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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.
Data from: Influence of landscape features on the microgeographic genetic structure of a resident songbird.
Landscape features influence individual dispersal and as a result can affect both gene flow and genetic variation within and between populations. The landscape of British Columbia, Canada, is already highly heterogeneous due to natural ecological and geological transitions, but disturbance from human-mediated processes has further fragmented continuous habitat, particularly in the central plateau region. In this study, we evaluated the effects of landscape heterogeneity on the genetic structure of a common resident songbird, the black-capped chickadee (Poecile atricapillus). Previous work revealed significant population structuring in British Columbia which could not be explained by physical barriers, so our aim was to assess the pattern of genetic structure at a microgeographic scale and determine the effect of different landscape features on genetic differentiation. A total of 399 individuals from 15 populations were genotyped for fourteen microsatellite loci revealing significant population structuring in this species. Individual and population-based analyses revealed as many as nine genetic clusters with isolation in the north, the central plateau and the south. Moreover, a mixed modelling approach that accounted for non-independence of pairwise distance values revealed a significant effect of land cover and elevation resistance on genetic differentiation. These results suggest that barriers in the landscape influence dispersal which has led to the unexpectedly high levels of population isolation. Our study demonstrates the importance of incorporating landscape features when interpreting patterns of population differentiation. Despite taking a microgeographic approach, our results have opened up additional questions concerning the processes influencing dispersal and gene flow at the local scale.
Data from: The role of parasite-driven selection in shaping landscape genomic structure in red grouse (Lagopus lagopus scotica)
Landscape genomics promises to provide novel insights into how neutral and adaptive processes shape genome-wide variation within and among populations. However, there has been little emphasis on examining whether individual-based phenotype-genotype relationships derived from approaches such as genome-wide association (GWAS) manifest themselves as a population-level signature of selection in a landscape context. The two may prove irreconcilable as individual-level patterns may become diluted by high levels of gene flow and complex phenotypic or environmental heterogeneity. We illustrate this issue with a case study that examines the role of the highly prevalent gastrointestinal nematode Trichostrongylus tenuis in shaping genomic signatures of selection in red grouse (Lagopus lagopus scotica). Individual-level GWAS involving 384 SNPs has previously identified five SNPs that explain variation in T. tenuis burden. Here, we examine whether these same SNPs display population-level relationships between T. tenuis burden and genetic structure across a small-scale landscape of 21 sites with heterogeneous parasite pressure. Moreover, we identify adaptive SNPs showing signatures of directional selection using FST outlier analysis and relate population- and individual-level patterns of multi-locus neutral and adaptive genetic structure to T. tenuis burden. The five candidate SNPs for parasite-driven selection were neither associated with T. tenuis burden on a population level, nor under directional selection. Similarly, there was no evidence of parasite-driven selection in SNPs identified as FST outliers. We discuss these results in the context of red grouse ecology and highlight the broader consequences for the utility of landscape genomics approaches for identifying signatures of selection.
Data from: The relative influence of habitat amount and configuration on genetic structure across multiple spatial scales
Despite strong interest in understanding how habitat spatial structure shapes the genetics of populations, the relative importance of habitat amount and configuration for patterns of genetic differentiation remains largely unexplored in empirical systems. In this study, we evaluate the relative influence of, and interactions among, the amount of habitat and aspects of its spatial configuration on genetic differentiation in the pitcher plant midge, Metriocnemus knabi. Larvae of this species are found exclusively within the water-filled leaves of pitcher plants (Sarracenia purpurea) in a system that is naturally patchy at multiple spatial scales (i.e., leaf, plant, cluster, peatland). Using generalized linear mixed models and multimodel inference, we estimated effects of the amount of habitat, patch size, interpatch distance, and patch isolation, measured at different spatial scales, on genetic differentiation (FST) among larval samples from leaves within plants, plants within clusters, and clusters within peatlands. Among leaves and plants, genetic differentiation appears to be driven by female oviposition behaviors and is influenced by habitat isolation at a broad (peatland) scale. Among clusters, gene flow is spatially restricted and aspects of both the amount of habitat and configuration at the focal scale are important, as is their interaction. Our results suggest that both habitat amount and configuration can be important determinants of genetic structure and that their relative influence is scale dependent.
