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5,538 results for “Population data”
Data from: Population genetic data of a model symbiotic cnidarian system reveal remarkable symbiotic specificity and vectored introductions across ocean basins
The Aiptasia-Symbiodinium symbiosis is a promising model for experimental studies of cnidarian-dinoflagellate associations, yet relatively little is known regarding the genetic diversity of either symbiotic partner. To address this we collected Aiptasia from 17 localities throughout the world and examined the genetic diversity of both anemones and their endosymbionts. Based on newly-developed SCAR markers, Aiptasia consisted of two genetically-distinct populations, one Aiptasia lineage from Florida and a second network of Aiptasia genotypes found at other localities. These populations did not conform to the distributions of described Aiptasia species, suggesting that taxonomic re-evaluation is needed in light of molecular genetics. Associations with Symbiodinium further demonstrated the distinctions among Aiptasia populations. According to 18S-RFLP, ITS2-DGGE, and microsatellite flanker region sequencing, Florida anemones engaged in diverse symbioses predominantly with members of Symbiodinium Clades A and B, but also C, whereas anemones from elsewhere harboured only S. minutum within Clade B. Symbiodinium minutum apparently does not form a stable symbiosis with other hosts, which implies a highly-specific symbiosis. Fine-scale differences among S. minutum populations were quantified using six microsatellite loci. Populations of S. minutum had low genotypic diversity and high clonality (R=0.14). Furthermore, minimal population structure was observed among regions and ocean basins, due to allele and genotype sharing. The lack of genetic structure and low genotypic diversity suggest recent vectoring of Aiptasia and S. minutum across localities. This first ever molecular-genetic study of a globally-distributed cnidarian and its Symbiodinium assemblages reveals host-symbiont specificity and widely-distributed populations in an important model system.
Data from: Ghosts of habitats past: environmental carry-over effects drive population dynamics in novel habitat
The phenotype of adults can be strongly influenced by the environmental conditions experienced during development. Consequently, variation in habitat quality across space and through time also leads to differences in the phenotypes of adults. This could create carry-over effects where differences in the natal habitat quality of colonizers influence population dynamics in new habitats. We tested this hypothesis experimentally by simulating dispersal of Tribolium castaneum from low or high quality natal habitat into new patches of low or high quality habitat. Differences in natal habitat quality of colonizers altered population growth trajectories and led to carrying capacities that differed by up to 85% within a habitat type, indicating that patch dynamics are determined by the interaction of past and current habitat quality. Interestingly, even after multiple generations, natal habitat of colonizers determined differences in adult traits that were related to density-dependent population regulation. These changes in adult phenotype could at least partially explain why carry-over effects continued to alter population dynamics for multiple generations until the end of the experiment. These results highlight the importance of variable habitat quality and carry-over effects for population dynamics.
Data from: Adaptive potential of ash (Fraxinus excelsior) populations against the novel emerging pathogen Hymenoscyphus pseudoalbidus
An emerging infectious pathogen Hymenoscyphus pseudoalbidus has spread across much of Europe within recent years causing devastating damage on European common ash trees (Fraxinus excelsior) and associated plant communities. The present study demonstrates the presence of additive genetic variation in susceptibility of natural F. excelsior populations to the new invasive disease. We observe high levels of additive variation in the degree of susceptibility with relatively low influence of environmental factors (narrow sense heritability = 0.37-0.52). Most native trees are found highly susceptible, and we estimate that only around 1% has the potential of producing offspring with expected crown damage of less than 10% under the present disease pressure. The results suggest that the presence of additive genetic diversity in natural F. excelsior populations can confer the species with important ability to recover, but that low resistance within natural European populations is to be expected due to a low frequency of the hypo-sensitive trees. Large effective population sizes will be required to avoid genetic bottlenecks. The role of artificial selection and breeding for protection of the species is discussed based on the findings.
