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Fig. 6 in Favourite plants of wild bees

Fig. 6. Favourite plants in existing seed mixtures. Percentage of commercial seed mixtures containing seeds of the identified 34 "high visitor richness" plant species (according to Fig. 3). Total number of seed mixtures n = 55.

Fig. 5 in Favourite plants of wild bees

Fig. 5. Favourite plants as hosts for polylectic, oligolectic and threatened species. Percentage of wild bee species visiting each of the identified 34 "high visitor richness" species (according to Fig. 3). 100% of observed bee species is the total number of polylectic, oligolectic and threated species that are included in the Wildbienen-Kataster dataset, which includes ~ 75% of all wild bee species in Germany (440 species in total, containing 87 oligolectic and 177 red-listed species). The percentage of wild bee species for plants that are not widespread in the study area, such as Chondrilla juncea or Ballota nigra, are underestimated.

Fig. 2 in Favourite plants of wild bees

Fig. 2. Overview of the way that the datasets were combined in the analyses (detailed descriptions are given in the Material & Methods section).

Fig. 3 in Favourite plants of wild bees

Fig. 3. Favourite plants of bees. Plant species are grouped into "high visitor richness", "medium visitor richness" and "low visitor richness" based on the bee visits observed in the BienABest-project. On each sampling date and each habitat and location, the plant species were ranked based on the increasing number of visiting bee species. Mean ranks ¯R i for each plant species during all months (yellow), during April and May (green), during June (blue) and during July and August (purple) are shown. As the BienABest dataset contains a high proportion of interactions of polylectic and common species (male and female individuals), we additionally highlighted the top plant species with the greatest number of visiting oligolectic (+, n = 18 plant species) and red listed wild bee species (*, n = 17 plant species) according to Wildbienen-Kataster dataset.

opencc-zeroDec 2023View details →

Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)

The rapid expansion of wild pigs (Sus scrofa) throughout the United States (US) has been fueled by unlawful introductions, with invasive populations causing extensive crop losses, damaging native ecosystems, and serving as a reservoir for disease. Multiple states have passed laws prohibiting the possession or transport of wild pigs. However, genetic and phenotypic similarities between domestic pigs and invasive wild pigs – which overwhelmingly represent domestic pig-wild boar hybrids – pose a challenge for the enforcement of such regulations. We sought to exploit wild boar ancestry as a common attribute among the vast majority of invasive wild pigs as a means of genetically differentiating wild pigs from breeds of domestic pigs found within the US. We organized reference high-density single nucleotide polymorphism genotypes (1,039 samples from 33 domestic breeds and 382 samples from 16 wild boar populations) into five genetically cohesive reference groups: mixed-commercial breeds, Durocs, heritage breeds, primitive breeds, and wild boar. Building upon well-established genetic clustering approaches, we structured the test statistic to describe the difference in the likelihood of a given genotype's ancestry vectors (sensu genetic clustering analysis) if derived strictly from the four described domestic pig reference groups versus allowing for admixture from the wild boar group. By fitting statistical distributions to test statistics of reference domestic pigs, we characterized the distribution of the null hypothesis – that a given genotype descends strictly from domestic pig reference groups. We tested the approach with simulated genotypes and empirical data from an additional 29 breeds of domestic pig represented by 435 unique genotypes; all associated test statistics for simulated and empirical domestic pig challenge sets fell within the distribution of reference domestic pigs. We then evaluated 6,566 invasive wild pigs sampled across the contiguous United States, of which 63% exceeded the maximum threshold for domestic pigs and could be statistically classified as possessing wild boar ancestry. This approach provides a scientific foundation to enforce regulations prohibiting the possession of this destructive invasive species. Further, this computationally efficient and generalizable approach could be readily adapted to quantify gene flow among ecological systems of conservation or management concern.

opencc-zeroDec 2023View details →

An inbreeding perspective on the effectiveness of wildlife population defragmentation measures: A case study on wild boar (Sus scrofa) of Veluwe, The Netherlands