Data from: Feather melanin and micro-structure variation in dark-eyed junco (Junco hyemalis) across an elevational gradient in the Selkirk Mountains
Variation in feather melanism and microstructure can arise through sexual selection and ecological functional drivers. Melanin-based plumage traits are associated with sexual dichromatism and the intensity of sexual selection in many avian species, but also have several ecological benefits such as protection against ultra-violet (UV) radiation, camouflage, and feather strength. Additionally, feather microstructure influences thermoregulation. Plumage variation across species is well documented; however, the relative role of sexual selection and ecological drivers in intra-specific and within-population variation is less established. We investigated UV reflectance, melanism, and feather microstructure in a population of Oregon dark-eyed juncos Junco hyemalis oreganus between high (1900–2200 m a.s.l.) and low (450–800 m a.s.l.) elevations in the Selkirk Mountains to evaluate potential sexual selection and ecological drivers of variation. We found no difference in UV reflectance or lightness (melanism) of head feathers between elevations, but individuals at high elevation had lighter (less melanism) and less brown (less pheomelanin) body contour feathers than at low elevations. High elevation individuals also had longer contour feathers with more pronounced plumulaceous regions. Sexual dichromatism did not vary between elevations, leading us to reject sexual selection in favour of ecological functional drivers of plumage variation in this system. To our knowledge, this is the first study to identify within-population differences in feather melanism and microstructure between different elevations.
Data from: Patterns and thresholds of grazing-induced changes in community structure and ecosystem functioning: species-level responses and the critical role of species traits
Overgrazing has resulted in widespread decline in biodiversity and ecosystem functioning in grasslands worldwide in recent decades. However, few studies have examined the patterns and thresholds of grazing-induced changes in community structure and ecosystem functioning along a grazing gradient and based on species-level responses and plant functional traits. To identify the thresholds of grazing intensity at both species and community levels, we conducted a grazing manipulation experiment with seven levels of grazing intensity (0–9 sheep ha-1) and two topographies (flat versus slope) in a typical steppe. Four plant functional traits were measured, including specific leaf area (SLA), plant height, leaf nitrogen content (LNC) and stem: leaf ratio (SLR). The threshold of grazing intensity that significantly altered community composition was at 3.75 sheep ha-1 for the flat system and 3.0 sheep ha-1 for the slope system. For both flat and slope systems, the threshold grazing intensity for changes in primary productivity was at 3.0 sheep ha-1, beyond which the productivity decreased substantially. At species level, the abundances of common species, most of which are perennial grasses, declined at moderate grazing intensities (3.0–4.5 sheep ha-1). The abundances of most rare species, which are perennial forbs, declined at low grazing intensities (1.5–3.0 sheep ha-1). Specific leaf area and leaf nitrogen content are good predictors of species-level responses to grazing. Low SLA and high LNC species are negatively affected by high grazing intensity, while high SLA and low LNC species are little affected by grazing. The negative effect of grazing intensity on species abundance was greater in the slope system than in the flat system. Synthesis and applications. Our results indicate that the structural and functioning thresholds of grazing intensity depend on plant traits and species composition, which is mediated by topographic location. These findings, integrating plant functional traits and threshold approaches, have important implications for determining sustainable grazing intensity in grassland management and biodiversity conservation in semi-arid regions.
Data from: The geographic structure of selection on a coevolving interaction between social parasitic wasps and their hosts hampers social evolution
Social parasites exploit societies, rather than organisms, and rear their brood in social insect colonies at the expense of their hosts, triggering a coevolutionary process that may affect host social structure. The resulting coevolutionary trajectories may be further altered by selection imposed by predators, which exploit the abundant resources concentrated in these nests. Here, we show that geographic differences in selection imposed by predators affects the structure of selection on coevolving hosts and their social parasites. In a multi-year study, we monitored the fate of the annual breeding attempts of the solitary-founding females of Polistes biglumis social wasps in four geographically distinct populations that varied in levels of attack by the congeneric social parasite, P. atrimandibularis. Foundress fitness depended mostly on whether, during the long founding phase, a colony was invaded by social parasites or attacked by predators. Foundresses from each population differed in morphological traits and reproductive tactics that were consistent with selection imposed by their natural enemies and in ways that may affect host sociality. In turn, parasite traits were consistent with selection imposed locally by hosts, implying a geographic mosaic of coevolution in this brood parasitic interaction.
