Observations on post-fire black morel ascocarp development in an Israeli burnt forest site and their preferred micro-sites

Morchella species ascocarps (morels) are sought-after edible mushrooms that exhibit pyrophilous behavior, proliferating in fire-affected soils of certain types of forests. The factors governing fruiting in this habitat are poorly understood. An observational approach was used to determine the spatial distribution on preferred micro-sites of black morel fruiting in a forest after a summer fire, subjected to different post-fire forestry management activities. Clearing the burnt tree stumps from the site, compaction of the burnt soil by heavy machinery (bulldozers) and covering the soil with chopped wood created preferred micro-sites for black morel fruiting. Fewer fruit bodies developed on untouched burnt soil, and almost none on non-burnt soil at the same site. These observations enhance understanding the ecological principles underlying the distribution and abundance of morel ascocarp development in natural habitats; such an understanding could contribute to conservation and management of morel fruiting in the wild.     

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

The RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.     

Phylogenies and traits provide distinct insights about the historical and contemporary assembly of aquatic insect communities

The assumption that traits and phylogenies can be used as proxies of species niche has faced criticisms. Evidence suggested that phylogenic relatedness is a weak proxy of trait similarity. Moreover, different processes can select different traits, giving opposing signals in null model analyses. To circumvent these criticisms, we separated traits of stream insects based on the concept of α and β niches, which should give clues about assembling pressures expected to act independently of each other. We investigated the congruence between the phylogenetic structure and trait structure of communities using all available traits and all possible combinations of traits (4095 combinations). To account for hierarchical assembling processes, we analyzed patterns on two spatial scales with three pools of genera. Beta niche traits selected a priori – i.e., traits related to environmental variation (e.g., respiration type) – were consistently clustered on the smaller scale, suggesting environmental filtering, while α niche traits – i.e., traits related to resource use (e.g., trophic position) – did not display the expected overdispersion, suggesting a weak role of competition. Using all traits together provided random patterns and the analysis of all possible combinations of traits provided scenarios ranging from strong clustering to overdispersion. Communities were phylogenetically overdispersed, a pattern previously interpreted as phylogenetic limiting similarity. However, our results likely reflect the co‐occurrence of ancient clades due to the stability of stream habitats along the evolutionary scale. We advise ecologists to avoid using combinations of all available traits but rather carefully traits based on the objective under consideration. Both trait and phylogenetic approaches should be kept in the ecologist toolbox, but phylogenetic distances should not be used as proxies of traits differences. Although the phylogenetic structure revealed processes operating at the evolutionary scale, only specific traits explained local processes operating in our communities.     

Changes in habitat use and nesting density in a declining seabird colony

Seabirds in expanding colonies select the highest-quality nesting habitat, but habitat selection has seldom been studied in declining colonies. We studied a colony of Magellanic penguins (Spheniscus magellanicus) that declined from 314,000 active nests in 1987 to 201,000 in 2014. As expected, nest quality and reproductive success were higher in burrow habitats than in other habitats, and nest density decreased with distance from shore. Contrary to predictions, the steepest declines did not occur in the poorest-quality habitat (scrub) or near the inland colony edge and the colony area did not shrink. In agreement with predictions, penguins shifted from nests with less cover to nests with more cover. The highest nest densities and the steepest declines were in habitats of large bushes and bush clusters. As the population declined penguins abandoned nests on the edges of large bushes. Constraints on penguin habitat-use changes include strong area and nest-site fidelity, increased avian predation in high-density areas, soil characteristics, and the costs of making and maintaining nests. Contrary to conventional wisdom we found low-density, poor-quality scrub habitat (which covers >70 % of the colony area) contained 45 % of active nests, produced 44 % of fledglings, and was as important as high-quality habitat for reproductive output. Our research shows that all habitats in a declining colony of seabirds have value for conservation.     

Connectivity in the network macrostructure of Tursiops truncatus in the Pelagos Sanctuary (NW Mediterranean Sea): does landscape matter?

