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Rotational grazing with cattle-free zones supports the coexistence of cattle and wild herbivores in African rangelands

African wildlife populations are declining at an alarming rate. To stop further population declines and restore ecosystems, more areas for wildlife are needed. Community-based conservation with wildlife-livestock coexistence in the vast rangelands of Africa presents a major opportunity. However, the efficacy of wildlife conservation in mixed land-use areas remains an outstanding question. To assess the ecological outcomes of land-sharing between regulated livestock herds and wildlife populations in African savannas, we test how rotational cattle grazing affects spatiotemporal dynamics of 15 large herbivore species in the Maasai Mara, Kenya. First, we tested how wild herbivore distributions across the Greater Mara Ecosystem (the Mara, ~2,600 km2) are related to cattle density and environmental variables using 584,561 observations of wild herbivores (ecosystem scale). In a second analysis, we tested how rotational cattle grazing affects wild herbivore distributions in a 300 km2 subsection of the Mara using 30,583 observations (landscape scale). Finally, we tested how functional traits of wild herbivores affect species-level spatiotemporal responses to cattle grazing. At the ecosystem scale, the presence of five wild herbivore species was positively correlated with cattle density, while cattle effects on wild herbivore abundances were species-dependent with both increases and decreases. At the landscape scale, rotational cattle grazing strongly impacted the spatiotemporal habitat selection of wild herbivores, resulting in distinct lag periods with which different species are attracted to areas previously grazed by cattle. These lag periods were linked to functional traits, with body mass and herd size explaining 35% of the interspecific differences. Small to medium-sized herbivores with large herds select areas recently grazed by cattle, whereas large species with large herd sizes and small species with small herd sizes avoid recently grazed areas. Synthesis and applications Our results revealed that the effect of cattle on wild herbivores varies considerably among species, suggesting that cattle-wildlife interactions range from facilitation to competition. To maintain species that strongly avoid cattle, designated livestock-free zones remain essential, also in rotational grazing systems. Rotational grazing systems with regulated livestock densities present an important opportunity to better manage wildlife-livestock coexistence and thus improve wildlife conservation in African rangelands.

Reproductive output and telomere dynamics following calcium supplementation in wild Tree Swallows (Tachycineta bicolor)

This data was the result of an experiment investigating whether biologically relevant differences in reproductive investment influence fitness in a wild bird species. We employed calcium supplementation to experimentally modify reproductive output in Tree Swallow mothers and offspring and we used telomere dynamics during the breeding season as a proxy for fitness. To confirm that calcium supplementation positively impacts reproductive parameters at our study site, we initiated a 4-year trial of calcium supplementation with our Tree Swallow study population. In the following two breeding seasons, we used calcium supplementation to experimentally alter reproductive output and measured telomere length in mothers immediately before egg-laying and shortly before fledging to determine the direct relationship between reproductive investment and telomere shortening in this species. Our study includes one hundred eighty-eight nests initiated and monitored over six breeding seasons.

Chromosome-scale assembly of the wild wheat relative Aegilops umbellulata

Wild wheat relatives have been explored in plant breeding to increase the genetic diversity of bread wheat, one of the most important food crops. Aegilops umbellulata is a diploid U genome-containing grass species that serves as a genetic reservoir for wheat improvement. In this study, we report the construction of a chromosome-scale reference assembly of Ae. umbellulata accession TA1851 based on corrected PacBio HiFi reads and chromosome conformation capture. The total assembly size was 4.25 Gb with a contig N50 of 17.7 Mb. In total, 36,268 gene models were predicted. We benchmarked the performance of hifiasm and LJA, two of the most widely used assemblers using standard and corrected HiFi reads, revealing a positive effect of corrected input reads. Comparative genome analysis confirmed substantial chromosome rearrangements in Ae. umbellulata compared to bread wheat. In summary, the Ae. umbellulata assembly provides a resource for comparative genomics in Triticeae and for the discovery of agriculturally important genes.