Data from: Range‐wide population genetic structure of the Caribbean marine angiosperm Thalassia testudinum
Many marine species have widespread geographic ranges derived from their evolutionary and ecological history particularly their modes of dispersal. Seagrass (marine angiosperm) species have ranges that are unusually widespread, which is not unexpected following recent reviews of reproductive strategies demonstrating the potential for long distance dispersal combined with longevity through clonality. An exemplar of these dual biological features is turtlegrass (Thalassia testudinum) which is an ecologically important species throughout the tropical Atlantic region. Turtlegrass has been documented to have long distance dispersal via floating fruits and also extreme clonality and longevity. We hypothesise that across its range, Thalassia testudinum will have very limited regional population structure due to these characteristics and under typical models of population structure would expect to detect high levels of genetic connectivity. There are very few studies of range-wide genetic connectivity documented for seagrasses or other sessile marine species. This study presents a population genetic data set that represents a geographic area exceeding 14,000 km2. Population genetic diversity was evaluated from 32 Thalassia testudinum populations sampled across the Caribbean and Gulf of Mexico. Genotypes were based on nine microsatellites and haplotypes were based on chloroplast DNA sequences. Very limited phylogeographic signal from cpDNA reduced the potential comparative analyses possible. Multiple analytical clustering approaches on population genetic data revealed two significant genetic partitions: 1) The Caribbean, and 2) The Gulf of Mexico. Genetic diversity was high (HE = 0.641) and Isolation by Distance was significant, gene flow and migration estimates across the entire range were however modest, we suggest that the frequency of successful recruitment across the range is uncommon. Thalassia testudinum maintains genetic diversity across its entire distribution range. The genetic split may be explained by genetic drift during recolonsation from refugia following relatively recent reduction in available habitat such as the last glacial maxima.
Data from: Clinal variation in colony breeding structure and level of inbreeding in the subterranean termites Reticulitermes flavipes and R. grassei
Social insects exhibit remarkable variation in their colony breeding structures, both within and among species. Ecological factors are believed to be important in shaping reproductive traits of social insect colonies, yet there is little information linking specific environmental variables with differences in breeding structure. Subterranean termites (Rhinotermitidae) show exceptional variation in colony breeding structure, differing in the number of reproductives and degree of inbreeding; colonies can be simple families headed by a single pair of monogamous reproductives (king and queen) or they can be extended families headed by multiple inbreeding neotenic reproductives (wingless individuals). Using microsatellite markers, we characterized colony breeding structure and levels of inbreeding in populations over large parts of the range of the subterranean termites Reticulitermes flavipes in the USA and R. grassei in Europe. Combining these new data with previous results on populations of both species, we found that latitude had a strong effect on the proportion of extended-family colonies in R. flavipes and on levels of inbreeding in both species. We examined the effect of several environmental variables that vary latitudinally; while the degree of inbreeding was greatest in cool, moist habitats in both species, seasonality affected the species differently. Inbreeding in R. flavipes was most strongly associated with climatic variables (mean annual temperature and seasonality), whereas nonclimatic variables, including the availability of wood substrate and soil composition, were important predictors of inbreeding in R. grassei. These results are the first showing that termite breeding structure is shaped by local environmental factors and that species can vary in their responses to these factors.
Data from: Applying the multistate capture-recapture robust design to characterize metapopulation structure
1. Population structure must be considered when developing mark-recapture (MR) study designs as the sampling of individuals from multiple populations (or subpopulations) may increase heterogeneity in individual capture probability. Conversely, the use of an appropriate MR study design which accommodates heterogeneity associated with capture-occasion varying covariates due to animals moving between 'states' (i.e. geographic sites) can provide insight into how animals are distributed in a particular environment and the status and connectivity of subpopulations. 2. The Multistate Closed Robust Design was chosen to investigate: 1) the demographic parameters of Indo-Pacific bottlenose dolphins (Tursiops aduncus) subpopulations in coastal and estuarine waters of Perth, Western Australia; and 2) how they are related to each other in a metapopulation. Using four years of year-round photo-identification surveys across three geographic sites, we accounted for heterogeneity of capture probability based on how individuals distributed themselves across geographic sites and characterized the status of subpopulations based on their abundance, survival and interconnection. 3. MSCRD models highlighted high heterogeneity in capture probabilities and demographic parameters between sites. High capture probabilities, high survival and constant abundances described a subpopulation with high fidelity in an estuary. In contrast, low captures, permanent and temporary emigration and fluctuating abundances suggested transient use and low fidelity in an open coastline site. 4. Estimates of transition probabilities also varied between sites, with estuarine dolphins visiting sheltered coastal embayments more regularly than coastal dolphins visited the estuary, highlighting some dynamics within the metapopulation. 6. Synthesis and applications. To date, bottlenose dolphin studies using mark-recapture approach have focussed on investigating single subpopulations. Here, in a heterogeneous coastal-estuarine environment, we demonstrated that spatially structured bottlenose dolphin subpopulations contained distinct suites of individuals and differed in size, demographics and connectivity. Such insights into the dynamics of a metapopulation can assist in local-scale species conservation. The MSCRD approach is applicable to species/populations consisting of recognizable individuals and is particularly useful for characterizing wildlife subpopulations that vary in their vulnerability to human activities, climate change or invasive species.
