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opencc-zeroMar 2024View details →

Genetic insight into a polygenic trait using a novel Genome Wide Association approach in a wild amphibian population

Body size variation is central in the evolution of life history traits in amphibians, but the underlying genetic architecture of this complex trait is still largely unknown. Herein, we studied the genetic basis of body size and fecundity of the alternative morphotypes in a wild population of the Greek smooth newt (Lissotriton graecus). By combining a Genome-wide association approach with linkage disequilibrium network analysis, we were able to identify clusters of highly correlated loci thus maximizing sequence data for downstream analysis. The putatively associated variants explained 12.8% to 44.5% of the total phenotypic variation in body size and were mapped to genes with functional roles in the regulation of gene expression and cell cycle processes. Our study is the first to provide insights into the genetic basis of complex traits in newts and provides a useful tool to identify loci potentially involved in fitness related traits in small data sets from natural populations in non-model species.

opencc-zeroMar 2024View details →

Can livestock grazing dampen density dependent fluctuations in wild herbivore populations?

Conservation policy for the high mountains of Asia increasingly recognises the need to encompass large multi-use landscapes beyond the protected area network. Due to limited long-term research in this region, our understanding of even fundamental processes, such as factors regulating large mammal populations is poor. Understanding the factors that regulate animal populations, especially those generating cyclicity, is a long-standing problem in ecology. Long-term research across multiple taxa (mainly from Europe and North America) has focused on the relative roles of food and predation in generating cyclicity in population dynamics. It remains unclear how trophic interactions that are influenced by anthropogenic stressors can affect population dynamics in human-modified landscapes. We present a 10-year study to compare the effects of livestock grazing on density dependent dynamics in two populations of bharal, Pseudois nayaur, in the Himalaya. We combine this with a mechanistic understanding of whether density dependence in these two sites acts predominantly by affecting adult survival or recruitment. We compared and quantified density dependence in the bharal population by fitting Bayesian Gompertz state‐space (GSS) models. We found evidence for negative density dependence which indicates possible cyclic dynamics in the bharal population of the site (Tabo) with low livestock density. The population dynamics of this site were driven by recruited offspring – with a 2-year density dependent lag effect – rather than adult survival. In the site with high livestock density (Kibber), this density dependence was not detected. We postulate the potential role of excessive grazing by livestock in affecting offspring recruitment, thereby affecting the bharal population in Kibber. Synthesis and applications: Our results suggest that conservation action to facilitate wild herbivore population recovery, such as the development of protected areas and village reserves, needs to account for density dependent regulation. Sites with trophy hunting require continuous monitoring to understand the effects of density dependence so that appropriate hunting quotas can be formulated.

opencc-by-4.0Mar 2024View details →

Code For: Invasive wild pig carcass availability does not affect coyote abundance

Open the record for dataset details and reuse information.

opencc-zeroApr 2024View details →

Data from: Phenotypic resources immortalized in a panel of wild-derived strains of five species of house mice

The house mouse, Mus musculus, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. To assess the proportion of variation added by wild progenitors, we estimated phenotypic variation in 84 WDS representing 5 species (M. musculus, M. spretus, M. spicilegus, M. macedonicus, M. caroli), 3 subspecies (M. m. musculus, M. m. domesticus, M. m. castaneus), and compared it with 5 CLS. The spectrum of WDS captures long-term mouse evolution, estimated to be over 5 million years ago since the split of M. caroli from the remaining mouse species. All mice are housed in a conventional breeding facility (without a nanofilter barrier or specific-pathogen free condition) at the Institute of Vertebrate Biology, Czech Academy of Sciences, in Studenec. They are maintained under standard conditions: light/dark regime of 14/10 hours, temperatures of 23 ± 1 °C during summer (April-September) and 22 ± 1 °C during winter (October-March), respectively, and relative humidity within 40-70 %. Mice have access to food pellets and tap water ad libitum. Further data on this mouse repository and WDS can be obtained at <a href="https://housemice.cz/en/strains/">https://housemice.cz/en/strains/</a>. Morphological traits were measured in 4335 mice and include body weight, spleen weight, body length, tail length, weight of both ovaries, sperm count, the weight of testes, left epididymis, and seminal vesicles. Reproductive ability was estimated in 87 WDS and 8 CLS. This dataset was obtained from 90,077 offspring born to 8,298 mothers in 17,049 litters recorded in Studenec studbooks between 2000 and 2023. Reproductive performance was characterized by litter size, newborn mortality (calculated as the proportion of stillborn or cannibalized mice across all litters), and the number of generations produced per year. We also estimated the time since a WDS was established from wild progenitors until completing 20 generations of strict brother-sister mating, i.e., the generation at which a strain of mice can be considered inbred. Although CLS resemble M. m. domesticus and M. m. musculus WDS, they differ from them in 8 and 11 out of 15 phenotypic traits, respectively. The data suggest that WDS can be a useful tool in evolutionary studies, providing a basis for comparative analyses with other mammal taxa, particularly classical laboratory mice. The detected stunning phenotypic variation supplemented by genetic variation have great potential for medical applications.

