Terrestrial resource pulses can significantly affect the community dynamics of freshwater ecosystems. Previously, its effect on the river community is considered to be stronger in summer, while weaker in winter when terrestrial invertebrates are less abundant. The movement of the terrestrial earthworms are triggered in winter, so they may be supplied to winter rivers as terrestrial resource pulse, but little is known about it. Here, we report that the massive numbers of the terrestrial earthworms were supplied intensively to an upstream of the small river in early winter. In particular, we found large numbers of Megascolecidae earthworms were supplied in an upstream of the small river in Northern Japan. Furthermore, we observed that supplied earthworms were consumed by salmonid fish species (masu salmon, white spotted char and rainbow trout) and aquatic invertebrates (gammarid amphipod, planarian flatworm and stonefly larvae). These findings suggests that the terrestrial earthworms may play a key role in ecosystem functioning in winter when severe and other resources are scarce.

Designing appropriate management plans requires knowledge of both the dispersal ability and what has shaped the current distribution of the species under consideration. Here we investigated the evolutionary history of the endangered grey reef shark (Carcharhinus amblyrhynchos) across its range by sequencing thousands of RAD-seq loci in 173 individuals in the Indo-Pacific (IP) . We first bring evidence of the occurrence of a range expansion (RE) originating close to the Indo-Australian Archipelago (IAA) where two stepping-stone waves (east and westward) colonized almost the entire IP. Coalescent modeling additionally highlighted a homogenous connectivity (Nm~10 per generation) throughout the range, and an isolation by distance model suggested the absence of barriers to dispersal despite the affinity of C. amblyrhynchos to coral reefs. This coincides with long-distance swims previously recorded, suggesting that the strong genetic structure at the IP scale (FST ~ 0.56 between its ends) is the consequence of its broad current distribution and organization in a large number of demes. Our results strongly suggest that management plans for the grey reef shark should be designed on a range-wide rather than a local scale due to its continuous genetic structure. We further contrasted these results with those obtained previously for the sympatric but strictly lagoon-associated Carcharhinus melanopterus, known for its restricted dispersal ability. C. melanopterus exhibits similar RE dynamic, but is characterized by stronger genetic structure and a non-homogeneous connectivity largely dependent on local coral reefs availability. This sheds new light on shark evolution, emphasizing the roles of IAA as source of biodiversity and of life history traits in shaping the extent of genetic structure and diversity.

Plasmids are extra-chromosomal genetic elements that encode a wide variety of phenotypes and can be maintained in bacterial populations through vertical and horizontal transmission, thus increasing bacterial adaptation to hostile environmental conditions like those imposed by antimicrobial substances. To circumvent the segregational instability resulting from randomly distributing plasmids between daughter cells upon division, non-transmissible plasmids tend to be carried in multiple copies per cell, which also results in a metabolic burden to the bacterial host, therefore reducing the overall fitness. This trade-off poses an existential question for plasmids: What is the optimal plasmid copy number? We address this question using a combination of population genetics modeling with microbiology experiments consisting of Escherichia coli K12 bearing a multi-copy plasmid encoding for blaTEM-1, a gene conferring resistance to b-lactam antibiotics. We use a Wright-Fisher model to evaluate the interaction between the above mentioned opposing forces. By numerically determining the optimal plasmid copy number for constant and fluctuating selection regimes, we conclude that plasmid copy number is an optimized evolutionary trait that depends on the rate of environmental fluctuation and balances the benefit between increased stability in the absence of selection with the burden associated with carrying multiple copies of the plasmid.

1. The Environmental Data Initiative (EDI) is a trustworthy, stable data repository and data management support organization for the environmental scientist. In a bottom-up community process EDI was built with the premise that freely and easily available data are necessary to advance the understanding of complex environmental processes and change, to improve transparency of research results, and to democratize ecological research. 2. EDI provides tools and support that allow the environmental researcher to easily integrate data publishing into the research workflow. 3. Almost ten years since going into production, we analyze metadata to provide a general description of EDI’s collection of data and its data management philosophy and placement in the repository landscape. We discuss how comprehensive metadata and the repository infrastructure lead to highly findable, accessible, interoperable, and reusable (FAIR) data by evaluating compliance with specific community proposed FAIR criteria. 4. Finally, we review measures and patterns of data (re)use, assuring that EDI is fulfilling its stated premise.

