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558 results for “wild populations”
Data from: The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries)
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Supplementary material and data from: Cranial volume and palate length of cats, Felis spp., under domestication, hybridisation and in wild populations
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Data from: Can dominance genetic variance be ignored in evolutionary quantitative genetic analyses of wild populations?
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Data from: Mortality, perception, and scale: understanding how predation shapes space use in a wild prey population
Attempts to assess behavioral responses of prey to predation risk are often confounded by depredation of prey. Moreover, the scale at which the response of prey is assessed has important implications for discovering how predation risk alters prey behavior. Herein, we assessed space use of wild Ring-necked Pheasants (Phasianus colchicus) in response to spatial and temporal variation in recreational hunting. We radio-marked pheasants and monitored space use at two spatial scales: short-term seasonal home range, and nightly resting locations. Additionally, we considered temporal variation in predation risk by monitoring space use prior to and during the pheasant hunting season. Although we found no change in nightly resting location, pheasants subjected to predation risk expanded their home range and shifted home range location even when invulnerable to predation. Home range formation was plastic, with home ranges expanding and contracting as risk fluctuated before and during the hunting season. Depredation reduced the measured response within the population, obscuring the potential importance of perceived predation risk in shaping prey communities, particularly when not measured at the appropriate scale. By assessing space use of a wild prey population at multiple scales, considering spatial and temporal variation in predation risk, we show that not only does predation risk affect space use, but that the effects at the population level may be challenging to assess when not measured at the appropriate ecological scale because of the direct effects of differential mortality on the same behaviors.
Limited evidence of cloning and selfing within wild populations of coral-eating crown-of thorns seastar (Acanthaster cf. solaris)
<p>Population outbreaks of crown-of-thorns seastars (CoTS; <i>Acanthaster</i> spp.) are contributing to extensive coral loss and reef degradation throughout the Indo west-Pacific, but the causes and underlying mechanisms of population maintenance and outbreaks are equivocal. Two recent publications suggest that, in addition to outbreeding sexual reproduction, asexual reproduction through larval fission and selfing may contribute to rapid increases in the local abundance of <i>Acanthaster</i> spp. We re-analysed two large microsatellite datasets (collectively representing 3,714 individuals) that investigated connectivity in the Great Barrier Reef and Pacific region to investigate if potential cloning or selfing can be evidenced in the population genetic structure. Within this dataset we identified only a small number (18, < 0.5%) of putative clones (repeated multi locus genotypes). We argue that several of these are due to sampling and processing errors rather than direct evidence of cloning. Analysis of the population genetic structure (i.e., pairwise genetic differences between individuals, deviations from Hardy-Weinberg-Equilibrium, and linkage disequilibrium) also yielded no genetic evidence for asexual reproduction. There was a tendency towards slight heterozygote deficits, so we cannot refute that selfing does occur, but this is mostly likely attributable to sampling artefacts. Although we cannot exclude that asexual reproduction occurs to some extent in <i>Acanthaster</i> populations, we find no evidence that these processes make <span>a</span> contribution to population structure or directly enhance larval supply.</p>
Ecological drivers of African swine fever virus persistence in wild boar populations: insight for control
Environmental sources of infection can play a primary role in shaping epidemiological dynamics, however the relative impact of environmental transmission on host-pathogen systems is rarely estimated. We developed and fit a spatially-explicit model of African swine fever virus (ASFV) in wild boar to estimate what proportion of carcass-based transmission is contributing to the low-level persistence of ASFV in Eastern European wild boar. Our model was developed based on ecological insight and data from field studies of ASFV and wild boar in Eastern Poland. We predicted that carcass-based transmission would play a substantial role in persistence, especially in low-density host populations where contact rates are low. By fitting the model to outbreak data using Approximate Bayesian Computation, we inferred that between 53 to 66% of transmission events were carcass-based – i.e., transmitted through contact of a live host with a contaminated carcass. Model fitting and sensitivity analyses showed that the frequency of carcass-based transmission increased with decreasing host density, suggesting that management policies should emphasize the removal of carcasses and consider how reductions in host densities may drive carcass-based transmission. Sensitivity analyses also demonstrated that carcass-based transmission is necessary for the autonomous persistence of ASFV under realistic parameters. Autonomous persistence through direct transmission alone required high host densities; otherwise re-introduction of virus periodically was required for persistence when direct transmission probabilities were moderately high. We quantify the relative role of different persistence mechanisms for a low-prevalence disease using readily collected ecological data and viral surveillance data. Understanding how the frequency of different transmission mechanisms vary across host densities can help identify optimal management strategies across changing ecological conditions.
Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)
Mitochondrial genomes extracted from wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is a SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study either sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1, atp9 and cox1 found in D. carota individuals collected from 24 populations in the eastern U.S. More than half of the 128 individuals surveyed had a CAA or AAA, rather than TAA, genotype at the position usually thought to function as an atp9 stop codon in this species. We also found no evidence for mitochondrial RNA editing (Cytosine to Uridine) of the CAA stop codon in either floral or leaf tissue. Evidence for intra-genic recombination, as opposed the more common inter-genic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other two genes surveyed, were non-randomly associated with the three atp9 stop codon variants, though further analysis suggested that multi-locus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an Fst of 0.34.
Data from: Polyandry and postcopulatory sexual selection in a wild population
When females mate multiply, postcopulatory sexual selection can occur via sperm competition and cryptic female choice. Although postcopulatory selection has the potential to be a major force in driving evolution, few studies have estimated its strength in natural populations. Likewise, though polyandry is widespread across taxa and is the focus of a growing body of research, estimates of natural female mating rates are still limited in number. Microsatellites can be used to estimate the number of mates represented in females' sperm stores and the number of sires contributing to their offspring, enabling comparisons both of polyandry and of two components of postcopulatory selection: the proportion of males that mate but fail to sire offspring, and the degree of paternity skew among the males that do sire offspring. Here we estimate the number of mates and sires among wild females in the Hawaiian swordtail cricket Laupala cerasina. We compare these estimates to the actual mating rates and paternity shares we observed in a semi-natural population. Our results show that postcopulatory sexual selection operates strongly in this species: wild females mated with an average minimum of 3.6 males but used the sperm from only 58% of them. Furthermore, among the males that did sire offspring, paternity was significantly skewed. These patterns were similar to those observed in the field enclosure, where females mated with an average of 5.7 males and used the sperm from 62% of their mates, with paternity significantly skewed among the sires.
Data from: Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population
Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade-off between them, either at the phenotypic or genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker-based approaches - chromosome partitioning, quantitative trait locus (QTL) mapping and a genome-wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome-wide significant QTL, and no individual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, non-significant, negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait.
Data from: Twelve years of repeated wild hog activity promotes population maintenance of an invasive clonal plant in a coastal dune ecosystem
Invasive animals can facilitate the success of invasive plant populations through disturbance. We examined the relationship between the repeated foraging disturbance of an invasive animal and the population maintenance of an invasive plant in a coastal dune ecosystem. We hypothesized that feral wild hog (Sus scrofa) populations repeatedly utilized tubers of the clonal perennial, yellow nutsedge (Cyperus esculentus) as a food source and evaluated whether hog activity promoted the long-term maintenance of yellow nutsedge populations on St. Catherine's Island, Georgia, United States. Using generalized linear mixed models, we tested the effect of wild hog disturbance on permanent sites for yellow nutsedge culm density, tuber density, and percent cover of native plant species over a 12-year period. We found that disturbance plots had a higher number of culms and tubers and a lower percentage of native live plant cover than undisturbed control plots. Wild hogs redisturbed the disturbed plots approximately every 5 years. Our research provides demographic evidence that repeated foraging disturbances by an invasive animal promote the long-term population maintenance of an invasive clonal plant. Opportunistic facultative interactions such as we demonstrate in this study are likely to become more commonplace as greater numbers of introduced species are integrated into ecological communities around the world.