Data from: Resources alter the structure and increase stochasticity in bromeliad microfauna communities
Although stochastic and deterministic processes have been found to jointly shape structure of natural communities, the relative importance of both forces may vary across different environmental conditions and across levels of biological organization. We tested the effects of abiotic environmental conditions, altered trophic interactions and dispersal limitation on the structure of aquatic microfauna communities in Costa Rican tank bromeliads. Our approach combined natural gradients in environmental conditions with experimental manipulations of bottom-up interactions (resources), top-down interactions (predators) and dispersal at two spatial scales in the field. We found that resource addition strongly increased the abundance and reduced the richness of microfauna communities. Community composition shifted in a predictable way towards assemblages dominated by flagellates and ciliates but with lower abundance and richness of algae and amoebae. While all functional groups responded strongly and predictably to resource addition, similarity among communities at the species level decreased, suggesting a role of stochasticity in species-level assembly processes. Dispersal limitation did not affect the communities. Since our design excluded potential priority effects we can attribute the differences in community similarity to increased demographic stochasticity of resource-enriched communities related to erratic changes in population sizes of some species. In contrast to resources, predators and environmental conditions had negligible effects on community structure. Our results demonstrate that bromeliad microfauna communities are strongly controlled by bottom-up forces. They further suggest that the relative importance of stochasticity may change with productivity and with the organizational level at which communities are examined.
Data from: Assortative mating and the maintenance of population structure in a natural hybrid zone
Understanding the factors that give rise to natural hybrid zones and govern their dynamics and structure is important to predicting the evolutionary consequences of hybridization. Here we use a combination of multi-generational population genetic data, mating patterns from a natural population, behavioral assays, and mark-recapture data within clinal hybrid zones of the genus Xiphophorus to test the role of assortative mating in maintaining population structure and the potential for ongoing genetic exchange between heterospecifics. Our data demonstrate that population structure is temporally robust and driven largely by assortative mating stemming from pre-copulatory isolation between pure species. Furthermore, mark-recapture data revealed that rates of migration within the same stream reach are far below the level needed to support population structure. Contrasting with many empirical studies of natural hybrid zones, there appeared to be no hybrid male dysfunction nor discrimination against hybrid males by pure parental females, and hybrid females mated and associated with pure species and hybrid males at random. Despite strong isolation between pure parentals, hybrids therefore can act as a conduit for genetic exchange between heterospecifics, which has been shown to increase the tempo of evolutionary change. Additionally, our findings highlight the complexity of natural hybrid zone dynamics, demonstrating that multivariate selection can give rise to patterns that do not fit classical models of hybrid zone evolution.
Data from: Contrasted invasion processes imprint the genetic structure of an invasive scale insect across southern Europe
Deciphering the colonization processes by which introduced pests invade new areas is essential to limit the risk of further expansion and/or multiple introductions. We here studied the invasion history of the maritime pine bast scale Matsucoccus feytaudi. This host-specific insect does not cause any damage in its native area, but it devastated maritime pine forests of South-Eastern France where it was detected in the 1960s, and since then reached Italy and Corsica. We used population genetic approaches to infer the populations' recent evolutionary history from microsatellite markers and Approximate Bayesian Computation. Consistent with previous mitochondrial data, we showed that the native range is geographically strongly structured, which is probably due to the patchy distribution of the obligate host and the limited dispersal capacity of the scale. Our results show that the invasion history can be described in three successive steps involving different colonization and dispersal processes. During the mid-XXth century, massive introductions occurred from the Landes planted forest to South-Eastern France, probably due to transportation of infested wood material after World War II. Stepping-stone expansion, consistent with natural dispersal, then allowed M. feytaudi to reach the maritime pine forests of Liguria and Tuscany in Italy. The island of Corsica was accidentally colonized in the 1990s, and the most plausible scenario involves the introduction of a limited number of migrants from the forests of South-Eastern France and Liguria, which is consistent with an aerial dispersal due to the dominant winds that blow in spring in this region.