A document by George Lohay. Click on the document to view its contents.

Aim: To test whether the occupancy of shorebirds has changed in the eastern Canadian Arctic, and whether these changes could indicate that shorebird distributions are shifting in response to long-term climate change Location: Foxe Basin and Rasmussen Lowlands, Nunavut, Canada Methods: We used a unique set of observations, made 25 years apart, using general linear models to test if there was a relationship between changes in shorebird species’ occupancy and their Species Temperature Index, a simple version of a species climate envelope. Results: Changes in occupancy and density varied widely across species, with some increasing and some decreasing. This is despite that overall population trends are known to be negative for all of these species, based on surveys during migration. The changes in occupancy that we observed were positively related to the Species Temperature Index, such that the warmer-breeding species appear to be moving into these regions, while colder-breeding species appear to be shifting out of the regions, likely northwards. Main Conclusions: Our results suggest that we should be concerned about declining breeding habitat availability for bird species whose current breeding ranges are centred on higher and colder latitudes.

The behavior of animals potentially affects their survival and reproduction. The activity budget of the Critically Endangered giraffe Giraffa camelopardalis camelopardalis has been investigated in populations across Africa and found to be influenced by body size, diet and sex. Foraging patterns show how an animal chooses to forage in its environment, and is influenced by resource availability, competition and predation risk. The activity budget and foraging patterns of Nubian giraffes vary considerably between ecosystems. The Nubian giraffe is a recently identified subspecies G. camelopardalis camelopardalis). This Critically Endangered giraffes which includes Rothschild’s giraffes, occurs only within Kenya, Uganda, Ethiopia, and Southern Sudan. We observed the behavior of a population of Nubian giraffes in Lake Nakuru National Park, Kenya, to assess seasonal activity budgets and foraging patterns. In the wet and dry seasons, giraffes spent approximately the same amount of time (53 and 57%, respectively) foraging. Movement and resting duration decreased slightly from the dry to the wet season (22 to 20% and 25 to 22%, respectively. Across both seasons, Vachellia xanthophloea (67%), Maytenus senegalensis (19%), and Solanum incanum (9%) made up the bulk of the giraffe’s diet. In the dry season, giraffe additionally foraged on Maerua triphylla (2%), Vachellia gerrardi (2%), and Grewia similis (1%); in the wet season, they added Vachellia abyssinica (2%) and Rhus natalensis (2%) to their diet. The most utilized browsing height was 3.5 m below their average height.. Overall, season did not appear to influence the Nubian giraffe’s activity time budget or foraging patterns in Lake Nakuru National Park. Improved knowledge of the behavioral patterns of this subspecies will allow managers to manage and conserve the species and its habitat better. For instance, planting perennial plants in all vegetation types used by giraffes in the park minimizes browsing pressure on the already over browsed Vachellia.

Increased access to genome-wide data provides new opportunities for plant conservation. However, information on neutral genetic diversity in a small number of marker loci can still be valuable because genomic data are not available to most rare plant species. In the hope of bridging the gap between conservation science and practice, we outline how conservation practitioners can more efficiently employ population genetic information in plant conservation. We first review the current knowledge about the within-population genetic variation and among-population differentiation in neutral genetic variation (NGV) and adaptive genetic variation (AGV) in seed plants. We then introduce the estimates of among-population genetic differentiation in quantitative traits (QST) and neutral markers (FST) to plant biology and summarize conservation applications derived from QST–FST comparisons, particularly on how to capture most AGV and NGV on both in-situ and ex-situ programs. Based on a review of published studies, we found that, on average, two and four populations would be needed for woody perennials (n = 18) to capture 99% of neutral and adaptive genetic variation, respectively, whereas four populations would be needed in case of herbaceous perennials (n = 14). On average, QST is about 3.6, 1.5, and 1.1 times greater than FST in woody plants, annuals, and herbaceous perennials, respectively. We suggest using maximum QST rather than average QST among trait comparisons. Hence, conservation and management policies or suggestions based solely on inference on FST could be misleading, particularly in woody species. We recommend conservation managers and practitioners consider this when formulating further conservation and restoration plans for plant species, and for woody species in particular.