Data from: Mhc-linked survival and lifetime reproductive success in a wild population of great tits
Major histocompatibility complex (Mhc) genes are frequently used as a model for adaptive genetic diversity. Although associations between Mhc and disease resistance are frequently documented, little is known about the fitness consequences of Mhc variation in wild populations. Further, most work to date has involved testing associations between Mhc genotypes and fitness components. However, the functional diversity of the Mhc, and hence the mechanism by which selection on Mhc acts, depends on how genotypes map to the functional properties of Mhc molecules. Here, we test three hypotheses that relate Mhc diversity to fitness: (1) the maximal diversity hypothesis; (2) the optimal diversity hypothesis, and (3) effect of specific Mhc types. We combine mark-recapture methods with analysis of long-term breeding data to investigate the effects of Mhc class I functional diversity (Mhc supertypes) on individual fitness in a wild great tit (Parus major) population. We found that the presence of three different Mhc supertypes was associated with three different components of individual fitness: survival, annual recruitment and lifetime reproductive success (LRS). Great tits possessing Mhc supertype 3 experienced higher survival rates than those that did not, whereas individuals with Mhc supertype 6 experienced higher LRS and were more likely to recruit offspring each year. Conversely, great tits that possessed Mhc supertype 5 had reduced LRS. We found no evidence for a selective advantage of Mhc diversity, either in terms of maximal or optimal supertype diversity. Our results support the suggestion that specific Mhc types are an important determinant of individual fitness.
Data from: Partitioning of genetic variation across the genome using multimarker methods in a wild bird population
The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high-density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex-, age- and environment-specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems.
Data from: Slower senescence in a wild insect population in years with a more female-biased sex ratio
Life-history theories of senescence are based on the existence of a trade-off in resource allocation between body maintenance and reproduction. This putative trade-off means that environmental and demographic factors affecting the costs of reproduction should be associated with changes in patterns of senescence. In many species, competition among males is a major component of male reproductive investment, and hence variation in the sex ratio is expected to affect rates of senescence. We test this prediction using nine years of demographic and behavioural data from a wild population of the annual field cricket Gryllus campestris. Over these generations the sex ratio at adulthood varied substantially, from years with an equal number of each sex to years with twice as many females as males. Consistent with the predictions of theory, we found that in years with a greater proportion of females, both sexes experienced a slower increase in mortality rate with age. Additionally, phenotypic senescence in males was slower in years when there were more females. Sex ratio did not affect the baseline mortality rate in males, but females suffered higher age-independent mortality rates when males were in short supply.
Data from: Estimated six percent loss of genetic variation in wild populations since the industrial revolution
Genetic variation is fundamental to population fitness and adaptation to environmental change. Human activities are driving declines in many wild populations and could have similar effects on genetic variation. Despite the importance of estimating such declines, no global estimate of the magnitude of ongoing genetic variation loss has been conducted across species. By combining studies that quantified recent changes in genetic variation across a mean of 27 generations for 91 species, we conservatively estimate a 5.4-6.5% decline in within-population genetic diversity of wild organisms since the industrial revolution. This loss has been most severe for island species, which show a 30% average decline. We identified taxonomic and geographic gaps in temporal studies that must be urgently addressed. Our results are consistent with single time-point meta-analyses, which indicated that genetic variation is likely declining. However, our results represent the first confirmation of a global decline, and provide an estimate of the magnitude of the genetic variation lost from wild populations.
