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.     

Interspecific networks in ground beetle (Coleoptera: Carabidae) assemblages

Although changes to interspecific relationships can significantly alter the composition of insect assemblages, they are often ignored when assessing impacts of environmental change. Long-term ground beetle data were used in this study to analyse ecological networks from three habitats at two sites in Scotland. A Bayesian Network inference algorithm was used to reveal interspecific relationships. The significance and strength of relationships between species (nodes) were estimated along with other network properties. Links were identified as positive relationships if co-occurrences of beetles correlated positively, and as negatives relationships if there was a negative correlation between the occurrences of the species. Most of the species had few links and only 10% of the nodes were connected with several links. Calathus fuscipes, a common carabid in the samples, was the most connected, with nine links to other species. More interspecific relationships were found to be positive than negative, with 48 and 23 links, respectively. The modular structure of the network was assessed and eight separate sub-networks were found. Habitat preferences of the species were clearly represented in the structure of the sets of those five sub-networks containing more than one species and were in line with the findings of the indicator species analysis. In our study, we showed that generated Bayesian networks can model interspecific relationships between carabid species. Due to the relative ease of the collection of field data and the high information content of the results, this method could be incorporated into everyday ecological analysis.     

A thermodynamic approach for assessing agroecosystem sustainability

By revisiting theoretical concepts in biogeography and the importance of thermodynamic laws in biosphere-atmosphere interactions, ecological sustainability in agricultural systems may be better defined. In this case study, we employed a multidisciplinary methodology for exploring agroecosystem sustainability by using eddy covariance (EC) data to compute thermodynamic entropy production (σ) and relate it to water, energy and carbon cycling in croplands and grasslands of the Central US. From 2002 to 2012, the biophysical metric of σ was compared across AmeriFlux sites, each with site-specific land management practices of irrigation, crop rotation, and tillage. Results show that σ is most correlated with net ecosystem exchange (NEE) of carbon, and when cropland and grassland sites are close to being carbon neutral, σ values range from 0.51–1.0 W K⁻¹ m⁻² for grasslands, 0.81–1.0 W K⁻¹ m⁻² for rainfed croplands, and 0.81–1.1 W K⁻¹ m⁻² for irrigated croplands. Irrigated maize stressed by hydrologic and high temperature anomalies associated with the 2012 drought exhibit the greatest increase in σ, indicating the possibility of decreased sustainability compared to rainfed croplands and grasslands. These results suggest that maximizing carbon uptake with irrigation and fertilizer use tends to move agroecosystems further away from thermodynamic equilibrium, which has implications for ecological sustainability and greenhouse gas (GHG) mitigation in climate-smart agriculture. The underlying theoretical concepts, multidisciplinary methodology, and use of eddy covariance data for biophysical indicators in this study contribute to a unique understanding of ecological sustainability in agricultural systems.     

Stability,sensitivity and uncertainty rates in the flow equations of ecological models

In previous work by the authors about dynamic system modeling, basic ecosystems concepts and their application to ecological modeling theory were formalized. Measuring how a variable effects certain processes leads to improvements in dynamic systems modelling and facilitates the author’s study of system diversity in which model sensitivity is a key theme. Initially, some variables and their numeric data are used for modeling. Predictions from the constructed models depend on these data. Generic study of sensitivity aims to show to what degree model behavior is altered by modification of some specific data. If small variations cause important modifications in the model’s global behavior then the model is very sensitive in relation to the variables used. If uncertain systems are considered, then it is important to submit the system to extreme situations and analyze its behavior. In this article, some indexes of uncertainty will be defined in order to determine the variables' influence in the case of extreme changes. This will permit analysis of the system’s sensitivity in relation to several simulations.     