Data from: Clone configuration and spatial genetic structure of two Halophila ovalis populations with contrasting internode lengths
Fine-scale spatial genetic structure (SGS) is predominantly determined by gene flow. While sexually reproducing plants can disperse their genes through pollen and seed grains, clonal plants can additionally disperse genes through clonal growth. Plants' clonal reproduction strategy, however, often varies within and between species. Still, the effect of differential clonal reproduction strategy on fine-scale SGS remains somewhat unclear. Halophila ovalis is a fast-growing clonal seagrass, whose internode length (which defines a species' clonal reproduction strategy) varies among populations. Using eight polymorphic microsatellites, here we compare the genetic diversity, clonal structure and fine-scale SGS of two H. ovalis populations with contrasting internode lengths (Yingluo versus Xialongwei populations). We found moderate to high genotypic and allelic richness and heterozygosities in both populations. Compared to Xialongwei population, genetic and genotypic diversity was significantly lower in Yingluo population. Although their internode length was relatively short, clones of Yingluo population spread farther than those of Xialongwei population. Sexual-to-vegetative dispersal variance ratios were 34.6 and 445.5 in Yingluo and Xialongwei populations, respectively. In both populations, clonal growth significantly intensified the SGS, especially in short distance classes. The SGS at small distance classes were weaker in Yingluo than Xialongwei, in part, due to more intermingled distribution of genets and more extensive clonal expansion in the former population. Our results indicate that vegetative dispersal variance/distance, rather than internode length, plays a crucial role in shaping the fine-scale genetic structure.
Data from: Mosaic structure of native ant supercolonies
According to the inclusive fitness theory, some degree of positive relatedness is required for the evolution and maintenance of altruism. However, ant colonies are sometimes large interconnected networks of nests which are genetically homogenous entities, causing a putative problem for the theory. We studied spatial structure and genetic relatedness in two supercolonies of the ant Formica exsecta, by using nuclear and mitochondrial markers. We show that there may be multiple pathways to supercolonial social organization leading to different spatial genetic structures. One supercolony formed a genetically homogenous population dominated by a single mtDNA haplotype, as expected if founded by a small number of colonizers, followed by nest propagation by budding and domination of the habitat patch. The other supercolony had several haplotypes and the spatial genetic structure was a mosaic of nuclear and mitochondrial clusters. Genetic diversity probably originated from long-range dispersal, and the mosaic population structure is likely a result of stochastic short-range dispersal of individuals. Such a mosaic spatial structure is apparently discordant with the current knowledge about the integrity of ant colonies. Relatedness was low in both populations when estimated among nestmates, but increased significantly when estimated among individuals sharing the same genetic cluster or haplogroup. The latter association indicates the important historical role of queen dispersal in the determination of the spatial genetic structure.
Data from: Comparative analyses of reproductive structures in harvestmen (Opiliones) reveal multiple transitions from courtship to precopulatory antagonism
Explaining the rapid, species-specific diversification of reproductive structures and behaviors is a long-standing goal of evolutionary biology, with recent research tending to attribute reproductive phenotypes to the evolutionary mechanisms of female mate choice or intersexual conflict. Progress in understanding these and other possible mechanisms depends, in part, on reconstructing the direction, frequency and relative timing of phenotypic evolution of male and female structures in species-rich clades. Here we examine evolution of reproductive structures in the leiobunine harvestmen or "daddy long-legs" of eastern North America, a monophyletic group that includes species in which males court females using nuptial gifts and other species that are equipped for apparent precopulatory antagonism (i.e., males with long, hardened penes and females with sclerotized pregenital barriers). We used parsimony- and Bayesian likelihood-based analyses to reconstruct character evolution in categorical reproductive traits and found that losses of ancestral gift-bearing penile sacs are strongly associated with gains of female pregenital barriers. In most cases, both events occur on the same internal branch of the phylogeny. These coevolutionary changes occurred at least four times, resulting in clade-specific designs in the penis and pregenital barrier. The discovery of convergent origins and/or enhancements of apparent precopulatory antagonism among closely related species offers an unusual opportunity to investigate how major changes in reproductive morphology have occurred. We propose new hypotheses that attribute these enhancements to changes in ecology or life history that reduce the duration of breeding seasons, an association that is consistent with female choice, sexual conflict, and/or an alternative evolutionary mechanism.
