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opencc-by-4.0Mar 2022View details →

Non-invasive genomics of respiratory pathogens infecting wild great apes using hybridization capture

This dataset complements a manuscript reporting genomic analyses of respiratory pathogens cuasing lethal outbreaks in the wild chimpanzee community living in Tai National Park, Ivory Coast.

opencc-zeroDec 2021View details →

Immigrant males' memory acts to reduce ranging overlap and mating competition in wild baboons

Mechanistic models suggest that information acquired by animals ("knowledge") could shape home range patterns and dynamics, and how neighbours share space. In social species this would suggest that immigrants could bring new knowledge into social groups, potentially affecting the dynamics of home range overlap. We tested this "immigrant knowledge hypothesis" in a wild population of chacma baboons (Papio ursinus). We used data collected between 2005 and 2013 on two neighbouring troops in Namibia, comprising GPS records of daily ranges, male natal origins, daily females' reproductive status, and a satellite index of vegetation growth. We found that when the ratio of fertile females to adult males in the focal troop increased (i.e. increasing inter-troop mating competition costs for focal troop males), the focal troop tended to overlap less with a neighbouring troop's home range only when the alpha male had immigrated from that neighbouring troop and so was "knowledgeable" about its home range. When the alpha male was "not knowledgeable" the reverse was observed, with troops showing greater overlap, most likely reflecting an influence of fertile females on ranging patterns. Our findings support the immigrant knowledge hypothesis of group ranging behaviour, and suggest that dispersal and spatial memory may sometimes act to increase rather than decrease spatial segregation between groups. Very few previous studies have reported an effect of mating competition on ranging dynamics in social species, perhaps because previous studies did not consider divergent adaptive interest among group members and how they can be solved through collective-decision processes.

opengpl-2.0Dec 2021View details →

Dataset - Swarm of Micro Flying Robots in the Wild

Dataset for manuscripts "Swarm of Micro Flying Robots in the Wild". The file "data_benchmark.zip" contains data files of the simulation and real-world experiments of the manuscript: "Swarm of Micro Flying Robots in the Wild". And it also contains MATLAB scripts to recreate the plots and graphs as presented in the manuscript. Please see [data_out/ReadMe.txt] for code usage. The file "hardware.zip" contains PCB files and mechanical drawings of our micro flying robots. The file "realworldflight_software.zip" contains the source code of object detection and localization drift correction used in real-world experiments.

Cold winters have morph-specific effects on natal dispersal distance in a wild raptor

Dispersal is a key process with crucial implications in spatial distribution, density and genetic structure of species' populations. Dispersal strategies can vary according to both individual and environmental features, but putative phenotype-by-environment interactions have rarely been accounted for. Melanin-based color polymorphism is a phenotypic trait associated with specific behavioral and physiological profiles and is therefore a good candidate trait to study dispersal tactics in different environments. Here, using a 40 years dataset of a population of color polymorphic tawny owls (Strix aluco), we investigated natal dispersal distance of recruiting gray and pheomelanic reddish-brown (hereafter brown) color morphs in relation to post-fledging winter temperature and individual characteristics. Since morphs are differently sensitive to cold winters, we predicted that morphs' natal dispersal distances vary according to winter conditions. Winter temperature did not affect the proportion of brown (or gray) among recruits. We found that dispersal distances correlate with winter temperature in an opposite manner in the two morphs. While the gray morph undertakes larger movements in harsher conditions, likely because it copes better with winter severity, the brown morph disperses shorter distances when winters are harsher. We discuss this morph-specific natal dispersal pattern in a context of competition for territories between morphs and in terms of costs and benefits of these alternative strategies. Our results stress the importance of considering the interaction between phenotype and environment to fully disentangle dispersal movement patterns and provide further evidence that climate affects behavior and local distribution of this species.