The bottlenose dolphin (Tursiops truncatus Montagu, 1821) is a regularly observed species in the Mediterranean Sea, but its network organization has never been investigated on a large scale. We described the network macrostructure of the bottlenose dolphin (meta)population inhabiting the Pelagos Sanctuary (a wide protected area located in the north-western portion of the Mediterranean basin) and we analysed its connectivity in relation to the landscape traits. We pooled effort and sighting data collected by 13 different research institutions operating within the Pelagos Sanctuary from 1994 to 2011 to examine the distribution of bottlenose dolphins in the Pelagos study area and then we applied a social network analysis, investigating the association patterns of the photo-identified dolphins (806 individuals in 605 sightings). The bottlenose dolphin (meta)population inhabiting the Pelagos Sanctuary is clustered in discrete units whose borders coincide with habitat breakages. This complex structure seems to be shaped by the geo-morphological and ecological features of the landscape, through a mechanism of local specialization of the resident dolphins. Five distinct clusters were identified in the (meta)population and two of them were solid enough to be further investigated and compared. Significant differences were found in the network parameters, suggesting a different social organization of the clusters, possibly as a consequence of the different local specialization.     

A habitat quality indicator for common birds in Europe based on species distribution models

The EU 2020 Biodiversity Strategy requires the gathering of information on biodiversity to aid in monitoring progress towards its main targets. Common species are good proxies for the diversity and integrity of ecosystems, since they are key elements of the biomass, structure, functioning of ecosystems, and therefore of the supply of ecosystem services. In this sense, we aimed to develop a spatially-explicit indicator of habitat quality (HQI) at European level based on the species included in the European Common Bird Index, also grouped into their major habitat types (farmland and forest). Using species occurrences from the European Breeding Birds Atlas (at 50 km × 50 km) and the maximum entropy algorithm, we derived species distribution maps using refined occurrence data based on species ecology. This allowed us to cope with the limitations arising from modelling common and widespread species, obtaining habitat suitability maps for each species at finer spatial resolution (10 km × 10 km grid), which provided higher model accuracy. Analysis of the spatial patterns of local and relative species richness (defined as the ratio between species richness in a given location and the average richness in the regional context) for the common birds analysed demonstrated that the development of a HQI based on species richness needs to account for the regional species pool in order to make objective comparisons between regions. In this way, we proved that relative species richness compensated for the bias caused by the inherent heterogeneous patterns of the species distributions that was yielding larger local species richness in areas where most of the target species have the core of their distribution range. The method presented in this study provides a robust and innovative indicator of habitat quality which can be used to make comparisons between regions at the European scale, and therefore potentially applied to measure progress towards the EU Biodiversity Strategy targets. Finally, since species distribution models are based on breeding birds, the HQI can be also interpreted as a measure of the capacity of ecosystems to provide and maintain nursery/reproductive habitats for terrestrial species, a key maintenance and regulation ecosystem service.     

The use of environmental DNA of fishes as an efficient method of determining habitat connectivity

This study demonstrated the use of environmental DNA (eDNA) to determine habitat connectivity for migration of fishes between the sea and river. Environmental DNA is DNA fragments released by fishes in water, which can be used as a species-specific marker of the presence/absence of the target species. A year-round water sampling regime at 15 sites on the Yodo River, Japan, was conducted to determine whether three major man-made barriers on the river inhibited the migration of fishes using species-specific detection of DNA fragments from three target migrant species, temperate seabass, Lateolabrax japonicus, flathead grey mullet, Mugil cephalus, and ayu, Plecoglossus altivelis altivelis. The presence/absence of eDNA from target species was consistent with known patterns of species’ seasonal migration. The detection of the DNA of temperate seabass and flathead grey mullet at sites upstream of the dam closest to the river mouth indicated successful upstream migration of these species via a fish ladder bypassing the dam. On the other hand, DNA of these two species was not detected from the upstream side of the two remaining dams, which are not equipped with fish ladders. Ayu is the only species among the three target species with a land-locked population in Lake Biwa located at the headwater of Yodo River. Ayu DNA was detected at most of the sites in the freshwater area during the warm months; however, in the coldest month of February, eDNA was only detected in the uppermost site of Yodo River at the southern tip of Lake Biwa. The eDNA we detected at this site suggests that it was derived from juvenile ayu spending their winter months in the lake. These results suggest that the eDNA analysis presented here can accurately track the seasonal migration of fishes in a river, demonstrating its application as an indicator of habitat connectivity for fishes in association with man-made barriers in a river. The sampling of eDNA involves merely scooping a tank full of water; therefore, it is a simple, rapid, and cost-effective method for long-term monitoring of habitat connectivity associated with the construction of barriers in a river.     