East Yunnan-Guizhou Plateau is rich in biodiversity in China. Complex geographical and climatic conditions, and rich bird resources made this area an ideal system for studying the spatial distribution mechanism and influencing factors of birds, which were still unknown. Bird community data from 37 sites in this region were collected, including 505 bird species and 164 species of resident passerine bird analyzed. The taxonomic diversity, phylogenetic diversity, functional diversity, and community structure index were calculated. Redundancy analysis (RDA), ordinary least square (OLS), and structural equation model (SEM), were used to explore the relationship between bird diversity index and 12 environmental factors used to describe the habitat conditions of birds. Results indicated that the vascular plant species richness, habitat area, and vertical altitude difference were the three most critical factors affecting bird diversity. The phylogenetic structure of bird community was dispersed in west and clustered in east, and significantly related to latitude, habitat area, and vertical altitude difference. The functional structure was dispersed in all sites, and significantly related to mean annual precipitation and longitude. This suggest that the distribution pattern of bird diversity was caused by the comprehensive action of various habitat factors which were mainly related to food availability and habitat heterogeneity. Considering the protection of birds in this area, it is necessary to continuously promote the construction of nature reserve system proposed by the Chinese government, and pay attention to the protection of urban green space such as campus and urban parks, to maintain the area and integrity of bird habitat, while only a high plant species and area is not enough, improving the habitat heterogeneity is of great significance.

Earth systems are nearing a global tipping point, beyond which the dynamics of biological systems will become unstable. One major driver of instability is species invasion, especially by organisms that act as “ecosystem engineers” through their modification of abiotic and biotic factors. In a mosaic landscape of non-invaded and invaded habitat, ecosystems modified through invasion may serve as “sink” habitat. To understand how native organisms respond to habitat that is becoming increasingly modified, it is essential to examine biological communities within invaded and non-invaded habitat, identifying compositional shifts between native and non-native taxa as well as measuring how modification has affected interactions among community members. Using dietary metabarcoding, our study examines the response of a native Hawaiian generalist predator to habitat modification by comparing biotic interactions across metapopulations of spiders collected in native forest and sites invaded by kahili ginger. Our study shows that, although there are shared components of the dietary community, spiders in invaded habitat are eating a less consistent and more diverse diet consisting of more non-native arthropods which are rarely or entirely undetected in spiders collected from native forest. Additionally, the frequency of novel interactions with parasites was significantly higher in invaded sites, reflected by the frequency and diversity of non-native Hymenoptera parasites and entomopathogenic fungi. The study highlights the role of habitat modification driven by an invasive plant in altering community structure and biotic interactions, appearing to serve as a “sink” for native arthropods and thereby threatening the stability of the ecosystem.

Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.

Abstract 1. Classic evolutionary theory suggests that sexual dimorphism evolves primarily via sexual and fecundity selection. However, theory and evidence is beginning to accumulate suggesting that resource competition can drive the evolution of sexual dimorphism, via ecological character displacement between sexes. A key prediction of this hypothesis is that the extent of ecological divergence between sexes will be associated with the extent of sexual dimorphism. 2. As the stable isotope ratios of animal tissues provide a quantitative measure of various aspects of ecology, we carried out a meta-analysis examining associations between the extent of isotopic divergence between sexes and the extent of body size dimorphism. Our models demonstrate that large amounts of between-study variation in isotopic (ecological) divergence between sexes is due to systematic heterogeneity, which may be associated with the traits of study subjects. We then completed meta-regressions to examine whether the extent of isotopic divergence between sexes is associated with the extent of sexual size dimorphism. 3. We found a modest but significantly positive association between size dimorphism and sex differences in trophic level. Furthermore, the strength of this positive association varied between ecological contexts, increasing in species whose diets provide the greatest scope for trophic variation and in those for which body size is of greater relevance to feeding. 4. Our results therefore provide further evidence that ecologically mediated selection, unrelated to reproduction, can contribute to the evolution of sexual dimorphism.

