of large herbivores and their effects on vegetation and may interact with other drivers such as edaphic variations to influence local variation in vegetation structure and composition.     

Fine‐scale habitat heterogeneity explains the local distribution of two Amazonian frog species of concern for conservation

To test the hypothesis that subtle differences in abiotic requirements can result in almost total spatial segregation, we sampled two species of diurnal frogs, Atelopus spumarius and Allobates sumtuosus, in a primary forest reserve in central Brazilian Amazonia. We conducted visual and acoustic surveys on three occasions over 2 months, in 40 streamside (riparian) plots distributed throughout the reserve's two major drainage basins, using a grid system that covers 64 km². On average, drainages differed in the pH of stream water and the number of connected and isolated streamside pools. Differences in abiotic characteristics of drainages were associated with the spatial distribution of frog species. The occurrence and density of Allobates sumtuosus was negatively related to stream pH and discharge and positively related to the number of isolated pools in plots. The occurrence and density of Atelopus spumarius was associated with streams with high discharge and pH near neutral. These results indicate that although very large reserves will probably contain sufficient landscape heterogeneity to accommodate different species of diurnal frogs, due to strongly patchy distributions, in situ studies using fine‐scale species‐distribution models will be necessary to assess the adequacy of small reserves in Amazonia that cover hundreds of square kilometers or less for the conservation of some anuran species.     

Increased water‐use efficiency translates into contrasting growth patterns of Scots pine and sessile oak at their southern distribution limits

In forests, the increase in atmospheric CO₂ concentrations (C_a) has been related to enhanced tree growth and intrinsic water‐use efficiency (iWUE). However, in drought‐prone areas such as the Mediterranean Basin, it is not yet clear to what extent this “fertilizing” effect may compensate for drought‐induced growth reduction. We investigated tree growth and physiological responses at five Scots pine (Pinus sylvestris L.) and five sessile oak (Quercus petraea (Matt.) Liebl.) sites located at their southernmost distribution limits in Europe for the period 1960–2012 using annually resolved tree‐ring width and δ¹³C data to track ecophysiological processes. Results indicated that all 10 natural stands significantly increased their leaf intercellular CO₂ concentration (C_i), and consequently iWUE. Different trends in the theoretical gas‐exchange scenarios as a response to increasing C_a were found: generally, C_i tended to increase proportionally to C_a, except for trees at the driest sites in which C_i remained constant. C_i from the oak sites displaying higher water availability tended to increase at a comparable rate to C_a. Multiple linear models fitted at site level to predict basal area increment (BAI) using iWUE and climatic variables better explained tree growth in pines (31.9%–71.4%) than in oak stands (15.8%–46.8%). iWUE was negatively linked to pine growth, whereas its effect on growth of oak differed across sites. Tree growth in the western and central oak stands was negatively related to iWUE, whereas BAI from the easternmost stand was positively associated with iWUE. Thus, some Q. petraea stands might have partially benefited from the “fertilizing” effect of rising C_a, whereas P. sylvestris stands due to their strict closure of stomata did not profit from increased iWUE and consequently showed in general growth reductions across sites. Additionally, the inter‐annual variability of BAI and iWUE displayed a geographical polarity in the Mediterranean.