Data from: Heterogeneity of genetic architecture of body size traits in a free-living population
Knowledge of the underlying genetic architecture of quantitative traits could aid in understanding how they evolve. In wild populations, it is still largely unknown whether complex traits are polygenic or influenced by few loci with major effect, due to often small sample sizes and low resolution of marker panels. Here, we examine the genetic architecture of five adult body size traits in a free-living population of Soay sheep on St Kilda using 37 037 polymorphic SNPs. Two traits (jaw and weight) show classical signs of a polygenic trait: the proportion of variance explained by a chromosome was proportional to its length, multiple chromosomes and genomic regions explained significant amounts of phenotypic variance, but no SNPs were associated with trait variance when using GWAS. In comparison, genetic variance for leg length traits (foreleg, hindleg and metacarpal) was disproportionately explained by two SNPs on chromosomes 16 (s23172.1) and 19 (s74894.1), which each explained >10% of the additive genetic variance. After controlling for environmental differences, females heterozygous for s74894.1 produced more lambs and recruits during their lifetime than females homozygous for the common allele conferring long legs. We also demonstrate that alleles conferring shorter legs have likely entered the population through a historic admixture event with the Dunface sheep. In summary, we show that different proxies for body size can have very different genetic architecture and that dense SNP helps in understanding both the mode of selection and the evolutionary history at loci underlying quantitative traits in natural populations.
Data from: Patterns of diversity and spatial variability of β-defensin innate immune genes in a declining wild population of tree swallows
Assessing the genetic variation and distribution of immune genes across heterogeneous environmental conditions in wild species is essential to further our understanding of the role of pathogen pressure and potential resistance or prevalence in hosts. Researchers have recently investigated β-defensin genes in the wild, because their variability suggests that they may play an important role in innate host defense. This study investigated the variation occurring at 6 innate immune genes of the β-defensin family in a declining population of tree swallows (Tachycineta bicolor) in southern Québec, Canada (N = 160). We found that all 6 genes showed synonymous and nonsynonymous single nucleotide polymorphisms (SNPs) within the exon coding for the mature peptide. These results indicated that this group of genes was diverse in tree swallows. Our results suggested a potential interaction of this group of genes with fluctuating pathogen diversity, however, we found no sign of positive or negative selection. We assessed whether or not the distribution of genetic diversity of β-defensin genes in our study population differed between 2 regions that strongly differ in their level of agricultural intensification. Adults are highly philopatric to their breeding sites and their immunological responses differ between these 2 regions. However, we found little evidence that the level and distribution of genetic variability differed between these heterogeneous environmental conditions. Further studies should aim to assess the link between genetic diversity of β-defensin genes and fitness-related traits in wild populations.
Data from: A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations
Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artefacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.
Data from: Fine-scale population dynamics in a marine fish species inferred from dynamic state-space models
Identifying the spatial scale of population structuring is critical for the conservation of natural populations and for drawing accurate ecological inferences. However, population studies often use spatially aggregated data to draw inferences about population trends and drivers, potentially masking ecologically relevant population sub-structure and dynamics. The goals of this study were to investigate how population dynamics models with and without spatial structure affect inferences on population trends and the identification of intrinsic drivers of population dynamics (e.g. density dependence). Specifically, we developed dynamic, age-structured, state-space models to test different hypotheses regarding the spatial structure of a population complex of coastal Atlantic cod (Gadus morhua). Data were from a 93-year survey of juvenile (age 0 and 1) cod sampled along >200 km of the Norwegian Skagerrak coast. We compared two models: one which assumes all sampled cod belong to one larger population, and a second which assumes that each fjord contains a unique population with locally determined dynamics. Using the best supported model, we then reconstructed the historical spatial and temporal dynamics of Skagerrak coastal cod. Cross-validation showed that the spatially structured model with local dynamics had better predictive ability. Furthermore, posterior predictive checks showed that a model which assumes one homogeneous population failed to capture the spatial correlation pattern present in the survey data. The spatially structured model indicated that population trends differed markedly among fjords, as did estimates of population parameters including density-dependent survival. Recent biomass was estimated to be at a near-record low all along the coast, but the finer scale model indicated that the decline occurred at different times in different regions. Warm temperatures were associated with poor recruitment, but local changes in habitat and fishing pressure may have played a role in driving local dynamics. More generally, we demonstrated how state-space models can be used to test evidence for population spatial structure based on survey time-series data. Our study shows the importance of considering spatially structured dynamics, as the inferences from such an approach can lead to a different ecological understanding of the drivers of population declines, and fundamentally different management actions to restore populations.
