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opencc-by-4.0Jun 2022View details →

Potential wild hosts of Echinococcus vogeli

O helminto Echinococcus vogeli Rausch & Bernstein, 1972 é o agente causador da Equinococose Neotropical, uma doença zoonótica crônica e endêmica da região Neotropical.  Este parasito é transmitido entre o cachorro-vinagre (Speothos venaticus) e suas presas, como pacas (Cuniculus paca Linnaeus, 1766) e cutias (Dasyprocta spp.). No Brasil, a maioria dos casos humanos de Equinococose Neotropical é registrada nos estados do Acre e Pará, embora existam poucos dados disponíveis sobre a ocorrência de potenciais hospedeiros definitivos e intermediários de E. vogeli na Amazônia. No presente estudo, foram investigadas áreas de floresta ao redor de 46 comunidades humanas localizadas dentro e fora de quatro áreas protegidas de uso sustentável no sudoeste da bacia amazônica, Brasil por meio de armadilhas fotográficas digitais para verificar a presença de potenciais hospedeiros silvestres de E. vogel, onde os mesmos foram registrados circulando na região.

opencc-zeroJun 2022View details →

Environment and mate attractiveness in a wild insect

Abstract The role of female choice in sexual selection is well established, including the recognition that females choose their mates based on multiple cues. These cues may include intrinsic aspects of a male's phenotype as well as aspects of the environment associated with the male. The role of the spatial location of a potential mate has been well studied in territorial vertebrates. However, despite their role as laboratory models for studies of sexual selection, the potential for insects to choose their mates on the basis of location has scarcely been studied. We studied a natural population of individually tagged crickets (Gryllus campestris) in a meadow in Northern Spain. Adults typically move between burrows every few days, allowing us to examine how pairing success of males can be predicted by the burrow they occupy, independent of their own characteristics. We observed the entirety of ten independent breeding seasons to provide replication and to determine whether the relative importance of these factors is stable across years. We find that both male ID and the ID his burrow affect the likelihood that he is paired with a female, but the burrow has a consistently greater influence. Furthermore, the two factors interact: the relative attractiveness of an individual male depends on which burrow he occupies. Our finding demonstrates a close interaction between naturally and sexually selected traits. It also demonstrates that mate choice studies may benefit from considering not only obvious secondary sexual traits, but also more cryptic traits such as microhabitat choice.

opencc-zeroJun 2021View details →

Study of the genetic and phenotypic variation among wild and cultivated clary sages provides interesting avenues for breeding programs of a perfume, medicinal and aromatic plant

A road-map of the genetic and phenotypic diversities in both crops and their wild-related species can help identifying valuable genetic resources for further crop breeding. The clary sage (Salvia sclarea L.), a perfume, medicinal and aromatic plant, is used for sclareol production and ornamental purposes. Despite its wide use in the field of cosmetics, the phenotypic and genetic diversity of wild and cultivated clary sage remains to be explored. We characterized the genetic and phenotypic variation of a collection of six wild S. sclarea populations from Croatia, sampled along an altitudinal gradient, and of populations of three S. sclarea cultivars. We showed low level of genetic diversity for the two S. sclarea traditional cultivars used for essential oil production and for ornamental purposes, respectively. In contrast, a recent cultivar resulting from new breeding methods, which involve hybridizations among several genotypes rather than traditional recurrent selection and self-crosses over time, showed high genetic diversity. We also observed a marked phenotypic differentiation for the ornamental clary sage compared with other cultivated and wild clary sages. Instead, the two cultivars used for essential oil production, a traditional and a recent, respectively, were not phenotypically differentiated from the wild Croatian populations. Our results also featured some wild populations with high sclareol content and early-flowering phenotypes as good candidates for future breeding programs. This study opens up perspectives for basic research aiming at understanding the impact of breeding methods on clary sage evolution, and highlights interesting avenues for clary breeding programs.