Data for: Dietary nucleotides can prevent glucocorticoid-induced telomere attrition in a fast-growing wild vertebrate

Telomeres are chromosome protectors that shorten during eukaryotic cell replication and in stressful conditions. Developing individuals are susceptible to telomere erosion when their growth is fast and resources are limited. This is critical because the rate of telomere attrition in early life is linked to health and life span of adults. The metabolic telomere attrition hypothesis (MeTA) suggests that telomere dynamics can respond to biochemical signals conveying information about the organism's energetic state. Among these signals are glucocorticoids, hormones that promote catabolic processes, potentially impairing costly telomere maintenance, and nucleotides, which activate anabolic pathways through the cellular enzyme target of rapamycin (TOR), thus preventing telomere attrition. During the energetically demanding growth phase, the regulation of telomeres in response to two contrasting signals—one promoting telomere maintenance and the other attrition—provides an ideal experimental setting to test the MeTa. We studied nestlings of a rapidly developing free-living passerine, the great tit (Parus major), that either received glucocorticoids (Cort-chicks), nucleotides (Nuc-chicks), or a combination of both (NucCort-chicks), comparing these with controls (Cnt-chicks). As expected, Cort-chicks showed telomere attrition, while NucCort- and Nuc-chicks did not. NucCort-chicks was the only group showing increased expression of a proxy for TOR activation (the gene telo2), of mitochondrial enzymes linked to ATP production (cytochrome oxidase and ATP-synthase) and a higher efficiency in aerobically producing ATP. NucCort-chicks had also a higher expression of telomere maintenance genes (shelterin protein TERF2 and telomerase TERT) and of enzymatic antioxidant genes (glutathione peroxidase and superoxide dismutase). The findings show that nucleotide availability is crucial for preventing telomere erosion during fast growth in stressful environments.

Wild pedigrees inform mutation rates and historic abundance in baleen whales

Phylogeny-based estimates suggesting a low germline mutation rate (μ) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated μ directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of μ reduces previous genetic–based estimates of pre-exploitation whale abundance by 86% and suggests that μ cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate μ directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.

Data from: The contributions of flower strips to wild bee conservation in agricultural landscapes can be predicted using pollinator habitat suitability models

Sowing flower strips along field edges is a widely adopted method for conserving pollinating insects in agricultural landscapes. To maximize the effect of flower strips given limited resources, we need spatially explicit tools that can prioritize their placement, and for identifying plant species to include in seed mixtures. We sampled bees and plant species as well as their interactions in a semi-controlled field experiment with roadside/field edge pairs with/without a sown flower strip at 31 sites in Norway and used a regional spatial model of solitary bee species richness to test if the effect of flower strips on bee species richness was predictable from the modelled solitary bee species richness. We found that sites with flower strips were more bee species rich compared to sites without flower strips and that this effect was greatest in areas that the regional solitary bee species richness model had identified to be particularly important for bees. Spatial models revealed that even within small landscapes there were pronounced differences between field edges in the predicted effect of sowing flower strips. Of the plant species that attracted the most bee species, the majority mainly attracted bumblebees and only few species also attracted solitary bees. Considering both the taxonomic diversity of bees and the species richness of bees attracted by plants we suggest that seed mixes containing Hieracium spp. such as Hieracium umbellatum and Pilosella officinarum; Taraxacum spp; Trifolium repens; Lotus corniculatus; Stellaria graminea; and Achillea millefolium would provide resources for diverse bee communities in our region. Spatial prediction models of bee diversity can be used to identify locations where flower strips are likely to have the largest effect and can thereby provide managers with an important tool for prioritizing how funding for agri-environmental schemes such as flower strips should be allocated. Such flower strips should contain plant species that are attractive to both solitary and bumblebees, and do not need to be particularly plant species rich as long as the selected plants complement each other.

A tale of three vines: current and future threats to wild Eurasian grapevine by vineyards and invasive rootstocks