Artificial size selection experiment reveals telomere length dynamics and fitness consequences in a wild passerine

Telomere dynamics could underlie life-history trade-offs among growth, size, and longevity, but our ability to quantify such processes in natural, unmanipulated populations is limited. We investigated how 4 years of artificial selection for either larger or smaller tarsus length, a proxy for body size, affected early-life telomere length (TL) and several components of fitness in two insular populations of wild house sparrows over a study period of 11 years. The artificial selection was expected to shift the populations away from their optimal body size and increase the phenotypic variance in body size. Artificial selection for larger individuals caused TL to decrease, but there was little evidence that TL increased when selecting for smaller individuals. There was a negative correlation between nestling TL and tarsus length under both selection regimes. Males had longer telomeres than females and there was a negative effect of harsh weather on TL. We then investigated whether changes in TL might underpin fitness effects due to the deviation from the optimal body size. Mortality analyses indicated disruptive selection on TL because both short and long early-life telomeres tended to be associated with the lowest mortality rates. In addition, there was a tendency for a negative association between TL and annual reproductive success, but only in the population where body size was increased experimentally. Our results suggest that natural selection for optimal body size in the wild may be associated with changes in TL during growth, which is known to be linked to longevity in some bird species.

opencc-by-4.0Jan 2022View details →

GWAS on salt stress responses in root system architecture parameters of wild tomato (S. pimpinellifolium)

The population of +/2 200 accessions of wild tomato was screened with the protocol described <a href="https://www.protocols.io/view/studying-root-system-architecture-changes-in-tomat-2mqgc5w">here</a> with the only exception that the plants were transferred 4 days after germination (rather than 3 - described in the protocol). The images were analyzed using the <a href="https://smartroot.github.io/">SmartRoot</a> for days 0, 1, 2, 3, and 4 after transfer to treatment plates (0 or 100 mM NaCl, 1/4 MS, 0.5% sucrose, 0.1% MES, 1% Dashin agar). The data analysis was performed as described <a href="https://rpubs.com/mjulkowska/BIGpimp_RSA_salt">here</a>, while the pareto front calculations were done according to Chandrasekhar & Julkowska paper (<a href="https://www.biorxiv.org/content/10.1101/2021.08.12.456185v1">preprint here</a>). The GWAS was performed using the ASReml script similar to <a href="https://onlinelibrary.wiley.com/doi/10.1111/tpj.15310">Awlia et al. (2021)</a>.

Grandmaternal age at reproduction affects grandoffspring body condition, reproduction and survival in a wild population of lizards

Age at reproduction can influence the survival and future reproduction of an individual as well as that of their offspring. Remarkably, it has been shown that grandmaternal age at reproduction can also affect the characteristics of grandoffspring in humans and in laboratory or semi-captive animals. However, currently we do not know whether grandmaternal age effects exist in wild populations. We gathered data on female age at reproduction, offspring and grandoffspring characteristics using a 16-year long-term survey of a natural population of the common lizard, Zootoca vivipara. The dataset contains 579 grandoffspring from 135 litters. Body size at birth was not correlated with grandmaternal age at reproduction. However, grandoffspring body condition at birth, grandoffspring survival and reproductive performance of granddaughters were dependent on grandmaternal age. These relationships were independent of maternal age. An age-structured model showed that the global effect of grandmaternal age was nonlinear and was largely driven by its effect on grandoffspring survival. Fitness was higher for granddaughters produced by grandmothers of intermediate ages. The study shows that age can shape life-history traits for more than one generation, documenting the importance that grandmaternal age can have in wild populations.

Hunting suitability model: A new tool for managing wild ungulates

Rising numbers of wild ungulates in human-dominated landscapes of Europe can induce negative effects like damages to forests. Therefore, effective wildlife management, including harvesting through hunting is becoming increasingly important. However, current hunting practices often fail to diminish those negative effects, as many ungulate species retreat to areas unsuitable for hunting. This predator-avoidance behaviour makes it difficult to fulfill the demand of reducing population numbers. Thus, there is an urgent need for innovative and effective wildlife management tools to counteract this problem. Here we provide for the first time a hunting suitability model for wild ungulate management in mountainous landscapes to visualise hunting suitability objectively and realistically. Using red deer as a model species, we modelled hunting suitability with high spatial resolution (10 x 10 m), based on remote sensing information, field surveys, and expert knowledge of professional hunters. We analysed spatio-temporal habitat selection by radio-collared deer in relation to locations of varying hunting suitability. The suitability of various locations regarding hunting influenced the spatio-temporal habitat selection by this species, consistent with our hypothesis. Red deer avoided areas suitable for hunting during daylight hours in the hunting season, but not during the night. This species seems to perceive a landscape of heterogeneous anthropogenic predation risk, shaped by locations of various hunting suitability, as we modelled it. This confirms the empirical realism of the model. Concerning wild ungulate management, our hunting suitability model provides high-resolution predictions of where species like red deer will retreat when perceived anthropogenic predation risk increases. The model also yields useful insights regarding the hunting suitability of particular locations, which is valuable information especially for non-locals. Furthermore, the model can serve as planning tool to inform decisions about where particular hunting strategies can be performed most efficiently to manage wild ungulates and therefore minimize human-wildlife conflicts.