Data from: Condition dependence of male and female genital structures in the seed beetle Callosobruchus maculatus (Coleoptera: Bruchidae)
Theory predicts that costly secondary sexual traits will evolve heightened condition dependence, and many studies have reported strong condition dependence of signal and weapon traits in a variety of species. However, although genital structures often play key roles in intersexual interactions and appear to be subject to sexual or sexually antagonistic selection, few studies have examined the condition dependence of genital structures, especially in both sexes simultaneously. We investigated the responses of male and female genital structures to manipulation of larval diet quality (new versus once-used mung beans) in the bruchid seed beetle Callosobruchus maculatus. We quantified effects on mean relative size and static allometry of the male aedeagus, aedeagal spines, flap and paramere and the female reproductive tract and bursal spines. None of the male traits showed a significant effect of diet quality. In females, we found that longer bursal spines (relative to body size) were expressed on low-quality diet. Although the function of bursal spines is poorly understood, we suggest that greater bursal spine length in low-condition females may represent a sexually antagonistic adaptation. Overall, we found no evidence that genital traits in C. maculatus are expressed to a greater extent when nutrients are more abundant. This suggests that, even though some genital traits appear to function as secondary sexual traits, genital traits do not exhibit heightened condition dependence in this species. We discuss possible reasons for this finding.
Data from: Sex-biased dispersal creates spatial genetic structure in a parthenogenetic ant with a dependent-lineage reproductive system
Reproduction and dispersal are key aspects of species life history that influence spatial genetic structure in populations. Several ant species in the genus Cataglyphis have evolved a unique breeding system in which new reproductives (that is, queens and males) are produced asexually by parthenogenesis; in contrast, non-reproductives (that is, workers) are produced via sexual reproduction by mates from distinct genetic lineages. We investigated how these two coexisting reproductive methods affect population-level spatial genetic structure using the ant Cataglyphis mauritanica as a model. We obtained genotypes for queens and their male mates from 338 colonies, and we found that the two lineages present in the study population occurred with equal frequency. Furthermore, analysis of spatial genetic structure revealed strong sex-biased dispersal. Because queens were produced by parthenogenesis and because they dispersed over short distances, there was an extreme level of spatial structuring: a mosaic of patches composed of clonal queens was formed. Males, on the other hand, dispersed over several hundred metres and, thus, across patches, ensuring successful interlineage mating.
Data from: Similarity in G matrix structure among natural populations of Arabidopsis lyrata
Understanding the stability of the G matrix in natural populations is fundamental for predicting evolutionary trajectories, yet, the extent of its spatial variation and how this impacts responses to selection remain open questions. With a nested paternal half-sib crossing design and plants grown in a field experiment, we examined differences in the genetic architecture of flowering time, floral display and plant size among four Scandinavian populations of Arabidopsis lyrata. Using a multivariate Bayesian framework, we compared the size, shape and orientation of G matrices and assessed their potential to facilitate or constrain trait evolution. Flowering time, floral display and rosette size varied among populations and significant additive genetic variation within populations indicated potential to evolve in response to selection. Yet, some characters, including flowering start and number of flowers, may not evolve independently because of genetic correlations. Using a multivariate framework, we found few differences in the genetic architecture of traits among populations. G matrices varied mostly in size rather than shape or orientation. Differences in multivariate responses to selection predicted from differences in G were small, suggesting overall matrix similarity and shared constraints to trait evolution among populations.
Data from: Population clustering and clonal structure evidence the relict state of Ulmus minor Mill. in the Balearic Islands
Field elm (Ulmus minor) is a riparian tree that grows in rare, small populations scattered along temporary watercourses in the Balearic Islands, nowadays mostly covered with Mediterranean vegetation. Agriculture and farming on the fertile land along the periodically flooded plains have reduced the elm populations to sparse tree lines along the creek beds. The presence of field elm in this very anthropic landscape has led some authors to consider it as an introduced species in the Balearics. However, pollen data suggest these elms may be the remains of larger populations experiencing continuous population shrinkage during the Holocene, and hence be native to the isles. In this paper, we apply genetic markers to assess whether field elm is or is not indigenous to the Balearic Islands. We compare the genetic variation in nine nuclear microsatellites of six Balearic populations (three in each of the largest islands, Majorca and Minorca) with that of three natural Iberian populations located in two regions, one geologically (Baetic mountains, SE Iberia) and another historically (Catalonia, NE Iberia) related to the islands. Principal coordinates analysis and Bayesian clustering methods reveal a strong genetic differentiation of the Balearic populations from the Iberian ones, and even among islands, which support their native origin. Genotypic variation in the islands is very low and clonal reproduction is very high compared with the mainland, as it is frequently observed in populations of clonal species where sexual reproduction is limited. We discuss the practical implications of these findings for the conservation of elm genetic resources of these findings.
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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.