This dataset has been used for the paper A tale of three vines: current and future threats to wild Eurasian grapevine by vineyards and invasive rootstocks by Petitpierre et al. It contains the species distribution of five Vitis species in North America and Europe (Vitis acerifolia, Vitis aestivalis, Vitis rupestris, Vitis riparia and Vitis berlandieri), so as the distribution of the Eurasian wild grapevine (Vitis vinifera ssp. sylvestris) and cultivated grapevine in Europe (Vitis vinifera ssp. vinifera). 40 bioclimatic variables are associated to these distributions. These variables were derived from the Climond dataset (Kriticos et al., 2012). Species distribution data were gathered using several databases and sources. The list of the different sources is cited in methods section of the related manuscript. The distribution of each Vitis taxa was rasterized at a resolution of 0.167° (coordinate reference system WGS84; EPSG:4326). X and Y coordinates correspond to the center of each cell. Environmental variables were extracted from the CliMond database (Kriticos et al., 2012) for each site. It consists of a set of 40 bioclimatic variables at a resolution of 0.167°, grouped into 4 categories: temperature, precipitation, moisture, and solar radiation. The description of these 40 variables can be found in the original CliMond publication (Kriticos et al., 2012).   Each file contains the distribution of one Vitis taxa. v_ace.csv contains the distribution of Vitis acerifolia in North America. v_aes.csv contains the distribution of Vitis aestivalis in North America. v_ber.csv contains the distribution of Vitis berlandieri in North America. v_rip.csv contains the distribution of Vitis riparia in North America. v_rup.csv contains the distribution of Vitis rupestris in North America. v_root.csv contains the distribution of the American vitis taxa (Vitis acerifolia, Vitis aestivalis, Vitis berlandieri, Vitis riparia and Vitis rupestris) in Europe. v_vin.csv contains the distribution of the vineyards (i.e. Vitis vinifera ssp. vinifera, the cultivated grapevine) in Europe. v_syl.csv contains the distribution of the vineyards (i.e. Vitis vinifera ssp. sylvestris, the wild European grapevine) in Europe. Reference Kriticos, D.J., Webber, B.L., Leriche, A., Ota, N., Macadam, I., Bathols, J., Scott, J.K., 2012. CliMond: Global high-resolution historical and future scenario climate surfaces for bioclimatic modelling. Methods Ecol. Evol. 3, 53–64. https://doi.org/10.1111/j.2041-210X.2011.00134.x GBIF data for Vitis vinifera ssp. vinifera. GBIF.org (11 November 2020) GBIF Occurrence Download  https://doi.org/10.15468/dl.hacmjx GBIF data for Vitis ssp. sylvestris. GBIF.org (11 November 2020) GBIF Occurrence Download  https://doi.org/10.15468/dl.qu7txv GBIF data for Vitis berlandieri. GBIF.org (11 November 2020) GBIF Occurrence Download  https://doi.org/10.15468/dl.w6dt7r GBIF data for Vitis riparia. GBIF.org (11 November 2020) GBIF Occurrence Download  https://doi.org/10.15468/dl.aqh55u GBIF data for Vitis acerifolia. GBIF.org (11 November 2020) GBIF Occurrence Download  https://doi.org/10.15468/dl.csd7wc GBIF data for Vitis aestivalis. GBIF.org (11 November 2020) GBIF Occurrence Download  https://doi.org/10.15468/dl.f5jfzf GBIF data for Vitis rupestris. GBIF.org (02 September 2020) GBIF Occurrence Download https://doi.org/10.15468/dl.gqjm7w

Contaminated sediment in the Detroit River selects for evolved CYP1A and p53 responses in wild brown bullhead (Ameiurus nebulosus) populations

<div> <div> In a previous study, adaptive responses to a single polycyclic aromatic hydrocarbon (PAH), benzo[a]pyrene (BaP), were identified in brown bullhead (Ameiurus nebulosus) captured from contaminated sites across the Great Lakes. The tumor suppressor p53 and phase I toxin metabolizing CYP1A genes showed a protective and refractory response, respectively, up to the F1 generation (Williams and Hubberstey, 2014). As an extension to the first study, bullhead were exposed to sediment collected from sites along the Detroit River to see if these adaptive responses are attainable when fish from a contaminated site are exposed to a mixture of contaminants, instead of a single compound. p53 and CYP1A proteins were measured in both studies with the addition of phase II glutathione-s-transferase (GST) activity in the second. Three treatment groups were measured: acute (treated immediately), cleared (depurated for three months and subsequent treatment), and farm raised F1 offspring. All three treatment groups were exposed to clean and contaminated sediment for 24 and 96 hours. Acute fish from contaminated sites exposed to contaminated sediment revealed an initial elevated p53 response that was not reached in cleared fish exposed to contaminated sediment. Instead, cleared and F1 bullhead from clean and contaminated sites had overlapping p53 expression patterns in response to contaminated sediment by 96 hours. Acute fish from contaminated sites exposed to contaminated sediment revealed refractory CYP1A expression, which disappeared in cleared fish and whose F1 refractory response overlapped with clean site F1 offspring. Decreasing GST activity was evident in both clean and contaminated fish over time, with clean site fish responding to contaminated sediment more deliberately. By 96 hours, the response patterns of F1 offspring from clean and contaminated sites to clean and contaminated sediment exposures were similar. </div> <div> Because p53, CYP1A and GST activity responses to contaminated sediment dosing overlapped in clean and contaminated farm-raised F1 offspring, these results suggest that contaminated fish have acclimated to the contaminants present in their environments by reaching a tolerance threshold and no evidence of adaptation was detected in these biomarkers. </div> </div>