opencc-zeroJun 2022View details →

The occurrence data of wild apple in the Mountains of Central Asia Biodiversity Hotspot

To obtain high-quality occurrence records for wild apple across its whole distribution range, we compiled data from field surveys, herbariums and the literature. The field surveys were conducted in all of the countries with wild apple distribution in Central Asia. Precisely, we had several exhaustive investigations of wild apple populations in Xinjiang, China from 2008 to 2021, including distribution range and abundance of wild apple across its whole elevational ranges in six counties. For herbarium data, we combined the records from Global Biodiversity Information Facility and Chinese Virtual Herbarium. Finally, we obtained 8344 occurrence records for wild apple.

opencc-zeroJun 2022View details →

Does mast seeding shape mating time in wild boar? A comparative study

In seasonal environments, the timing of reproduction often matches with the peak of food resources. One well-known effect of global warming is an earlier phenology of resources, leading to a possible mismatch between timing of reproduction for consumers and food peak. However, global warming may also change the dynamics of food resources, such as the intensity and frequency of pulsed mast seeding. How quantitative changes in mast seeding influence the timing of reproduction of seed consumers remains unexplored. Here, we assess how yearly variation in mast seeding influences mating time in wild boar (Sus scrofa), a widespread seed consumer species. We took advantage of the intensive monitoring of both female reproduction (1,636 females) and acorn production over 6 consecutive years across 15 populations of wild boar in the wild. We found that mating time occurs earlier when acorn production increases in most but not all populations. In three out of fifteen populations, heavy females mated earlier than light ones. Our findings demonstrate that mast seeding does shape mating time in wild boar females, but differently across populations. This high plasticity of mating times in wild boar indicates that females locally adapt to environmental conditions.

Seasonal dynamics of the wild rodent faecal virome

Viral discovery studies in wild animals often rely on cross‐sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host–virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Utilizing noninvasive faecal samples from a long‐term wild rodent study, we characterized viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis and Myodes glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most common virus families, Picornaviridae, show pronounced temporal changes in viral richness and evenness, which were associated with concurrent and up to ~3‐month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.

opencc-by-4.0Jun 2022View details →

The gut microbiome of wild American marten in the Upper Peninsula of Michigan

Directory Information for The gut microbiome of wild American marten in the Upper Peninsula of Michigan ####### "R Code" contains: --- "marten_phyobj.rds" is the phyloseq object that can be directly imported for statistical analysis if the user prefers not to go entire QIIME2 pipeline. The phyloseq object was created from QIIME2 artifacts from the "QIIMEpipe.html" pipeline: the cleaned rooted tree, the cleaned taxonomy table and the cleaned ASV table. This requires the command "readRDS()" to import. The "load()" command will not work. --- "Stat.Rmd" Markdown file for "Stat.html" --- "Stat.html" knitted statistical analysis file to view the studies outputs quickly --- "Stat.R" R code if user prefers over Rmarkdown ####### "QIIME" contains: --- "martendemux.qza" demultiplexed QIIME2 artifact --- "martendemux.qzv" visualization output of demultiplexed sequence that can be viewed at qiimeview.org --- "MartenMeta.tsv" metadata file for QIIME2 pipeline and statistical analysis --- "QIIMepipe.html" code for bioinformatic pipeline for downstream analysis - "Sequences" folder: --- "R1_demultiplxed_pairedend_marten.fastq.gz" forward reads of demultiplexed, EMP paired end sequences (Illumina Miseq) if the user prefers to use another bioinformatic platform besides QIIME2. --- "R2_demultiplxed_pairedend_marten.fastq.gz" reverse reads of demultiplexed, EMP paired end sequences (Illumina Miseq) if the user prefers to use another bioinformatic platform besides QIIME2.

opencc-by-4.0Jul 2022View details →

Dataset for: Conformational and Thermodynamic Differences Underlying Wild-type and Mutant YEATS Domain Specificity for Epigenetic Marks