Figure 5 in Contributions to the wild bee fauna in Argentina (Hymenoptera: Anthophila)

Figure 5. Georeferenced new records of bee species for Argentina. The Ecoregions corresponding to each record are presented. Symbols represent localities with more than one new record: Star = Parque Nacional Iguazú; Plus = M. Belgrano; Diamond = Loreto; Triangle = Pueblo Liebig.

Figure 1 in Contributions to the wild bee fauna in Argentina (Hymenoptera: Anthophila)

Figure 1. (A-D) Callonychium (Callonychium) petuniae Cure & Wittmann male. (E-G) Melitoma danunciae Oliveira & Engel female. (H-J) Gaesischia (Gaesischia) nigra Moure female. A, E, H = head in frontal view. B, G, J = lateral view. B, C = S3 and T7. f = basitial plate. i = metasoma in dorsal view. Scale bars: 1 mm.

Figure 4 in Contributions to the wild bee fauna in Argentina (Hymenoptera: Anthophila)

Figure 4. (A, B) Pseudaugochlora callaina Almeida female. (C, D) Rhectomia catarina Gonçalves female. (E-G) Thectochlora hamata Gonçalves & Melo female. (H, I) Bothranthidium lauroi Moure female. A, C, E, H = head in frontal view. B, G, I = lateral view. D = mesoscutum in dorsal view. F = foreleg trochanter. Scale bars: 1 mm.

Figure 2 in Contributions to the wild bee fauna in Argentina (Hymenoptera: Anthophila)

Figure 2. (A, B) Trichocerapis mirabilis (Smith) female. (C, D) Hylaeus bertonii (Schrottky) female. (E, F) Hy. paradoxus (Schrottky) female. (G, H) Hy. polybiaeformis (Schrottky) female. A, G = head in frontal view. B, D, F, H = lateral view. C, E = mesoscutum in dorsal view. Scale bars: 1 mm.

opencc-zeroDec 2023View details →

Winter feeding preferences and personality vary with territory characteristics in wild great tits

Differences in habitat characteristics experienced during rearing associate with variation in a range of behavioral phenotypes such as exploratory behavior, foraging behavior and food preference. The habitat-dependent selection hypothesis predicts that animals develop behavioral characteristics fitted to their rearing environment. Yet, little is known about how habitat characteristics during rearing shape how animals face winter conditions and adjust their winter foraging behavior. The aim of this study was to explore how fine-scale rearing habitat characteristics associate with exploratory behavior, food selection and foraging performance during winter. For this, we measured habitat characteristics during the breeding season in territories of wild great tits (Parus major), and tested first-year juvenile birds that fledged from these territories for exploratory and foraging behavior at feeders during winter. We found evidence that faster explorers were raised in territories with lower quality-related habitat characteristics. In addition, fast exploring fledglings visited the feeders significantly more (total visits). Moreover, the rearing environment, via caterpillar availability and tree species composition, determined diet selection during winter in first year birds. These results show support for the habitat-dependent selection hypothesis, since exploratory behavior as well as food preferences during winter associate with habitat features of the rearing territories during development. This pattern can be caused either by the kinds of foods prevalent at these sites or because of intrinsic individual differences. Further experiments are needed to disentangle these two.

opencc-zeroApr 2024View details →

Data from: genetic evidence of differential dispersal pattern in Asiatic wild dog: comparing populations with different pack size and tiger densities