Data from: Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern
Deleterious recessive alleles that are masked in outbred populations are predicted to be expressed in small, inbred populations, reducing both individual fitness and population viability. However, there are few definitive examples of phenotypic expression of lethal recessive alleles under inbreeding conditions in wild populations. Studies that demonstrate the action of such alleles, and infer their distribution and dynamics, are required to understand their potential impact on population viability and inform management responses. The Scottish population of red-billed choughs (Pyrrhocorax pyrrhocorax), which currently totals <60 breeding pairs and is of major conservation concern, has recently been affected by lethal blindness in nestlings. We used family data to show that the pattern of occurrence of blindness within and across affected families that produced blind nestlings was exactly 0·25, matching that expected given a single-locus autosomal lethal recessive allele. Furthermore, the observed distribution of blind nestlings within affected families did not differ from that expected given Mendelian inheritance of such an allele. Relatedness estimates showed that individuals from affected families were not more closely related to each other than they were to individuals from unaffected families that did not produce blind nestlings. Blind individuals tended to be less heterozygous than non-blind individuals, as expected if blindness was caused by the expression of a recessive allele under inbreeding. However, there was no difference in the variance in heterozygosity estimates, suggesting that some blind individuals were relatively outbred. These results suggest carriers of the blindness allele may be widely distributed across contemporary families rather than restricted to a single family lineage, implying that the allele has persisted across multiple generations. Blindness occurred at low frequency (affecting 1·6% of observed nestlings since 1981). However, affected families had larger initial brood sizes than unaffected families. Such high fecundity of carriers of a lethal recessive allele might reflect overdominance, potentially reducing purging and increasing allele persistence probability. We thereby demonstrate the phenotypic expression of a lethal recessive allele in a wild population of conservation concern, and provide a general framework for inferring allele distribution and persistence and informing management responses.
Data from: An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population
Because of their high variability, microsatellites are still considered the marker of choice for studies on parentage and kinship in wild populations. Nevertheless, single nucleotide polymorphisms (SNPs) are becoming increasing popular in many areas of molecular ecology, owing to their high-throughput, easy transferability between laboratories and low genotyping error. An ongoing discussion concerns the relative power of SNPs compared to microsatellites – that is, how many SNP loci are needed to replace a panel of microsatellites? Here, we evaluate the assignment power of 80 SNPs (HE=0.30, 80 independent alleles) and 11 microsatellites (HE =0.85, 194 independent alleles) in a wild population of about 400 sockeye salmon with two commonly used software packages (Cervus3, Colony2) and, for SNPs only, a newly developed software (SNPPIT). Assignment success was higher for SNPs than for microsatellites, especially for parent pairs, irrespective of the method used. Colony2 assigned a larger proportion of offspring to at least one parent than the other methods, though Cervus and SNPPIT detected more parent pairs. Identification of full sib groups without parental information from relatedness measures was possible using both marker systems, though explicit reconstruction of such groups in Colony2 was impossible for SNPs because of computation time. Our results confirm the applicability of SNPs for parentage analyses and refute the predictability of assignment success from the number of independent alleles.
Data from: Temporally variable multivariate sexual selection on sexually dimorphic traits in a wild insect population
A widely held view is that the strength and form of natural selection varies in time and space in response to varying ecological forces; however, adequate quantitative evaluations of this are relatively scarce. In this study, we measured the strength and form of sexual selection acting on a suite of male morphological traits in a wild ambush bug (Phymata americana) population at 10 sampling dates over 2 years. We tested the prediction that the strength and direction of sexual selection would be associated with one or more important ecological variables. We found that patterns of multivariate selection varied considerably over time, and even within a season. Yet, for this population, a sexually dimorphic color pattern trait was consistently a target of directional selection. The strength of sexual selection on this trait was related to both sex ratio and density, which is consistent with the idea that ecological factors can play an important role in generating patterns of sexual selection. We also demonstrate that the median strength of linear selection obtained from replicated cross‐sectional methods was qualitatively similar to the estimates obtained from longitudinal methods, providing multiple lines of evidence that the evolution of sexual color dimorphism in this species is attributable to sexual selection.