Resting stages of aquatic organisms that accumulate in the sediment over time are an exceptional resource that allows direct insights into past populations and addressing evolutionary questions. This is of particular interest in taxa that have recently faced environmental changes such as the Daphnia longispina species complex, a keystone zooplankton group in European freshwater ecosystems. However, genomic analysis might be challenging as many of these resting stages are very small and the DNA might be degraded. To reliably allow the resequencing of single Daphnia resting eggs from different sediment layers and characterize genomic changes through time, we performed whole genome amplification to obtain DNA amounts suitable for genome re-sequencing and tested multiple protocols involving egg isolation, whole genome amplification kits and library preparation. A pre-sequencing contamination screening was developed to quickly assess possible contamination. In total, we successfully amplified and sequenced nine genomes from Daphnia resting eggs that could be identified as Daphnia longispina species. We analyzed the genome coverage and SNP calling of these samples to optimize this method for future projects involving population genomic investigation of the resting egg bank.

Although the COVID-19 lockdowns in 2020 had some environmental benefits, the pandemic’s impact on the global economy has also had conservation repercussions, especially in biodiverse nations. Ecuador, which is heavily reliant on petroleum, agricultural exports, and ecotourism, experienced a rise in poverty in response to pandemic shutdowns. In this study, we sought to quantify levels of illegal timber extraction and poaching before and after the start of COVID-19 lockdowns throughout two protected areas (Reserva Jama Coaque [JCR] and Reserva Bosque Seco Lalo Loor [BSLL]) in the endangered Pacific Forest of Ecuador. We analyzed chainsaw and gunshot acoustic data recorded from devices installed in the forest canopy from December 2019 to March 2020 and October 2020 to March 2021. Results from generalized linear mixed effects models indicated less chainsaw activity before lockdowns (post.lockdown = 0.571 + 0.196 SE, p-value = 0.004), although increased average rainfall also seemed to negatively affect chainsaw activity (avg.rainfall = -0.005 + 0.001 SE, p-value < 0.001). Gunshots were too infrequent to conduct statistical models; however, 87% of gunshots were detected during the ‘lockdown’ period. Observational data collected by rangers from these protected areas also noted an increase in poaching activities beginning mid to late 2020 and persisting into 2021. These results add to the steadily growing literature indicating an increase in environmental crime, particularly in biodiverse nations, catalyzed by COVID-19-related economic hardships. Identifying areas where environmental crime increased during pandemic lockdowns is vital to address both socioeconomic drivers and enforcement deficiencies to prevent further biodiversity loss and disease outbreaks and to promote ecosystem resilience. Our study also demonstrates the utility of passive acoustic monitoring to detect illegal resource extraction patterns, which can inform strategies such as game theory modeling for ranger patrol circuits and placement of real-time acoustic detection technologies to monitor and mitigate environmental crimes.

Carnivore communities are extremely important for maintaining the structure/function of ecosystems. Exploring the carnivore coexistence can provide the data needed for the development of effective conservation strategies for endangered species. We aimed to (1) reveal the dietary composition of a carnivore community that inhabits the Everest region by analyzing molecular diets, (2) assess activity patterns by analyzing camera-trapping records. Dietary analysis revealed 22 food MOTUs of 7 orders and 2 classes. Snow leopard and wolf mainly preyed on ungulate mammals (%PR = 61%, 50%), while lynx and red fox mainly consumed small mammals (%PR = 62%, 76%). Higher dietary overlap (Pianka’s index = 0.95 ~ 0.97) was observed between similar-sized predators (snow leopard versus wolf, lynx versus fox); and there was no dietary difference between them (P > 0.05). Lower dietary overlap (Pianka’s index = 0.53 ~ 0.67) was observed between predators with large body size difference (snow leopard versus lynx, snow leopard versus red fox, wolf versus fox); and dietary difference was significant (P < 0.01), indicating the existence of dietary partitioning. In activity pattern analysis, predators exhibited higher temporal overlap with the more frequently consumed prey species, indicating that predator activity can be regulated by prey availability. Snow leopard and wolf had the higher activity overlap (Δ = 0.87) suggesting the lack of temporal partitioning. Red fox had the lower coefficients of overlap with snow leopard and wolf (Δ = 0.60, Δ = 0.59), suggesting that fox temporally avoid snow leopard and wolf slightly. We revealed the coexistence mechanisms of a carnivore community in the Everest region, by confirming that sympatric coexistence was facilitated by both dietary and temporal partitioning. These results will help to increase understanding of carnivore communities, and provide the scientific foundation for the conservation of threatened species in the Mount Everest region.