Data from: Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs
Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single-nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine-scale structure. In Hudson Bay, Canada, three polar bear (Ursus maritimus) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark–recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine-scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western—including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern—individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast—individuals from SH (Akimiski Island in James Bay); and (iv) Northeast—individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine-scale population delineation in polar bears.
Data from: Population density and size influence pollen dispersal pattern and mating system of the predominantly outcrossed Banksia nivea (Proteaceae) in a threatened ecological community
Gene flow is a critical component of plant mating systems and influences population fitness, yet pollen dispersal can be highly variable and influenced by natural and anthropogenic fragmentation. Gene flow through pollen dispersal was investigated in two populations of contrasting size and habitat context in Banksia nivea ssp. uliginosa, a rare species in the Busselton ironstone threatened ecological community with a naturally fragmented distribution. Paternity analysis was conducted with seven microsatellite loci to determine mating system parameters and patterns of pollen dispersal. Outcrossing was high in both populations with a similar level of selfing for both populations despite differences in population size, density and vegetation matrix. Most mating occurred within 10 m of a mother plant in the small, clumped population, while more dispersed mating, up to 50 m from a mother plant, was recorded in the large, less dense population. Our results show that population density and size are important influences on mating system parameters and level of pollen dispersal.
Data from: Does population distribution matter? Influence of a patchy versus continuous distribution on genetic patterns in a wind-pollinated shrub
Aim: Uniform spatial population distributions are predicted to result in lower among-population genetic differentiation and higher within-population genetic diversity than naturally patchy distributions, but there have been surprisingly few attempts to isolate this effect from confounding factors. We studied the widespread wind-pollinated shrub Allocasuarina humilis that is common in a geologically-stable landscape characterised by long-term population persistence to test the influence of semi-continuous versus patchy population distributions on genetic patterns. We also investigated whether A. humilis shows the high population connectedness and genetic diversity typically associated with wind pollination, a relatively uncommon and little-studied syndrome in this landscape. Location: Heath-shrublands ('heath') and forests of south-western Australia. Methods: Populations were sampled from heath and forest regions, which respectively exhibited semi-continuous and patchy population distributions. Genetic structure and diversity were assessed for 27 populations using eight nuclear microsatellite markers and three chloroplast regions. Phylogeographic history was examined using Bayesian phylogeny reconstruction, parsimony analysis and tests of expansion. Results: High haplotype diversity is consistent with long-term population persistence across most of the species' range. Nuclear markers showed low overall population differentiation and no geographical structure over ~900 km, reflecting extensive pollen dispersal. For both marker types, patchily-distributed forest populations were substantially more differentiated with significantly lower within-population diversity than semi-continuous heath populations. Phylogeographic analysis revealed evidence for earlier colonization of heath than forest and recent expansion into wetter forests, consistent with progressive long-term climatic drying. Main conclusions: High population connectedness and genetic diversity probably resulted from wind pollination in combination with dioecy and long life span. Patchy population distributions appear to have influenced genetic structure and diversity through lower pollen and seed dispersal, lower effective population sizes and greater genetic drift. Our approach illustrates the value of minimising confounding variables by testing the effect of a variable ecological trait within a single species.
Data from: Recovery of native genetic background in admixed Populations Using haplotypes, phenotypes, and pedigree information – using Cika cattle as a case breed
The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.
Data from: Breakdown of gametophytic self-incompatibility in subdivided populations
In many hermaphroditic flowering plants self-fertilization is prevented by self-incompatibility (SI), often controlled by a single locus, the S-locus. In single isolated populations, the maintenance of SI depends chiefly on inbreeding depression and the number of SI alleles at the S-locus. In subdivided populations, however, population subdivision has complicated effects on both the number of SI alleles and the level of inbreeding depression, rendering the maintenance of SI difficult to predict. Here, we explore the conditions for the invasion of a self-compatible mutant in a structured population. We find that the maintenance of SI is strongly compromised when a population becomes subdivided. We show that this effect is mainly caused by the decrease of the local diversity of SI alleles rather than by a change in the dynamics of inbreeding depression. Strikingly, we also find that the diversity of SI alleles at the whole population level is a poor predictor of the maintenance of SI. We discuss the implications of our results for the interpretation of empirical data on the loss of SI in natural populations.