The set of molecular dynamics trajectories generated and analyzed in the paper "Conformational and Thermodynamic Differences Underlying Wild-type and Mutant YEATS Domain Specificity for Epigenetic Marks."  Citations should refer directly to the manuscript.  The preprint version is available at: https://doi.org/10.1101/2022.07.14.500085 The uploaded zip file "trajectory_data.zip" contains trajectories for the (1) apo (2) h3k27ac and (3) h3k9ac systems.  In each directory is a subdirectory corresponding to the wild-type, deletion, and insertion mutations.  In each of those subdirectories are 10 XTC files, which correspond to the trajectories for the 10 different simulations performed for each system, along with an AMBER-formated PRMTOP file. Solvent molecules were removed from each file, and trajectories were strided such that there is one frame per 500 ps.

Data from: Wild bee abundance declines with urban warming, regardless of floral density

As cities expand, conservation of beneficial insects is essential to maintaining robust urban ecosystem services such as pollination. Urban warming alters insect physiology, fitness, and abundance, but the effect of urban warming on pollinator communities has not been investigated. We sampled bees at 18 sites encompassing an urban warming mosaic within Raleigh, NC, USA. We quantified habitat variables at all sites by measuring air temperature, percent impervious surface (on local and landscape scales), floral density, and floral diversity. We tested the hypothesis that urban bee community structure depends on temperature. We also conducted model selection to determine whether temperature was among the most important predictors of urban bee community structure. Finally, we asked whether bee responses to temperature or impervious surface depended on bee functional traits. Bee abundance declined by about 41% per °C urban warming, and temperature was among the best predictors of bee abundance and community composition. Local impervious surface and floral density were also important predictors of bee abundance, although only large bees appeared to benefit from high floral density. Bee species richness increased with floral density regardless of bee size, and bee responses to urban habitat variables were independent of other life-history traits. Although we document benefits of high floral density, simply adding flowers to otherwise hot, impervious sites is unlikely to restore the entire urban pollinator community since floral resources benefit large bees more than small bees.

opencc-by-4.0Jul 2022View details →

Supplementary figure: No evidence of any wild animal samples positive for SARS-CoV-2 RNA or antibodies were found in China.

A compilation of results of wildlife sampling from the Huanan market and from China showing no evidence of positive animal for SARS-CoV-2 in China

Six years of wild bee monitoring collections data using Blue Vane traps in Southern Pennsylvania, USA

Turley NE, Biddinger DJ, Joshi NK, López-Uribe MM. 2022. Six years of wild bee monitoring shows changes in biodiversity within and across years and declines in abundance. Ecology and Evolution. Wild bees form diverse communities that pollinate plants in both native and agricultural ecosystems making them both ecologically and economically important. The growing evidence of bee declines has sparked increased interest in monitoring bee community and population dynamics using standardized methods. Here, we studied the dynamics of bee biodiversity within and across years by monitoring wild bees adjacent to four apple orchard locations in Southern Pennsylvania, USA. We collected bees using passive Blue Vane traps continuously from April to October for six years (2014-2019) amassing over 26,000 bees representing 144 species. We quantified total abundance, richness, diversity, composition, and phylogenetic structure. There were large seasonal changes in all measures of biodiversity with month explaining an average of 72% of the variation in our models. Changes over time were less dramatic with years explaining an average of 44% of the variation in biodiversity metrics. We found declines in all measures of biodiversity especially in the last 3 years, though additional years of sampling are needed to say if changes over time are part of a larger trend. Analyses of population dynamics over time for the 40 most abundant species indicate that about one third of species showed at least some evidence for declines in abundance. Bee family explained variation in species-level seasonal patterns but we found no consistent family-level patterns in declines, though bumble bees and sweat bees were groups that declined the most. Overall, our results show that season-wide standardized sampling across multiple years can reveal nuanced patterns in bee biodiversity, phenological patterns of bees, and population trends over time of many co-occurring species. These datasets could be used to quantify the relative effects that different aspects of environmental change have on bee communities and to help identify species of conservation concern.