opencc-zeroDec 2021View details →

Wild zebra finches are attracted towards acoustic cues from conspecific social groups

Social information gathered by observing others often supplements personal information collected from direct interactions with the physical environment during decision making. Social information use may be particularly beneficial in harsh environments or if resources are distributed patchily, ephemeral and unpredictable, and hence difficult to locate. We experimentally tested the use of acoustic cues in wild zebra finches (Taeniopygia guttata) as they flew around their arid habitat as a way of locating conspecifics on the ground, and potentially accessing useful social information. Joining a conspecific group may reduce the predation risk, and if they are foraging may also improve foraging efficiency, as the distribution of zebra finch food (grass seed) is scattered and unpredictable in their natural habitat, the Australian arid zone. We conducted playback experiments along vegetated creek lines radiating out from an artificial dam where all birds in the population were coming for drinking water. We broadcast recordings of vocalizations from foraging conspecific groups to birds using these creek lines to move to or from the water into the wider habitat. Zebra finches were more likely to land near the loudspeaker when conspecific vocalizations were broadcast compared to white noise. Birds flying low and close to the loudspeaker were most likely to land. Our results indicate that zebra finches use acoustic cues of conspecifics as a source of social information for grouping decisions. Use of such information may also enhance foraging efficiency in environments with unpredictable and scarce foraging locations, and reduce predation risk for calling and responding individuals.

opencc-zeroFeb 2022View details →

Wild legumes maintain beneficial soil rhizobia populations despite decades of nitrogen deposition

Natural landscapes are increasingly impacted by nitrogen enrichment from aquatic and airborne pollution sources. Nitrogen enrichment in the environment can eliminate the net benefits that plants gain from nitrogen-fixing microbes such as rhizobia, potentially altering host-mediated selection on nitrogen fixation. However, we know little about the long-term effects of nitrogen enrichment on this critical microbial service. Here, we sampled populations of the legume Acmispon strigosus and its associated soil microbial communities from sites spanning an anthropogenic nitrogen deposition gradient. We measured the net growth benefits plants obtained from their local soil microbial communities and quantified plant investment into nodules that house nitrogen-fixing rhizobia. We found that plant growth benefits from sympatric soil microbes did not vary in response to local soil nitrogen levels, and instead varied mainly among plant lines. Soil nitrogen levels positively predicted the number of nodules formed on sympatric plant hosts, although this was likely due to plant genotypic variation in nodule formation, rather than variation among soil microbial communities. The capacity of all the tested soil microbial communities to improve plant growth is consistent with plant populations imposing strong selection on rhizobial nitrogen fixation despite elevated soil nitrogen levels, suggesting that host control traits in A. strigosus are stable under long-term nutrient enrichment.

opencc-zeroFeb 2022View details →

Empirical tests of habitat selection theory reveal that conspecific density and patch quality, but not habitat amount, drive long-distance immigration in a wild bird

Individuals that disperse long distances from their natal site must select breeding patches with no prior knowledge of patch suitability. Despite decades of theoretical studies examining which cues dispersing individuals should use to select breeding patches, few empirical studies have tested the predictions of these theories at spatial scales relevant to long-distance dispersal in wild animal populations. Here, we use a novel assignment model based on multiple intrinsic markers to quantify natal dispersal distances of Wood Thrush (Hylocichla mustelina) breeding in forest fragments. We show that long-distance natal dispersal in this species is more frequent than commonly assumed for songbirds and that habitat selection by these individuals is driven by density-dependence and patch quality but not the amount of habitat surrounding breeding patches. These results represent an important contribution to understanding habitat selection by dispersing individuals, especially with regards to long-distance dispersal.