Role of immigrant males and muzzle contacts in the uptake of a novel food by wild vervet monkeys

Data and script used to analyse data for the study: "Role of immigrant males and muzzle contacts in the uptake of a novel food by wild vervet monkeys"

Dataset to paper "ECN with QUIC: Challenges in the Wild"

In the following you can find the according measurements of our IMC'23 paper "ECN with QUIC: Challenges in the Wild" for the publicly available toplists. Please note that we cannot publicly share our CZDS-based measurements due to their proprietary license. All data is available as line-delimited json files which have been zstandard compressed. If you use any portion of our work, please consider citing our publication. <pre><code>@Inproceedings { 2023-sander-quic-ecn, title = {ECN with QUIC: Challenges in the Wild}, year = {2023}, month = {10}, publisher = {ACM}, booktitle = {Proceedings of the Internet Measurement Conference (IMC '23)}, DOI = {10.1145/3618257.3624821}, author = {Sander, Constantin and Kunze, Ike and Bl{\"o}cher, Leo and Kosek, Mike and Wehrle, Klaus} }</code></pre>

Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplant

Crop wild relatives possess desirable traits that confer resilience to various environmental stresses. We applied landscape genomics, that associates environment with genomic variation to understand the genetic basis of their adaptation. In this study, we applied landscape genomics to examine the differences in allele frequency of 15,416 Single Nucleotide Polymorphisms (SNPs) among 153 accessions of wild eggplant relatives from Africa, the principal hotspot of these wild relatives. Further, we explored the correlation between the genetic variations and the bio-climatic and soil conditions at their collection sites. Our results showed that the environment has a greater impact on the genetic variation in the eggplant wild relative populations compared to the geographical distances between collection sites while controlling for population structure. These findings indicate the relevance of the environment in shaping genetic variation in eggplant relatives over time. We detected also candidate SNPs associated with ten environmental factors. Some of these SNPs signal genes involved in pathways that help with adaptation to environmental stresses such as drought, heat, cold, salinity, pests, and diseases.

Supplementary data for: "The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches"

Supplementary data to https://doi.org/10.1101/2023.06.01.543285

Data from: hibernation telomere dynamics in a shifting climate: insights from wild greater horseshoe bats

Hibernation is linked with various hypotheses to explain the extended lifespan of hibernating mammals compared with their non-hibernating counterparts. Studies on telomeres, markers of ageing and somatic maintenance, suggest telomere shortening slows during hibernation and lengthening may reflect self-maintenance with favourable conditions. Bats in temperate zones adjust body temperatures during winter torpor to conserve energy and exploit mild conditions for foraging. Climate change may impact the hibernation cycle of bats, but more research is needed regarding the role of telomeres in understanding their response to a changing climate. Here relative telomere length (rTL) was measured in the long-lived greater horseshoe bat Rhinolophus ferrumequinum (n = 223 individuals) over three winters, considering climatic conditions. Cross-sectional analyses revealed between-individual variation in rTL with a strong year effect, likely linked to varying weather conditions and foraging success. Additionally, within-individual increases of rTL occurred in 51% of consecutive measurements, with evidence of increasing telomerase expression during hibernation in this species. These findings highlight the beneficial effects of hibernation on telomeres and potential consequences of changing climatic conditions for long-lived temperate bats. Understanding the interplay between hibernation, telomeres, and climate can provide insights into the adaptive capacity and survival of bat populations facing environmental challenges.