Different types of semi-natural habitat are required to sustain diverse wild bee communities across agricultural landscapes

1. Semi-natural habitats provide important resources for wild bees in agricultural landscapes. Landscapes under management are dynamic and floral resources fluctuate in space and time. Thus, promoting different semi-natural habitat types within landscapes could be key to support diverse bee meta-communities throughout the season. 2. Here, we integrate analyses of a-diversity (species richness) and b-diversity and species-habitat networks to examine the relative contribution of all major semi-natural habitats to wild bee meta-communities in agricultural landscapes. We sampled extensively and conventionally managed meadows, flower strips, hedgerows and forest edges in spring, early and late summer in 25 landscapes in Switzerland. 3. Habitat types varied in their importance for wild bees throughout the season: While extensively managed meadows supported more rare species, habitat specialists and bee species overall than the other habitat types, flower strips were most important later in the season. Each of the five investigated habitat types harboured relatively unique sets of species with different habitats generally acting as distinct modules in the overall bee-habitat network. 4. Not only flower richness in a habitat per se, but also flower-habitat network properties (habitat strength and functional complementarity) were good predictors of wild bee richness. In addition to local floral richness, landscape composition and configuration interactively influenced b-diversity patterns across habitats. 5. Synthesis and applications. Our study highlights the value of pollinator-habitat network analysis to inform pollinator conservation management at the landscape scale, especially when combined with information on floral resources and flower-habitat networks. Maintaining different types of semi-natural habitats offers diverse and complementary resources throughout the season, which are crucial to sustain diverse wild bee meta-communities in agricultural landscapes. Particularly meadow extensification schemes can play a key role in safeguarding rare and specialist species in these landscapes. While locally a high flower richness promoted bee abundance and richness in general, our results indicate that increasing connectivity between habitat patches in landscapes dominated by arable crops appears to improve species exchange between local bee communities of different habitats, thereby possibly increasing their resilience to disturbances.

Nuclear genetic diversity and structure of Anastrepha ludens wild populations evidenced by microsatellite markers

The Mexican fruit fly, Anastrepha ludens is an important pest that causes widespread damage to a number of fruit crops in Mexico. The Sterile Insect Technique (SIT) is commonly used for its control. However, the existence of natural barriers can give rise to a population structure in neutral loci and possibly behavioral or adaptive traits that interfere with SIT. For this reason, it is important to understand the genetic diversity and structure of A. ludens populations and to better understand the evolutionary ecology and population processes in view of possible expansions and possible host shifts due to climate change. We genotyped nine nuclear DNA (nDNA) microsatellite loci among fruit fly populations collected from five biogeographic areas within Mexico, Mexican Plateau, the Northeastern Coastal Plain, the Pacific Coast, the Gulf Coast of Mexico, the Soconusco and a laboratory strain. The nuclear genetic diversity was moderate (from He = 0.34 to He = 0.39) within the wild mexfly population. We found that populations were clustered in three genetic groups (K=3). The diversity and genetic structure of A. ludens are produced by environmental and geological conditions as well as local conditions like anthropogenic perturbation which would produce population expansion and the existence of possible predators that would affect the population density. Gene flow showed recent migration among populations. The laboratory strain showed less diversity than the wild samples. Large values of current and ancestral population size suggest high resistance to climatic changes, probably due to biological attributes, such as its polyphagous, multivoltine and high dispersal characteristics. In particular ecosystem fragmentation and perturbation as well as the existence of new plant hosts all of which would probably increase the abundance of flies.

Three-dimensional surface scans of tooth surfaces of Japanese wild boars.