opencc-zeroFeb 2022View details →

Introgressive hybridisation between domestic pigs (Sus scrofa domesticus) and endemic Corsican wild boars (S. s. meridionalis): effects of human-mediated interventions

Owing to the intensified domestication process with artificial trait selection, introgressive hybridisation between domestic and wild species poses a management problem. Traditional free-range livestock husbandry, as practiced in Corsica and Sardinia, is known to facilitate hybridisation between wild boars and domestic pigs (Sus scrofa). Here, we assessed the genetic distinctness and genome-wide domestic pig ancestry levels of the Corsican wild boar subspecies S. s. meridionalis, with reference to its Sardinian conspecifics, employing a genome-wide single nucleotide polymorphism (SNP) assay and mitochondrial control region (mtCR) haplotypes. We also assessed the reliance of morphological criteria and the melanocortin-1 receptor (MC1R) coat colour gene to identify individuals with domestic introgression. While Corsican wild boars showed closest affinity to Sardinian and Italian wild boars compared to other European populations based on principal component analysis, the observation of previously undescribed mtCR haplotypes and high levels of nuclear divergence (Weir's 0.14) highlighted the genetic distinctness of Corsican S. s. meridionalis. Across three complementary analyses of mixed ancestry (i.e., STRUCTURE, PCADMIX, and ELAI), proportions of domestic pig ancestry were estimated at 9.5% in Corsican wild boars, which was significantly higher than in wild boars in Sardinia, where free-range pig keeping was banned in 2012. Comparison of morphologically pure- and hybrid-looking Corsican wild boars suggested a weak correlation between morphological criteria and genome-wide domestic pig ancestry. The study highlighted the usefulness of molecular markers to assess the direct impacts of management practices on gene flow between domestic and wild species.

opencc-by-4.0Mar 2022View details →

WIld boar demographic parameters extracted from the literature

This is the data extraction and description of  parameters of WB population dynamics, including general drivers, population demography, mortality, reproduction, and spatial behaviour.  The definition of the most relevant parameters that describe the wild boar (WB) population dynamics is essential to guide African swine fever (ASF) control policies. These parameters should be framed considering different contexts, such as geographic, ecological and management contexts, and gaps of data useful for the parameter definition should be identified. This information would allow better harmonized monitoring of WB populations and higher impact of ASF management actions, as well as better parametrizing population dynamics and epidemiological models, which is key to develop more efficient cost-benefit strategies. ENETwild is a project funded by EFSA, www.enetwild.com.

opencc-by-4.0Mar 2022View details →

Genomic, transcriptomic and proteomic comparison of MRSA CC398 isolates collected from human and wild animal samples (Genome assembly and annotation dataset)

This dataset includes the assembled contigs (.fasta and .gbk files), the nucleotide sequences of the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) for the following methicillin-resistant Staphylococcus aureus (MRSA) strains: MRSA CC398 isolates recovered from humans, namely C5621 and C9017, and from a wild boar, namely OR418. All raw sequence reads used in this study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB35102).

opencc-zeroApr 2022View details →

Single-Cell RNA-sequencing of neural precursor cells from an Alzheimer's mouse model, wild-type mice, and Alzheimer's mice rescued with Usp16 haploinsufficiency

Alzheimer's disease (AD) is a progressive neurodegenerative disease observed with aging that represents the most common form of dementia. To date, therapies targeting end-stage disease plaques, tangles, or inflammation have limited efficacy. Therefore, we set out to identify an earlier targetable phenotype. Utilizing a mouse model of AD we found that cell intrinsic neural precursor cell (NPC) dysfunction precedes widespread inflammation and amyloid plaque pathology, making it one of the earlier defects in the evolution of the disease. We demonstrate that reversing impaired NPC self-renewal via genetic reduction of USP16, a histone modifier and critical physiological antagonist of the Polycomb Repressor Complex 1, can prevent downstream cognitive defects and decrease astrogliosis in vivo. To delineate potential self-renewal pathways that might contribute to the defect and rescue of Tg-SwDI NPCs and Tg-SwDI/Usp16+/- NPCs, respectively, we performed single-cell RNA-seq and gene set enrichment analysis (GSEA) on lineage depleted primary FACS-sorted CD31-CD45-Ter119-CD24- NPCs from Tg-SwDI, WT, and Tg-SwDI/Usp16+/- mice at 3-4 months and 1 year of age. Using the GSEA Hallmark gene sets, we found only three gene sets that were enriched in Tg-SwDI mice over WT mice and rescued in the Tg-SwDI/Usp16+/- mice at both ages: TGF-ß pathway, oxidative phosphorylation, and Myc Targets. The TGF-ß pathway consistently had the highest normalized enrichment score in pairwise comparisons between Tg-SwDI vs WT and Tg-SwDI vs Tg-SwDI/Usp16+/- of the three rescued pathways. These data suggest that USP16 may regulate neural precursor cell function in part through the BMP pathway.