Pervasive inbreeding is a major genetic threat of population fragmentation and can undermine the efficacy of population connectivity measures. Nevertheless, few studies have evaluated whether wildlife crossings can alleviate the frequency and length of genomic autozygous segments. Here, we provided a genomic inbreeding perspective on the potential effectiveness of mammal population defragmentation measures. We applied a SNP-genotyping case study on the ~2500 wild boar Sus scrofa population of Veluwe, The Netherlands, a 1000-km2 Natura 2000 protected area with many fences and roads but also, increasingly, fence openings and wildlife crossings. We combined a 20K genotyping assessment of genetic status and migration rate with a simulation that examined the potential for alleviation of isolation and inbreeding. We found that Veluwe wild boar subpopulations are significantly differentiated (FST-values of 0.02-0.07) and have low levels of gene flow. One noteworthy exception was the Central and Southeastern subpopulation, which were nearly panmictic and appeared to be effectively connected through a highway wildlife overpass. Estimated effective population sizes were at least 85 for the meta-population and ranging from 31 to 52 for the subpopulations. All subpopulations, including the two connected subpopulations, experienced substantial inbreeding, as evidenced through the occurrence of many long homozygous segments. Simulation output indicated that whereas one or few migrants per generation could undo genetic differentiation and boost effective population sizes rapidly, genomic inbreeding was only marginally reduced. The implication is that ostensibly successful connectivity restoration projects may fail to alleviate genomic breeding of fragmented mammal populations. We put forward that defragmentation projects should allow for (i) monitoring of levels of differentiation, migration and genomic inbreeding, (ii) anticipation of the inbreeding status of the meta-population, and, if inbreeding levels are high and/or haplotypes have become fixed, (iii) consideration of enhancing migration and gene flow among meta-populations, possibly through translocation.

opencc-zeroJan 2024View details →

An integrated population model reveals source-sink dynamics for competitively subordinate African wild dogs linked to anthropogenic prey depletion

<ol> <li>Many African large carnivore populations are declining due to decline of the herbivore populations on which they depend. The densities of apex carnivores like the lion and spotted hyena correlate strongly with prey density, but competitive subordinates like the African wild dog benefit from competitive release when the density of apex carnivores is low, so the expected effect of a simultaneous decrease in resources and dominant competitors is not obvious. </li> <li>Wild dogs in Zambia's Luangwa Valley Ecosystem occupy four ecologically similar areas with well-described differences in the densities of prey and dominant competitors, due to spatial variation in illegal offtake.</li> <li>We used long-term data to fit a Bayesian integrated population model (IPM) of the demography and dynamics of wild dogs in these four regions. The IPM used Leslie projection to link a Cormack-Jolly-Seber model of area-specific survival (allowing for individual heterogeneity in detection), a zero-inflated Poisson model of area-specific fecundity, and a state-space model of population size that used estimates from a closed mark-capture model as the counts from which (latent) population size was estimated.</li> <li>The IPM showed that both survival and reproduction were lowest in the region with the lowest density of preferred prey (puku, Kobus vardonii, and impala, Aepyceros melampus), despite little use of this area by lions. Survival and reproduction were highest in the region with the highest prey density, and intermediate in the two regions with intermediate prey density. The population growth rate (λ) was positive for the population as a whole, strongly positive in the region with the highest prey density, and strongly negative in the region with the lowest prey density.</li> <li>It has long been thought that the benefits of competitive release protect African wild dogs from the costs of low prey density. Our results show that the costs of prey depletion overwhelm the benefits of competitive release and cause local population decline where anthropogenic prey depletion is strong. Because competition is important in many guilds and humans are affecting resources of many types, it is likely that similarly fundamental shifts in population limitation are arising in many systems.</li> </ol>

opencc-zeroFeb 2024View details →

Effects of food supplementation and helminth removal on space use and spatial overlap in wild bank vole populations

Animal space use and spatial overlap can have important consequences for population-level processes such as social interactions and pathogen transmission. Identifying how environmental variability and inter-individual variation affect spatial patterns and in turn influence interactions in animal populations is a priority for the study of animal behavior and disease ecology. Environmental food availability and macroparasite infection are common drivers of variation, but there are few experimental studies investigating how they affect spatial patterns of wildlife. Bank voles (Clethrionomys glareolus) are a tractable study system to investigate spatial patterns of wildlife and are amenable to experimental manipulations. We conducted a replicated, factorial field experiment in which we provided supplementary food and removed helminths in vole populations in natural forest habitats and monitored vole space use and spatial overlap using capture-mark-recapture methods. Using network analysis, we quantified vole space use and spatial overlap. We compared the effects of food supplementation and helminth removal and investigated the impact of season, sex, and reproductive status on space use and spatial overlap. We found that food supplementation decreased vole space use while helminth removal increased space use. Space use also varied by sex, reproductive status, and season. Spatial overlap was similar between treatments despite up to three-fold differences in population size. By quantifying the spatial effects of food availability and macroparasite infection on wildlife populations, we demonstrate the potential for space use and population density to trade off and maintain consistent spatial overlap in wildlife populations. This has important implications for spatial processes in wildlife including pathogen transmission.

opencc-zeroFeb 2024View details →

Early developmental carry-over effects on exploratory behaviour and DNA methylation in wild great tits (Parus major)