Dispersal is a multi-causal, crucial life-history event in shaping the genetic and behavioral structure of mammals. We assessed the dispersal pattern of dholes aka Asiatic wild dog (Cuon alpinus), a social monogamous mammal at two tiger reserves of Maharashtra with different degrees of pack size and competition with tigers i.e. Tadoba-Andhari (TATR, smaller pack size, higher tiger density) and Nawegaon-Nagzira (NNTR, larger pack size, lower tiger density). We used the microsatellite data of 174 individual genotypes (98 males and 67 females) to assess the dispersal pattern of dholes from two populations with varying pack size, tiger density, and landscape connectivity using gene flow as a proxy. We compared the population structure, pairwise F statistics, assignment index, and relatedness across a spatial scale. Overall, the results suggested a difference in sex-bias dispersal pattern for the two sub-populations, exhibiting significant results for female-biased dispersal in the TATR population with a smaller pack size and higher tiger density. Our study highlights the variability in sex-biased dispersal patterns in two different populations which could be the consequence of different variables such as pack size, tiger density, and geographical scale. The study warrants further quantitative investigation including several factors including individual behavior, pack composition, pack size, tiger density, etc. In the present Anthropocene era, determining the sex bias in dispersal patterns for a short-range, pack-living carnivore will help in devising an effective conservation management plan for their long-term survival.

opencc-by-4.0Apr 2024View details →

Evaluation of the immunostimulant effect of microvesicles of Lactobacillus acidophilus isolated from wild Rattus norvegicus.

Lactic acid bacteria are components of the microbiota of the gastrointestinal tract in both humans and animals and are widely used as probiotics. The bacterial strain Lactobacillus sp. is the most related to probiotic activity and released membrane microvesicles (MVs). Some of their primary functions are to carry and transmit antigens to the host tissues and modulate the host defense responses. In the present study, Lactobacillus acidophilus was isolated from the ileum of free-living Rattus norvegicus to evaluate the immunostimulant effect of their MVs in two biological models. MVs from L. acidophilus were characterized using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, electron microscopy, and nanoparticle tracking analysis. The immunostimulant effect of MVs from L. acidophilus on ovine abomasal explants, previously stimulated with 30 µg/1h of MVs and subsequently challenged with third-stage larvae (L3) of Haemonchus contortus, was probed, demonstrating a decrease in the percentage of larvae association, and favoring the migration of inflammatory cells to the infection site. In contrast, cells line of the RAW 264.7 were stimulated by 10 µg/3h of MVs from L. acidophilus to evaluate their activation through the expression of transcripts coding for IL-1β and TNF-α. In both cases, the immunostimulatory effects of MVs from L. acidophilus isolated from free-living R. norvegicus were verified, demonstrating that these structures are capable of immunostimulated the evaluated biological models and could carried important antigen that can be considerate in a formulation to promote the intestinal health in livestock production.  The present study is the first report of MVs secreted by L. acidophilus isolated from free-living R. norvegicus caring that this rodent is resistant to many bacterial pathogens that normally affect the gastrointestinal tract of other mammals. In the atachment file we present the data obtained of the porcentage of asocciation and porcentage of mortality of L3 stage larvae from H. contortus in abomasal tissue stimulated with microvesicles from L. acidophilus. In the other hand the expression of IL-1β and TNFα.  mRNA from RAW 264.7 cells stimulated with microvesicles from L. acidophilus.

opencc-by-4.0Dec 2023View details →

Figure 6 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)

Figure 6 – Location of Tswalu Kalahari in southern Africa.

opencc-by-4.0Dec 2023View details →

Non-targeted metabolomics-based molecular networking enables the chemical characterization of Rumex sanguineus, a wild edible plant

This dataset delves into the chemical composition of Rumex sanguineus employing non-targeted metabolomics and Feature-Based Molecular Networking (FBMN), with compound annotation facilitated by SIRIUS. Utilizing UHPLC-HRMS, we conducted comprehensive analyses on samples extracted from Rumex roots, stems, and leaves, further enhancing our insights through molecular networking.

opencc-by-4.0Mar 2024View details →

Dataset for Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic

Dataset for Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic Code used for plotting of main figures and quantifying allelic shifts attached in the GitHub repository CareyMetheringham/MardenPark. Additional files for analysis of GEBV shifts between adults and juveniles, estimation of heritability, trends in green up and simulations of allelic shifts included as: <ul> <li>GEBV-regression.Rmd</li> <li>heritabilityEst.R</li> <li>GreeningAnalysis.R</li> <li>Simulated_selection_analysis.Rmd</li> <li>Distinguishing the effects of selection from genetic drift.pdf</li> </ul> Data files: <ul> <li>S1 - phenotypic measurements for adult and juvenile trees</li> <li>S2 - Effect sizes for SNPs used to calculate GEBV</li> <li>S3 - Allelic frequencies of sites used to calculate GEBV</li> <li>related_trees.csv - Predicted parentage of trees</li> <li>gebv_model_df.csv - Data used for greenup calculations in GreeningAnalysis.R</li> <li>maf1.pass2.miss25.snps.only.LD.vcf - Filtered file of high MAF SNPs used for parentage estimation</li> <li>unlinked_sites.csv - unlinked sites used in GEBV-regression.Rmd</li> <li>ebv_table_10000_250 - table of estimated breeding values in field trial populatio, used for heritability estimation</li> <li>MP_eefects_MIA_and_MAA.csv - Data for plotting Figure 3 - Estimated effect size of the major and minor allele, plus standard error on the estimate</li> </ul>

opencc-by-4.0Jun 2024View details →

Reconciling community-level responses of wild bees to highly anthropized landscapes