opencc-zeroApr 2022View details →

Low toxicity crop fungicide (Fenbuconazole) impacts reproductive male quality signals leading to a reduction of mating success in a wild solitary bee

Recent reports on bee health suggest that sub-lethal doses of pesticides have negative effects on wild bee reproduction and ultimately on their population growth. Females of the solitary horned mason bee, Osmia cornuta, evaluate thoracic vibrations and odours of males to assess male quality. When certain criteria are met, the female accepts the male and copulates. However, these signals were found to be modified by sub-lethal doses of pesticides in other hymenopterans. Here, we tested whether sub-lethal doses of a commonly used fungicide (Fenbuconazole) impact male quality signals and mating success in O. cornuta. Males exposed to Fenbuconazole exhibited reduced thoracic vibrations and an altered cuticular hydrocarbon profile compared to the control bees. Moreover, males exposed to the fungicide were less successful in mating than control males. Synthesis and applications: Our results indicate that a low toxicity fungicide can negatively affect male reproductive success by altering behavioural and chemical cues. This could explain the decreasing pollinator populations in a pesticide-polluted environment. This study highlights the need for a more comprehensive approach, including behaviour and chemical cues, when testing new pesticides and a more cautionary approach to the pesticides already used on crops.

opencc-by-4.0Apr 2022View details →

Annotated genomes of Pseudomonas spp. isolated from wild and cultivated cranberry bogs

Pseudomonas spp. were isolated from rhizospheres of wild and cultivated cranberry bogs in southeastern Massachusetts. Genomes were translated and annotated.

opencc-zeroApr 2022View details →

The quantitative genetics of fitness in a wild seabird

Additive genetic variance in fitness is a prerequisite for adaptive evolution, as a trait must be genetically correlated with fitness to evolve. Despite its relevance, additive genetic variance in fitness has not often been estimated in nature. Here, we investigate additive genetic variance in lifetime and annual fitness components in common terns (Sterna hirundo). Using 28 years of data comprising ca. 6000 pedigreed individuals, we find that additive genetic variances in the Zero-inflated and Poisson components of lifetime fitness were effectively zero, but estimated with high uncertainty. Similarly, additive genetic variances in adult annual reproductive success and survival did not differ from zero, but were again associated with high uncertainty. Simulations suggested that we would be able to detect additive genetic variances as low as 0.05 for the Zero-inflated component of fitness, but not for the Poisson component, for which adequate statistical power would require c. two more decades (four tern generations) of data collection. As such, our study suggests heritable variance in common tern fitness to be rather low if not zero, shows how studying the quantitative genetics of fitness in natural populations remains challenging, and highlights the importance of maintaining long-term individual-based studies of natural populations.

opencc-by-4.0Apr 2022View details →

Gene flow between wild trees and cultivated varieties shapes the genetic structure of sweet chestnut (Castanea sativa Mill.) populations

The sweet chestnut orchards (Castanea sativa Mill.) are traditionally planted in the northern Adriatic region. This study investigates their population structure, as well as the genetic background of three toponymous clonal varieties. Six genomic simple sequence repeat (gSSR) and nine EST-derived SSR (EST-SSR) loci were utilized in this study. We have identified five closely related clones, which represent a singular, polyclonal marron variety, found in all three cultivation areas, acompanied by many hybrids, resulting from the breeding between cultivated and wild chestnuts.