Data from: Genetic variation in variability: phenotypic variability of fledging weight and its evolution in a songbird population
Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation that within-family variance can be heritable. For offspring traits, such as birth weight, this implies that within-family variance in traits can vary among families and can thus be shaped by natural selection. Empirical evidence for this in wild populations is however lacking. We investigated whether within-family variance in fledging weight is heritable in a wild great tit (Parus major) population and whether these differences are associated with fitness. We found significant evidence for genetic variance in within-family variance. The genetic coefficient of variation (GCV) was 0.18 and 0.25, when considering fledging weight a parental or offspring trait, respectively. We found a significant quadratic relationship between within-family variance and fitness: families with low or high within-family variance had lower fitness than families with intermediate within-family variance. Our results show that within-family variance can respond to selection and provides evidence for stabilizing selection on within-family variance.
Data from: High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans) populations
Range expansion is a widespread biological process, with well described theoretical expectations for the genomic outcomes accompanying the colonization of novel ranges. However, comparatively few empirical studies address the genome-wide consequences associated with the range expansion process, particularly in recent or on-going expansions. Here, we assess two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been under selection during range expansion. Using a restriction enzyme assisted sequencing approach (RADseq), we genotyped 394 coyotes at 22,935 SNPs and found that overall population structure corresponded to their 19th century historical range and two distinct populations that expanded during the 20th century. Counter to theoretical expectations for populations to bottleneck during range expansions, we observed minimal evidence for decreased genomic diversity across coyotes sampled along either expansion front, which is likely due to hybridization with other Canis species. Furthermore, we identified 12 SNPs, located either within genes or putative regulatory regions, that were consistently associated with range expansion. Of these 12 genes, three (CACNA1C, ALK, and EPHA6) have putative functions related to dispersal, including habituation to novel environments and spatial learning, consistent with the expectations for traits under selection during range expansion. Although coyote colonization of eastern North America is well-publicized, this study provides novel insights by identifying genes associated with dispersal capabilities in coyotes on the two eastern expansion fronts.
Data from: Population history provides foundational knowledge for utilizing and developing native plant restoration materials
A species' population structure and history are critical pieces of information that can help guide the use of available native plant materials in restoration treatments and decide what new native plant materials should be developed to meet future restoration needs. In the western United States, Pseudoroegneria spicata (bluebunch wheatgrass; Poaceae) is an important component of grassland and shrubland plant communities and commonly used for restoration due to its drought resistance and competitiveness with exotic weeds. We used next-generation sequencing data to investigate the processes that shaped P. spicata's geographic pattern of genetic variation across the Intermountain West. Pseudoroegneria spicata's genetic diversity is partitioned into populations that likely differentiated since the Last Glacial Maximum. Adjacent populations display varying magnitudes of historical gene flow, with migration rates ranging from multiple migrants per generation to multiple generations per migrant. When considering the commercial germplasm sources available for restoration, genetic identities remain representative of the wildland localities from which germplasm sources were originally developed, and they maintain high levels of heterozygosity and nucleotide diversity. However, the commercial germplasm sources represent a small fraction of the overall genetic diversity of P. spicata in the Intermountain West. Given the low migration rates and long divergence times between some pairs of P. spicata populations, using commercial germplasm sources could facilitate undesirable restoration outcomes when used in certain geographic areas, even if the environment in which the commercial materials thrive is similar to that of the restoration site. As such, population structure and history can be used to provide guidance on what geographic areas may need additional native plant materials so that restoration efforts support species and community resilience and improve outcomes.