Three-dimensional surface scans of tooth surfaces of Japanese wild boars are saved in .sur format and surface analyses files in .mnt format, which are analyzed in: Miyamoto, K., Kubo, M. O. and Yokohata, Y. "Dental microwear texture of wild boars from Japan reflects inter- and intra-populational feeding preferences" submitted to Frontiers in Ecology and Evolution. Please see information in the paper for details.

opencc-zeroAug 2022View details →

Low levels of hybridization between domestic and wild Mallards wintering in the Lower Mississippi Flyway

Mallard ducks are a ubiquitous and socio-economically important game bird in North America. Despite their generally abundant midcontinent population, Mallards in eastern North America are declining, which may be partially explained by extensive hybridization with human-released domestically-derived game-farm Mallards. We investigated the genetic composition of Mallards in the middle and lower Mississippi flyway, key wintering regions for the species. We found that nearly 30% of wild Mallards carried mitochondrial haplotypes derived from domestic mallards present in North America, indicating that the individuals had female game-farm Mallard lineage in their past; however nuclear results identified only 4% of the same sample set as putative hybrids. Recovering 30% of samples with OW A mtDNA haplotypes is concordant with general trends across the Mississippi flyway and this percentage was stable across Mallards we sampled a decade apart. The capture and perpetuation of OW A mtDNA haplotypes is likely due to female breeding structure, whereas reversal of the nuclear signal back to wild ancestry is due to sequential backcrossing and lower and/or declining admixture with game-farm Mallards. Future studies of wild ancestry of Mississippi flyway Mallards will benefit from coupling molecular and spatial technology across flyways, seasons, and years to search for potential transitions of Mallard populations with different genetic ancestry, and whether the genetic ancestry is somehow linked to an individual's natal and subsequent breeding location.

opencc-zeroAug 2022View details →

Data for: Wild bee communities benefit from temporal complementarity of hedges and flower strips in apple orchards

1. Wild bees importantly pollinate both crop and wild plants. Yet, in intensive agricultural landscapes, wild bees are rare due to resource limitations of nectar and pollen. Flower strips and hedges are often used as resource enhancements for wild bees to overcome this shortage, but provide floral resources only during specific time periods. To sustain diverse and stable bee communities, bee-attractive flowers need to be available during the entire growing season. This may be achieved by combining flower strips and hedges to complement each other and provide continuous floral resources. 2. Over three subsequent years, we compared the phenology of flower and wild bee communities in perennial flower strips, hedges and improved hedges (complemented with a sown herb layer) in conventional apple orchards in Southern Germany, a pollination-dependent crop-system. 3. Hedges provided floral resources in the early season while the flower strips took over later in the season. 4. Bees visited the hedges mostly from March to June, whereas they visited the flower strips from June to August (first year), and in the second year already from April onwards. Flower strips were visited with an overall higher abundance and species richness than the improved and not modified hedges. 5. Synthesis and application: For enhancing wild bees in intensive apple orchards, hedges and perennial flower strips are complementary in providing flower resources. Yet, flower strips bloom more constantly and during periods of flower scarcity, and thus attract more bees than hedges. Perennial flower strips of different age classes should be preferred over annual strips, at best in a network with some well-maintained hedges, as perennial flower strips of different age attract different bee communities and thus potentially a higher bee diversity on the landscape level.

Rotational electron diffraction patterns of TIA-1 prion-like domain, wild type

Rotational electron diffraction patterns of TIA-1 prion-like domain, wild type. Collected with a JEOL CRYO ARM 300 electron microscope operated at an accelerating voltage of 300kV on a DirectElectron DE64 detector at RIKEN, SPring-8 Center. The PDB ID associated with this data is 7VI5.

Schematic and adapted figures from IPBES Sustainable Use of Wild Species Assessment - Chapter 3. Status of and trends in the use of wild species and its implications for wild species, the environment and people

Schematic and adapted figures from Chapter 3 of the thematic assessment of the sustainable use of wild species of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services.

Schematic and adapted figures from IPBES Sustainable Use of Wild Species Assessment - Chapter 6. Policy options for governing sustainable use of wild species

Schematic and adapted figures from Chapter 6 of the thematic assessment of the sustainable use of wild species of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services.