基于文献计量分析的生态修复现状研究

以中国知网学术期刊网络出版总库和WEB OF SCIENCE中1997—2015年的期刊论文为数据源,以"生态修复(ecological remediation和ecological restoration)"为关键词进行检索,利用共词分析方法,同时结合Bibexcel软件对检索结果进行分析,利用Ucinet和Netdraw软件绘制出共词网络可视图,并通过SPSS软件进行多维尺度分析,以此来研究高频关键词之间的内在联系,探讨国内外生态修复领域中的研究热点以及研究现状。以文献计量学的分析方法客观的评价国内外生态修复的研究概况及研究热点,明确生态修复技术研究探索的方向,从而为加强生态修复技术的研究提供理论依据。     

Phytolith‐rich biochar: A potential Si fertilizer in desilicated soils

Silicon (Si) is beneficial to plants since it increases photosynthetic efficiency, and alleviates biotic and abiotic stresses. In the most highly weathered and desilicated soils, plant phytoliths make up the reservoir of bioavailable Si. The regular removal of crop residues, however, substantially decreases this pool. Si supply may therefore be required to sustain continuous cropping. Available Si fertilizers are costly and usually poor in soluble Si. Biochar produced from the pyrolysis of phytolith‐rich biomass is thus a promising alternative Si source for plants. Taking into account the challenges of increasing food demand and environmental concerns, we evaluate the global potential of biochar produced from major crop residues and manures in terms of phytogenic Si (PhSi) supply. Crop residues contribute to 80% of the global production of biomass dry matter (8,201 Tg/year) of which 3,137 Tg/year are potentially available after pyrolysis, giving a potential application rate of 1.7 T ha^?1 year^?1 for highly weathered soils in the tropics. The potential PhSi supply from crop biochar amounts to 102 Tg Si/year. On its own, rice straws produce 57.7 Tg PhSi/year, accounting for 56.6% of the potential annual PhSi production. The Si release from crop biochar depends on inter altere feedstock type, pyrolysis temperature, soil pH, and buffer capacity. Furthermore, the amplitude of plant Si uptake and mineralomass depends on plant species, soil properties, and processes. These factors interact and can exert a decisive influence on the effectiveness of phytolithic biochar in releasing Si into highly weathered soils. We conclude that the use of phytolithic biochar as a Si fertilizer offers undeniable potential to mitigate desilication and to enhance Si ecological services due to soil weathering and biomass removal. This potential must be explored, as well as the conditions for using biochar in the field.     

Selection for barriers between honey bees and a devastating parasite

Rivaling pesticides and a dearth of flowers, the parasitic mite Varroa destructor presents a tremendous threat to western honey bees, Apis mellifera. A longstanding, but minor, pest for the Asian honey bee Apis cerana, these obligate bee parasites feast on developing and adult A. mellifera across several continents. Varroa reproduction is limited to a short window when developing bee pupae are concealed in wax cells. Mated females target developing bees just before pupation and then have about one day to initiate reproduction, eventually laying one male and up to several female offspring. Female mites often fail to reproduce at all, instead waiting in cells until their bee host finishes development and then hitching dangerous rides on a succession of adult bees for up to several weeks, before scouting for a new host pupa. In this issue of Molecular Ecology, Conlon et al. (2019) have explored mite reproductive success via a clever and thought‐provoking association study. In so doing, they have identified a protein whose actions could be integral to the dance between bees and their mite parasites.     

Genetic association with high‐resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula

Landraces are local populations of crop plants adapted to a particular environment. Extant landraces are surviving genetic archives, keeping signatures of the selection processes experienced by them until settling in their current niches. This study intends to establish relationships between genetic diversity of barley (Hordeum vulgare L.) landraces collected in Spain and the climate of their collection sites. A high‐resolution climatic data set (5 × 5 km spatial, 1‐day temporal grid) was computed from over 2,000 temperature and 7,000 precipitation stations across peninsular Spain. This data set, spanning the period 1981–2010, was used to derive agroclimatic variables meaningful for cereal production at the collection sites of 135 barley landraces. Variables summarize temperature, precipitation, evapotranspiration, potential vernalization and frost probability at different times of the year and time scales (season and month). SNP genotyping of the landraces was carried out combining Illumina Infinium assays and genotyping‐by‐sequencing, yielding 9,920 biallelic markers (7,479 with position on the barley reference genome). The association of these SNPs with agroclimatic variables was analysed at two levels of genetic diversity, with and without taking into account population structure. The whole data sets and analysis pipelines are documented and available at https://eead-csic-compbio.github.io/barley-agroclimatic-association . We found differential adaptation of the germplasm groups identified to be dominated by reactions to cold temperature and late‐season frost occurrence, as well as to water availability. Several significant associations pointing at specific adaptations to agroclimatic features related to temperature and water availability were observed, and candidate genes underlying some of the main regions are proposed.