Adverse, postnatal conditions experienced during development are known to induce lingering effects on morphology, behaviour, reproduction and survival. Despite the importance of early developmental stress for shaping the adult phenotype, it is largely unknown which molecular mechanisms allow for the induction and maintenance of such phenotypic effects once the early environmental conditions are released. Here we aimed to investigate whether lasting early developmental phenotypic changes are associated with post-developmental DNA methylation changes. We used a cross-foster and brood size experiment in great tit (Parus major) nestlings, which induced post-fledging effects on biometric measures and exploratory behaviour, a validated personality trait. We investigated whether these post-fledging effects are associated with DNA methylation levels of CpG sites in erythrocyte DNA. Individuals raised in enlarged broods caught up on their developmental delay after reaching independence and became more explorative as days since fledging passed, while the exploratory scores of individuals that were raised in reduced broods remained stable. Although we previously found that brood enlargement hardly affected pre-fledging methylation levels, we found 420 CpG sites that were differentially methylated between fledged individuals that were raised in small versus large sized broods. A considerable number of the affected CpG sites were located in or near genes involved in metabolism, growth, behaviour and cognition. Since the biological functions of these genes line up with the observed post-fledging phenotypic effects of brood size, our results suggest that DNA methylation provides organisms the opportunity to modulate their condition once the environmental conditions allow it. In conclusion, this study shows that nutritional stress during early development associates with indirect, carry-over effects on DNA methylation. We propose that treatment-associated DNA methylation differences arise as a consequence of pre-fledging phenotypic changes, rather than that they cause early environmentally-induced effects.

opencc-zeroFeb 2024View details →

Heritability of cognitive performance in wild Western Australian magpies

Individual differences in cognitive performance can have genetic, social and environmental components. Most research on the heritability of cognitive traits comes from humans or captive non-human animals, whilst less attention has been given to wild populations. Western Australian magpies (Gymnorhina tibicen dorsalis, hereafter magpies) show phenotypic variation in cognitive performance, which affects reproductive success. Despite high levels of individual repeatability, we do not know whether cognitive performance is heritable in this species. Here, we quantify broad-sense heritability of associative learning ability in a wild population of Western Australian magpies. Specifically, we explore whether offspring associative learning performance is predicted by maternal associative learning performance, or by the social environment (group size) when tested at three time points during the first year of life. We found no significant relationship between maternal and offspring associative learning performance, with an estimated broad-sense heritability of just -0.004 ± 0.024 (CI: -0.050/0.044). However, complementing previous findings, we find that at 300 days post-fledging, individuals raised in larger groups passed the test in fewer trials compared to individuals from small groups. Our results highlight the pivotal influence of the social environment on cognitive development.

opencc-by-4.0Mar 2024View details →

DailySense: a Daily Self-reports and Physiological Signals Sensing Dataset for Subjective Health Research in the Wild

Description: This is a daily self-reports and physiological signals sensing dataset for subjective health research in the wild (DailySense). This is a dataset from a consecutive 14-day experiment in real-life settings composed of smartphone-based subjective psychological evaluation and physiological sensing. A Total of 36 healthy Japanese adult remote workers (mean±SD, 35.8±7.5; range, 27–58 years; 21 male and 15 female participants) participated in the experiment through two terms (1st term [1], 18 participants from a Japanese company without rewards; 2nd term, 18 participants from a participant's pool with rewards). The study protocol was approved by the internal review board of Research & Development Group, Hitachi, Ltd., and was conducted in accordance with the Declaration of Helsinki. All participants provided informed consent prior to enrollment in this study. The permission to share the raw data with participants' anonymization was included in this approval and explicitly obtained in that informed consent. This dataset contains the following data:  - pre- and post-term data of     - responses to self-reporting questionnaires (i.e., the Japanese versions of NEO-FFI, STAI, CES-D, CFS, PSQI, WHO-QOL, and SF-36v2©).     - demographics     - survey regarding this experiment - mid-term data of     - responses to emotional self-reports (i.e., Affective Slider and I-PANAS-SF) and their behavior in ESM 6 times/day at maximum     - responses to subjective health (i.e., degree of fatigue, stress, anxiety, depression, and sleeplessness), wake-up/in-bed times, and work style 1time/day     - continuously monitored physiological data (i.e., EDA, PPG, Acc) and event tags obtained by a wristband sensor (E4 wristband, Empatica Inc.) during their waking hours     - response profile data estimated using the proposed method     - log data of an experience sampling support system (exkuma, Japan Experience Sampling Method Association) Details of data are mentioned in an xlsx file of the root directory. Due to the limitation of questionnaires, descriptions of original instructions of items in each questionnaire are omitted. The details of the experiment are described in [1][2]. Note that, in [1], participant #29 was excluded due to insufficient physiological data quality. In addition, in [2], participant #47 was excluded since he did not complete a personality questionnaire, but #29 was included since he completed responses to all the questionnaires.   License: This dataset is made available by Hitachi, Ltd. under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.   References: If you use this dataset, please cite the following papers: [1] Shunsuke Minusa, Chihiro Yoshimura, and Hiroyuki Mizuno "Emodiversity evaluation of remote workers through health monitoring based on intra-day emotion sampling," Front. Public Heal., vol. 11, no. August, pp. 1–12, 2023, doi: <a href="https://doi.org/10.3389/fpubh.2023.1196539" target="_blank" rel="noopener">10.3389/fpubh.2023.1196539</a> [2] Shunsuke Minusa, Tadayuki Matsumura, Kanako Esaki, Yang Shao, Chihiro Yoshimura, and Hiroyuki Mizuno, "Response Style Characterization for Repeated Measures Using the Visual Analogue Scale," arXiv preprint <a href="https://arxiv.org/abs/2403.10136" target="_blank" rel="noopener">arXiv:2403.10136</a>, 2024.   Contact: If there is any problem, please contact us: <ul> <li>Shunsuke Minusa, <a href="mailto:shunsuke.minusa.hd@hitachi.com" target="_blank" rel="noopener">shunsuke.minusa.hd@hitachi.com</a></li> </ul>