Data from: No evidence for MHC class I based disassortative mating in a wild population of great tits
Genes of the major histocompatibility complex (MHC) are regarded as a potentially important target of mate choice due to the fitness benefits that may be conferred to the offspring. According to the complementary genes hypothesis, females mate with MHC dissimilar males to enhance the immunocompetence of their offspring or to avoid inbreeding depression. Here, we investigate whether selection favours a preference for maximally dissimilar or optimally dissimilar MHC class I types, based on MHC genotypes, average amino acid distances and the functional properties of the antigen-binding sites (MHC supertypes); and whether MHC type dissimilarity predicts relatedness between mates in a wild great tit population. In particular, we explore the role that MHC class I plays in female mate choice decisions while controlling for relatedness and spatial population structure, and examine the reproductive fitness consequences of MHC compatibility between mates. We find no evidence for the hypotheses that females select mates on the basis of either maximal or optimal MHC class I dissimilarity. A weak correlation between MHC allele sharing and relatedness, and between MHC supertype sharing and relatedness suggests that MHC dissimilarity at functional variants may not provide an effective index of relatedness. Moreover the reproductive success of pairs did not vary with MHC dissimilarity. Our results provide no support for the suggestion that selection favours, or that mate choice realises, a preference for complimentary MHC types.
When more is not merrier: using wild population dynamics to understand the effect of density on ex situ seahorse mating behaviors
Seahorses are one of the most iconic examples of a monogamous species in the animal kingdom. Documenting monogamous behaviors of seahorses have proven to be quite complicated to study in the wild because of their low population densities and cryptic habits. Another challenge involves interpreting these behaviors in captivity because recreating realistic densities of wild populations in the laboratory can be difficult due to their patchy distributions. This study investigates the relationship between stocking density and mating and competitive behavior from the context of the field biology of the dwarf seahorse, Hippocampus zosterae (Jordan & Gilbert). Animals were housed in 38 liter tanks at a range of densities and sex ratios (from 2-8 animals per tank), and their reproductive and other social behaviors were monitored from tank introduction through copulation. At low tank densities and even sex ratios but comparatively high field densities, activity level in trials was low. A higher level of males in tanks across all densities increased competition, activity levels, and aggression leading to partial egg transfers and failed pregnancies, resulting in lower reproductive success. Across seahorse species, mean and maximum wild densities were consistently lower than those used in captive breeding, with adult sex ratios that were significantly female biased. However, significant variation exists in wild seahorse densities across species, with higher densities detected in focal/mark recapture studies and on artificial habitat structures than reported with belt transect sampling techniques. Interchange of knowledge gained in both captive and wild contexts will allow us to better understand the biology of this genus, and improve reproduction in captivity. Interpreting captive reproductive behaviors of seahorses within various densities reported from natural populations will help us predict the impact of conservation efforts and increase the likelihood of long-term persistence of populations for this threatened genus.
Data from: Does human-induced hybridization have long-term genetic effects? Empirical testing with domesticated, wild and hybridized fish populations
Current conservation practices exclude human-generated hybridized populations from protection, as the genetic effects of hybridization in the wild have been observed to be long-lasting based on neutral genetic markers and are considered potentially irreversible. Theory, however, predicts otherwise for genes under selection. We transplanted combinations of wild, domesticated and hybridized populations of a fish species to new environments. We then compared survival, phenotypic variation and plasticity to determine whether hybridization affects adaptive potential after multiple generations of selection in the wild. Although the fitness of our hybridized populations at the onset of hybridization cannot be assessed, our results suggest that within five to eleven generations, selection can remove introduced foreign genes from wild populations that have hybridized with domesticated conspecifics. The end result is hybridized populations that, in terms of survival, phenotypic plasticity, mean trait expression and overall general responses to environmental change, closely resemble neighbouring wild populations. These results have important implications for considering the potential conservation value of hybridized populations and illustrate the effectiveness of selection in a local environment.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.