The predicted temperature increase caused by climate change is a threat to biodiversity. Male reproduction is particularly sensitive to elevated temperatures resulting in sterility. Here we investigate temperature induced changes in reproductive tissues and the fertility reduction in male Drosophila melanogaster. We challenged males during development and either allowed them to recover or not in early adulthood, while measuring several determinants of male reproductive success. We found significant differences in recovery rate, organ sizes, sperm production and other key reproductive traits among males from our different temperature treatments. Spermatogenesis and hence sperm maturation was impaired before reaching the upper thermal sterility threshold. While some effects were reversible, this did not compensate the earlier damage imposed. Surprisingly, developmental heat stress was damaging to accessory gland growth and female post mating responses mediated by seminal fluid proteins were impaired regardless of the possibility of recovery. We suggest that sub-lethal thermal sterility and the subsequent fertility reduction is caused by a combination of malfunctioning reproductive traits: inefficient functionality of the accessory gland and alteration of spermatogenesis.

Environmental heterogeneity is an important driver of ecological communities. Here, we assessed the effects of local and landscape spatial environmental heterogeneity on ant community structure in temperate semi-natural upland grasslands of Central Germany. We surveyed 33 grassland sites representing a gradient in elevation and landscape composition. Local environmental heterogeneity was measured in terms of variability of temperature and moisture within and between grasslands sites. Grassland management type (pasture vs. meadows) was additionally included as a local environmental heterogeneity measure. The complexity of habitat types in the surroundings of grassland sites were used as a measure of landscape environmental heterogeneity. As descriptors of ant community structure, we considered species composition, community evenness, and functional response traits. We found that extensively grazed pastures and within-site heterogeneity in soil moisture at local scale, and a high diversity of land cover types at the landscape scale affected ant species composition by promoting nest densities. Ant community evenness was high in wetter grasslands with low within-site variability in soil moisture and surrounded by a less diverse landscape. Fourth-corner models revealed that ant community structure response to environmental heterogeneity was mediated mainly by worker size, colony size, and life history traits related with colony reproduction and foundation. We discuss how within-site local variability in soil moisture and low intensity grazing promote ant species densities, and highlight the role of habitat temperature and humidity affecting on community evenness. We hypothesize that a higher diversity of land cover types in a forest-dominated landscape buffers less favorable environmental conditions for ant species establishment and dispersal between grasslands. We conclude that spatial environmental heterogeneity at local and landscape scale plays an important role as deterministic force in filtering ant species and, along with neutral processes (e.g. stochastic colonization), in shaping ant community structure in temperate semi-natural upland grasslands.

Primula, well known for its heterostyly, is the largest genus in the family Primulaceae with more than 500 species. The considerable species number has introduced a huge challenge for taxonomy. Although several phylogenetic constructions have been carried out thoroughly, the relationships between Primula species were remained incompletely understood, especially for the relationship among sections within Chinese species. P. wilsonii Dunn is a PSESP (plant species with extremely small populations) with very limited genetic information to explore its endangered mechanism and conservation. In this study, we sequenced and assembled the complete chloroplast genomes of P. wilsonii using Illumina sequencing and compared its genomic sequences with those of four related Primula species. The chloroplast genomes of Primula species were similar in the basic structure, gene order and GC content. The detected 38 SSRs loci and 17 hyper-variable regions had many similarities in P. wilsonii, P. anisodora, P. miyabeana and P. poissonii, but showed a significant difference compared with those in P. secundiflora. Slight variations were observed among Primula chloroplast genomes, in consideration of the relatively stable patterns of IR contraction and expansion. Phylogenetic analysis based on chloroplast genomes confirmed three major clades in Chinese Primula, but the infrageneric sections were not in accordance with morphological traits. The P. poissonii complex was confirmed here and P. anisodora was the species that was most closely related to P. wilsonii. Overall, the chloroplast genome sequences provided useful genetic and evolutionary information for phylogeny, population genetics and conservation studies on Chinese Primula species.