Data from: Assessment of mesophotic coral ecosystem connectivity for proposed expansion of a marine sanctuary in the northwest Gulf of Mexico: population genetics
While there are several areas containing shallow coral habitats in the Gulf of Mexico (GOM), the availability of suitable reef habitat at mesophotic depths (~30–150 m) along the continental shelf margin suggests the potential for ecologically connected coral populations across hundreds of kilometers in the northwest (NW) GOM. The NW GOM includes a relatively high proportion of mesophotic habitats, including salt diapirs in Flower Garden Banks National Marine Sanctuary (FGBNMS), Bright Bank, and McGrail Bank, the latter two being Habitat Areas of Particular Concern (HAPCs). In response to a proposed expansion plan for the sanctuary boundaries to include additional mesophotic banks in the NW GOM, we investigated the genetic connectivity of the depth-generalist coral Montastraea cavernosa, a ubiquitous member of scleractinian communities throughout the Tropical Western Atlantic. Montastraea cavernosa populations in the NW GOM demonstrated strong connectivity with relatively high levels of gene flow and no significant genetic differentiation occurring over banks up to 120 km apart. Historical migration models based on genetic data predicted panmixia of M. cavernosa across the NW GOM. The comparisons between genetic and biophysical models (see Garavelli et al., 2018; associate manuscript) highlight not only the importance of incorporating multiple assessments of connectivity into management schemes, but also the potentially stochastic nature of oceanographic patterns in the NW GOM and their effect on migration estimates among coral habitats. These trends indicate that M. cavernosa populations have remained well-connected in the NW GOM and that coral populations on each bank have likely been receiving larval recruitment through time. Thus, M. cavernosa populations should be managed as a combined unit within the NW GOM, which supports the proposal to expand the NMS boundaries to include mesophotic habitats beyond West and East FGB.
Data from: Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps
Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here we examine genome-wide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST–based analyses. We tested only the most strongly differentiated SNPs for associations with a non-redundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genome-wide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.
Data from: Maternal lineages in native Canadian equine populations and their relationship to the Nordic and Mountain and Moorland pony breeds
A 378-bp section of the mitochondrial displacement loop was used to estimate genetic diversity in the native Canadian equine populations. The inclusion of 10 Mountain and Moorland, 3 Nordic pony breeds, 2 feral populations, and 5 horse breeds were also investigated as they may have influenced the development (or rejuvenation) of the native Canadian populations. A total of 281 samples were sequenced, which produced 75 haplotypes derived from 54 informative sites. On further investigation, 36 of these 75 haplotypes were found to be previously unreported. Overall, total diversity was lowest in the feral Sable Island population with a haplotype diversity (0.27 ± 0.12), nucleotide diversity (0.0007 ± 0.0004), and pairwise difference of 0.286 ± 0.317. This is not surprising due to the geographic isolation of this population. Haplotype diversity was highest (1.00 ± 0.13) in the New Forest population, pairwise difference was highest (8.061 ± 4.028) in the Icelandic breed, whereas nucleotide diversity was highest in the Exmoor breed (0.0209 ± 0.0025). Within the Canadian populations, haplotype diversity was highest in the Newfoundland pony (0.96 ± 0.08), whereas pairwise difference and nucleotide diversity was highest in the Canadian horse (7.090 ± 3.581 and 0.0188 ± 0.0042, respectively). Three different estimates of genetic distances were used to examine the phylogenetic relationships amongst these populations. All 3 estimates produced similar topologies. In general, the native Canadian populations were highly represented in the D clade, with particular emphasis in the D1 and D2 clades. This is an important factor when considering the phylogenetic conservation of these Canadian equine populations.
Data from: Effects of fire regime on the population genetics of natural pine stands, in Genetic structure of forest trees in biodiversity hotspots at different spatial scales (Ph.D. thesis).
The recurrence of wildfires is predicted to increase worldwide due to climate change, resulting in severe impacts on biodiversity and ecosystem functioning. We used simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers to examine the effects of fire regime on genetic diversity, demographic history and fine-scale spatial genetic structure (SGS) of Pinus pinaster and P. halepensis, two conifers with similar adaptations to fire in the eastern Iberian Peninsula. Stands growing under high (HiFi) or low (LoFi) frequency of crown fires had similar levels of genetic diversity and similar demographic history, with bottlenecks detected in all stands in both species. HiFi populations were not genetically depleted, suggesting that adaptations such as a diverse canopy seed bank due to serotinous cones, an early age of first flowering and high gene flow buffer against possible reductions of genetic diversity. Significantly stronger SGS at SNPs in HiFi than LoFi stands of P. halepensis suggested fire-related altered dispersal possibly combined with microenvironmental selection in this fire-sensitive "seeder" species. In contrast, SGS at SNP markers was unrelated to fire regime in P. pinaster. This could be a consequence of more pronounced fire-resistance in this species enabling some adults to survive fire, hence causing a lower dependence on post-fire regeneration. Our results highlight that the impact of fire differs in species with similar life-history traits. Therefore, species-specific studies are needed to understand the role of wildfires for the evolution of future forests
Data from: Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the Malagasy focus
Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar.
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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.