opencc-by-4.0Mar 2024View details →

Maintaining habitat diversity at small scales benefits wild bees and pollination services in mountain apple orchards

In 2021, we conducted our study in apple orchards in South Tyrol, an Alpine region in Italy, using pan-traps, direct observations of visitation frequency, and a pollinator exclusion experiment. We investigated the scale-dependent effects of landscape heterogeneity and other parameters on wild bee assemblages and the related pollination service they provide at five spatial scales (radius 100 – 2,000 m).

opencc-zeroMar 2024View details →

Data for: Harvest and decimation affect genetic drift and the effective population size in wild reindeer

Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long-term viability. The effective population size (Ne) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate Ne of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The Ne/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14-year period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2 % in 2005-2018 and 44.8 % in 2021). Increased harvest rates decreased Ne in the simulations, but less sex-biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased Ne. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long-term genetic viability of wildlife populations subject to disease will also depend on the population impacts of the disease and how these interact with management actions.

opencc-by-4.0Apr 2022View details →

Figure 2. Macrobrachium tenellum adult male who underwent a second spermatophore extraction using the electrostimulation technique. A in Sperm viability in wild-caught males of Macrobrachium tenellum (Smith, 1871) (Decapoda: Caridea: Palaemonidae) fed with different diets

Figure 2. Macrobrachium tenellum adult male who underwent a second spermatophore extraction using the electrostimulation technique. A= The dark brown, melanized spermatophore is different from that observed in healthy males.

opencc-by-4.0Apr 2022View details →

Figure 1 in Sperm viability in wild-caught males of Macrobrachium tenellum (Smith, 1871) (Decapoda: Caridea: Palaemonidae) fed with different diets

Figure 1. Relationship between (A) body weight and spermatophore weight, (B) sperm cell number and spermatophore weight, (C) spermatophore weight and body length, (D) sperm cell number and body weight, and (E) sperm cell number and body length of wild Macrobrachium tenellum, analyzed after collection.

Appendix 6 in Phenotypic variability in the shield morphology of wild- vs. lab-reared eumalacostracan larvae

Appendix 6. Principal components of Stomatopoda from principal component analysis on the shield outline and percentage of total variation in the data set explained by each principal component. A: Dorsal data set. B: Lateral data set.

Appendix 5 in Phenotypic variability in the shield morphology of wild- vs. lab-reared eumalacostracan larvae

Appendix 5. Principal components of Raninidae from principal component analysis on the lateral shield outline and percentage of total variation in the data set explained by each principal component.

Appendix 4 in Phenotypic variability in the shield morphology of wild- vs. lab-reared eumalacostracan larvae

Appendix 4. Principal components of Hippoidea from principal component analysis on the shield outline and percentage of total variation in the data set explained by each principal component. A: Dorsal data set. B: Lateral data set.

Appendix 3 in Phenotypic variability in the shield morphology of wild- vs. lab-reared eumalacostracan larvae

Appendix 3. Principal components of Galatheidae from principal component analysis on the shield outline and percentage of total variation in the data set explained by each principal component. A: Dorsal data set. B: Lateral data set.