Data for: Multiple mechanisms for inbreeding avoidance used simultaneously in a wild ape

Mating with close kin can have considerable negative fitness consequences, which are expected to result in selective pressure for inbreeding avoidance mechanisms, such as dispersal, mate choice and postcopulatory biases. Captive studies have suggested that inbreeding avoidance through mate choice is far less widespread than expected and may be absent where other mechanisms already limit inbreeding. However, few studies have examined multiple mechanisms of inbreeding avoidance simultaneously, particularly in the wild. We use 13 years of detailed dispersal, copulation, and paternity data from mountain gorillas to examine inbreeding avoidance. We find that partial dispersal of both sexes results in high kinship in multimale groups, but that copulations between close kin occur 40% less than expected. We find strong kin discrimination in mate choice, with significant avoidance of maternal kin but more limited avoidance of paternal kin. We find no evidence for post-copulatory inbreeding avoidance. Our analyses support familiarity-based mechanisms of kin identification and age-based avoidance that limits mating between fathers and daughters in their natal group. Our findings demonstrate that multiple complementary mechanisms for inbreeding avoidance can evolve in a single species and suggest that inbreeding avoidance through mate choice may enable more flexible dispersal systems to evolve.

Grassland extensification enhances nest densities of ground-nesting wild bees

<ol> <li>Ground-nesting wild bees provide essential pollination services in agroecosystems, but they are jeopardized by intensive agricultural management. To mitigate such negative impacts, agri-environment schemes have been implemented. While the success of enhancing floral food resources is relatively well studied, the role of agri-environmental schemes in providing suitable nesting habitat remains underexplored.</li> <li>We studied the effectiveness of meadow extensification according to the Swiss agri-environment scheme in promoting nesting of ground-nesting bees. Using a paired design, we quantified their nests during four rounds (March-June) in pairs of nine randomly selected extensively (i.e. no fertilizer input, postponed first mowing) and nine intensively managed meadows with similar soil properties, slope, exposure and landscape context. Nest numbers and vegetation characteristics were surveyed in areas of 250 m2. Vegetation properties were also assessed in 0.5 m × 0.5 m plots around nest locations and randomly selected locations without nests within each meadow to assess their role as drivers of nesting incidence (nest presence/absence) at this plot scale.</li> <li>We found substantially higher nest numbers of ground-nesting bees in extensively (mean ± SE per sampling round = 46.8 ± 14.2) compared to intensively managed meadows (0.8 ± 0.3; no nests in three out of nine intensively managed meadows). Extensively managed meadows harboured nests of several dominant crop pollinator species, including aggregations of e.g. Lasioglossum malachurum contributing to high nest densities in some of them. Number of nests was negatively related to grass cover and vegetation height, which were lower in extensively compared to intensively managed meadows. Plot-level nesting incidence increased with bare ground and moss cover, and decreased with grass cover.</li> <li> Synthesis and applications. Our study shows that extensively managed meadows are better nesting habitats for ground-nesting bees than intensively managed meadows, if reduced management intensity is associated with altered vegetation characteristics such as reduced grass cover and vegetation height, and small-scale availability of bare ground, driving these effects. This highlights that maintaining and promoting extensive management of meadows can promote ground-nesting wild bees, including dominant crop pollinators, not only by enhancing floral resources but also by improving nesting opportunities in agroecosystems.</li> </ol>

A field experiment reveals reciprocal effects of host personality and parasitism in wild lizards

Host behavior and parasite infection reciprocally interact, but this dynamic is rarely studied experimentally in the field with multiple behaviors. Using the dataset provided here, we investigated the interplay between parasitism and host behavior via an in situ experimental tick infestation of a wild population of sleepy lizards, Tiliqua rugosa. Using Bayesian models, we assessed the relationship between experimental infestation and lizard aggression and boldness before and after infestation. First, we tested whether lizard aggression and boldness prior to infestation predicted the probability of tick attachment in the infestation experiment. Second, we evaluated whether experimental infestation affected subsequent lizard aggression and boldness. We found that aggression and boldness related interactively with infestation: for unaggressive lizards, higher boldness was associated with reduced experimental infestation success, but the opposite occurred for aggressive individuals. Second, increased tick infestation did not affect post-infestation aggression, but tended to increase boldness. Taken together, these results highlight the potential for feedbacks between parasites and multi-dimensional host behaviors.