Data and source code for the analyses described in the manuscript.

opencc-by-4.0Oct 2024View details →

Data on the occurrence on anisakids and other parasites in fishery products from wild and farmed fish in all countries (Jan 2010 – Sept 2023)

This file contains data on anisakids and other parasites in fishery products from wild and farmed fish in all countries, covering studies published between January 2010 and September 2023. The systematic review protocol used to identify and extract the information is available at <a href="https://zenodo.org/records/10270810"> https://zenodo.org/records/10270810</a>. For data on anisakids for the period 2010-2020, this file is complementary to the zenodo file https://zenodo.org/records/14047972, and includes publications that were not selected in published meta-analyses.

opencc-zeroOct 2021View details →

Supplementary material and data from: Cranial volume and palate length of cats, Felis spp., under domestication, hybridisation and in wild populations

Reduced brain size, compared with wild individuals, is argued to be a key characteristic among domestic mammal species, and is often thought to be a component of the "domestication syndrome". However, brain size comparisons are often based on old, inaccessible literature and in some cases drew comparisons between domestic animals and wild species that are no longer thought to represent the true progenitor species of the domesticated variant in question. Here we set out to replicate results concerning cranial volumes in domestic cats that were published in the 1960s and 1970s and compared wildcats, domestic cats and their hybrids. In light of new research and ideas surrounding domestication and its effects on domestic animals a replication of these studies is highly relevant. Apart from replicating these studies we also present new data on palate length in Felis cat skulls. Here we provide all data (both new and old digitzed data) upon which we based the analysis discussed in this manuscript. We further provide a link to the code used in the analysis.

opencc-zeroOct 2021View details →

Data from: The birth hour of mammals: insights from intra-specific variation in wild blue monkeys

While most mammals show birth hour peaks at times of the 24-hour cycle when they are less active, there are exceptions to this general pattern. Such exceptions have been little explored, but may clarify evolutionary reasons for the diel timing of births. We investigated intraspecific variation in birth hour in wild blue monkeys (Cercopithecus mitis stuhlmanni), a diurnal primate, to identify factors that differentiated daytime vs. nighttime births. Behavioral and life history data from 14 groups over 14 years revealed that 4% of 484 births occurred during the day. Probability of daytime birth varied with mother's age, peaking at 15.7 years. Births whose annual timing deviated most from the population's peak birth months were five times more likely to occur during daytime than those that deviated less. There was no evidence that mother's rank or infant sex influenced birth hour, and mixed evidence that daytime births were more probable in larger groups. Survivorship did not differ significantly for infants born during the day vs. night. Prime-aged mothers may be able to handle the consequences of an unusual birth hour more successfully than mothers with less experience or those weakened by age. Daytime birth may be more advantageous in the off-season because nights are colder at that time of year. These findings are consistent with hypotheses relating birth hour to the risk of losing social protection in group-living animals, but are not consistent with those emphasizing risk of conspecific harassment. Patterns of within-species variation can help in evaluating evolutionary hypotheses for non-random birth hour.

opencc-zeroNov 2021View details →

Genomic prediction in the wild: a case study in Soay sheep

Genomic prediction, the technique whereby an individual's genetic component of their phenotype is estimated from its genome, has revolutionised animal and plant breeding and medical genetics. However, despite being first introduced nearly two decades ago, it has hardly been adopted by the evolutionary genetics community studying wild organisms. Here, genomic prediction is performed on eight traits in a wild population of Soay sheep. The population has been the focus of a >30 year evolutionary ecology study and there is already considerable understanding of the genetic architecture of the focal Mendelian and quantitative traits. We show that the accuracy of genomic prediction is high for all traits, but especially those with loci of large effect segregating. Five different methods are compared, and the two methods that can accommodate zero-effect and large-effect loci in the same model tend to perform best. If the accuracy of genomic prediction is similar in other wild populations, then there is a real opportunity for pedigree-free molecular quantitative genetics research to be enabled in many more wild populations; currently the literature is dominated by studies that have required decades of field data collection to generate sufficiently deep pedigrees. Finally, some of the potential applications of genomic prediction in wild populations are discussed.