Mapping habitat indices across river networks using spatial statistical modelling of River Habitat Survey data

Freshwater ecosystems are declining faster than their terrestrial and marine counterparts because of physical pressures on habitats. European legislation requires member states to achieve ecological targets through the effective management of freshwater habitats. Maps of habitats across river networks would help diagnose environmental problems and plan for the delivery of improvement work. Existing habitat mapping methods are generally time consuming, require experts and are expensive to implement. Surveys based on sampling are cheaper but provide patchy representations of habitat distribution. In this study, we present a method for mapping habitat indices across networks using semi-quantitative data and a geostatistical technique called regression kriging. The method consists of the derivation of habitat indices using multivariate statistical techniques that are regressed on map-based covariates such as altitude, slope and geology. Regression kriging combines the Generalised Least Squares (GLS) regression technique with a spatial analysis of model residuals. Predictions from the GLS model are ‘corrected’ using weighted averages of model residuals following an analysis of spatial correlation. The method was applied to channel substrate data from the River Habitat Survey in Great Britain. A Channel Substrate Index (CSI) was derived using Correspondence Analysis and predicted using regression kriging. The model explained 74% of the main sample variability and 64% in a test sample. The model was applied to the English and Welsh river network and a map of CSI was produced. The proposed approach demonstrates how existing national monitoring data and geostatistical techniques can be used to produce continuous maps of habitat indices at the national scale.     

环境筛选和扩散限制在地表和地下螨群落物种共存中的调控作用

识别扩散限制和环境筛选在群落物种共存中的相对作用,是土壤动物群落物种共存机制研究的重要内容,然而少有针对地表和地下土壤动物群落的探讨。在三江平原农田生态系统,设置一个50 m×50 m的空间尺度,探讨环境筛选和扩散限制对地表和地下土壤螨群落物种共存的调控作用。基于Moran特征向量图(MEMs)和变差分解的方法来区分环境筛选和扩散限制的调控作用;采用偏Mantel检验进一步分析环境距离和空间距离的相对贡献;使用RDA分析环境因子对螨群落物种组成的解释能力。变差分解结果表明,空间变量对地表、地下和地表-地下土壤螨群落具有较大的显著方差解释量,而环境变量和空间环境结构的解释量相对较小且不显著;偏Mantel检验没有发现环境距离或空间距离的显著贡献;RDA分析表明土壤p H值、大豆株高和土壤含水量对土壤螨群落具有显著的解释能力,说明环境变量对螨群落物种组成的重要作用。研究表明,在三江平原农田生态系统,地表和地下土壤螨群落物种共存主要受到扩散限制的调控作用,同时环境筛选的调控作用也不容忽视。     

秦岭山区中国大鲵生境因子的选择

通过对秦岭山区中国大鲵(Andrias davidianus)栖息地生境因子调查、统计,利用R语言分析了各因子与大鲵生境选择的相关性,得出研究结果:秦岭山区影响大鲵生存的主要因子为栖息地类型(相关系数r=0.98),其次是水温(相关系数r=-0.8)、河岸坡度(r=-0.6)和p H (r=-0.6);浊度(相关系数r=0.5)、电导率(r=0.49)、DO(r=0.4)、人为干扰(r=0.35)和海拔(r=0.31)对大鲵分布影响不大。研究结果为探讨中国大鲵对野生环境的适应性选择提供了参考。