Large captivity effect based on gene expression comparisons between captive and wild shrew brains

Compared to their free-ranging counterparts, wild animals in captivity are subject to different conditions with lasting effects on their physiology and behavior. Alterations in gene expression in response to environmental changes occur upstream of physiological and behavioral phenotypes, but there are no experiments analyzing differential gene expression in captive vs. free-ranging mammals. We assessed gene expression profiles of three brain regions (cortex, olfactory bulb, and hippocampus) of wild juvenile shrews (Sorex araneus) in comparison to shrews kept in captivity for two months. We found hundreds of differentially expressed genes in all three brain regions, suggesting a large and uniform captivity effect. Many of the downregulated genes in captive shrews significantly enrich pathways associated with neurodegenerative disease (p<0.001), oxidative phosphorylation (p<0.001), and genes encoding ribosomal proteins (p<0.001). Transcriptomic changes associated with captivity in the shrew resemble responses identified in several human pathologies, such as major depressive disorder and neurodegeneration. Thus, not only does captivity impact brain function and expression, but captivity effects may also confound analyses of natural physiological processes in wild individuals under captive conditions.

Seasonal roost selection of wild turkeys at their northern range edge

Wild turkeys (Meleagris gallopavo) are diurnally active birds that spend the dark hours roosting in trees. We tested the hypothesis that multiple benefits exist for roost tree selection by wild turkeys, including thermoregulation, resource acquisition, and protection from predators. We compared 48 roost trees used by eastern wild turkeys (M. g. silvestris) in Ontario, Canada to 48 non-roost trees sampled contemporaneously during 2017-2019 to determine roost site selection between seasons. Mean (± SE) roost tree height (21.4 ± 0.8 m) was taller than non-roost trees (18.2 ± 0.8 m), and roost trees were also larger in diameter at breast height (58.1 ± 5.5 cm versus 38.7 ± 3.1 cm). Using ibuttons to collect microclimate temperatures at the tree, we found that mean temperature (± SE) of a deciduous roost (14.5 ± 0.1°C) was higher than temperature at either a coniferous roost (13.9 ± 0.1°C) or ambient temperature (13.2 ± 0.1°C) during the summer months. In winter however, we did not find any relationship between temperature and tree type. Roosts were closer to buildings (150.8 ± 26.0 m) in the winter compared to summer and year-round roosts, and winter roosts were also farther away from crops (395.2 ± 63.7 m) compared to roost sites used year-round. Summer roosts were closer to roads (143 ± 36.3 m) than the roosts in the winter and roosts used year-round. Our data suggest that thermoregulation is not the driving force behind roost selection; instead, predator avoidance appears to play the most important role, with some weaker evidence in support of proximity to resources.

Sexes in sync: phenotypic plasticity, sexual selection, and phenological synchrony between the sexes in a wild hibernator

Desynchrony of phenological responses to climate change is a major concern in ecological communities. Potential uncoupling between one of the most fundamental divisions within populations, males and females, has not been well studied. To address this gap, we examined sex-specific plasticity in hibernation phenology in two populations of Columbian ground squirrels (Urocitellus columbianus). We find that both sexes display similar phenological plasticity to spring snowmelt dates in their timing of torpor termination and behavioural emergence from hibernation. As a result of this plasticity, the degree of protandry (i.e., males' emergences from hibernation preceding those of females) did not change significantly over the 27-year study. Earlier male behavioural emergence, relative to females, improved the likelihood of securing a breeding territory and increased annual reproductive success. Sexual selection favouring earlier male emergence from hibernation may maintain protandry in this population but did not contribute to further advances in male phenology. Older males also tended to emerge earlier and secure territories, and so it is unclear whether selection acts indirectly through age. Together, our results provide evidence that the sexes should remain synchronised, at least in response to the weather variation investigated here, and further support the role of sexual selection in the evolution of protandry in sexually reproducing organisms.