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Figure 5 in Genetic and morphological heterogeneity within Eucyclops serrulatus (Fischer, 1851) (Crustacea: Copepoda: Cyclopidae)
Figure 5. Eucyclops taiwanensis sp. n., female, ZIN RN 55090 (holotype): (A) habitus, dorsal; (B) urosome with P5, ventral side; (C) antennule with aesthetascs indicated by arrows; (D) hyaline membrane on segments 10–12 of antennule. Scale bar: A = 150 μm; B = 100 μm, C = 75 μm; D =37 μm.
Figure 4 in Genetic and morphological heterogeneity within Eucyclops serrulatus (Fischer, 1851) (Crustacea: Copepoda: Cyclopidae)
Figure 4. Distribution of Eucyclops serrulatus (Fischer) females from different localities on the base of caudal rami index INseta/OUTseta, and P4 exo Lseg/Sp1 (see Table 4 and text). Populations from Dniester Liman; Zakarpattia region; and from the type locality in Orlov Pond, Saint Petersburg: individuals from Orlov Pond resembling the Zakarpattia population ▲; individuals from Orlov Pond resembling Dniester Liman ♦ and individuals from Orlov Pond ○ looking like hybrids between the two Ukrainian populations.
Figure 1 in Genetic and morphological heterogeneity within Eucyclops serrulatus (Fischer, 1851) (Crustacea: Copepoda: Cyclopidae)
Figure 1. The localities of the Eucyclops serrulatus (Fischer) and Eucyclops taiwanensis sp. n., populations studied. Locality names are listed in Table 1.
Figure 2 in Genetic and morphological heterogeneity within Eucyclops serrulatus (Fischer, 1851) (Crustacea: Copepoda: Cyclopidae)
Figure 2. Phylogenetic tree constructed based on data from mitochondrial cytochrome c oxidase subunit I (CO1) region (651 bp) by the Bayesian method using the TPM1uf +G model. Numbers beside nodes indicate Bayesian posterior probabilities (BPP) and bootstrap values. Clade 1 includes sequences of Eucyclops serrulatus (Fischer) from the Zakarpattia region of Ukraine, Orlov Pond and Tavricheskii Pond in Saint Petersburg, Creteil Lake in Paris and the pond in Oslo; Clade 2: Eucyclops serrulatus sequences from the Dniester Liman in Ukraine, Orlov Pond in Saint Petersburg and Central Russia (Udmurtia). Clade 3: Eucyclops taiwanensis sp. n. sequences from ponds in Taiwan. Clade 4: Eucyclops cf. serrulatus sequences from the Xucar River in Spain.
Snow depth mapping with an Unmanned Aerial Vehicles in heterogeneous mountain site (Izas Catchment, Pyrenees)
<p>Recent developments in unmanned aircraft vehicles (UAV) and Structure for Motion (SfM photogrammetry or simply SfM) algorithms have proved their worth for determining snow depth distribution. This dataset presents UAV and Terrestrial Laser Scanner (TLS) snow depth obsrevations obtained in complex alpine terrain in the Pyrenees. UAV observations have been acqired with a fixed-wing UAV working in RTK mode with an RGB camera. During the 2018-19 season, seven field campaigns (13 UAV flights) were undertaken covering 0.48 km2 . Several UAV observations were obtained under different light conditions and flight block configurations (altitude and image overlaps) in the same day with the aim if evaluating UAV observations when compared ti a well-established close range remote sensing technique (TLS).</p>
An algorithm to quantify intratumor heterogeneity based on alterations of gene expression profiles: Data availability
<p>DEPTH evaluates the tumor heterogeneity level of each tumor sample based on gene expression profiles Heterogeneity score. </p>
Do heterogeneous seascapes of carbonate conditions across biogeographic breaks influence divergent phenotypic plasticity in natural populations?
<p><b>Aim:</b> Understanding how environmental variability influences stress tolerance, local adaptation, and phenotypic variation among populations is a key challenge for evolutionary ecology and climate change biology. Coastal biogeographic breaks are natural laboratories to explore this fundamental research question due to the contrasting environmental conditions experienced by natural populations across these regions.</p> <p><b>Location:</b> In the South East Pacific (SEP) coast a major break (30º-32ºS) is characterized by extreme natural variability in seawater carbonate chemistry parameters related to temporal and spatial dynamics in upwelling events. Mollusk species that reach their range limit at this zone are exposed to naturally acidified waters that can be corrosive and impact their calcification, physiology, and fitness, making them particularly prone to the effects of ocean acidification (OA). We investigated to what extent the interplay between biogeographic breaks and local variability of seawater carbonate conditions influences the tolerances and sensitivity of populations of the limpet <i>Scurria araucana</i> to OA.</p> <p><b>Methods: </b>During two years, we conducted field surveys of limpet populations at sites across the SEP break (27ºS, 30ºS and 32ºS). We collected individuals from each population to test for geographic differences in morphometric (e.g., total buoyancy weight, shell length) and physiological (e.g., oxygen consumption rate, cardiac activity, and thermal performance curves; TPC) responses to local conditions and to simulated OA scenarios.</p> <p><b>Results:</b> Analysis of the cardiac activity indicates that limpets from the central part of the break (30ºS) exhibit higher thermal performance compared to limpets from populations at both sides of the break. Thus, heterogeneous seascape of carbonate conditions and sea surface temperature across a biogeographic break in the SEP coast influence phenotypic differences among populations of this ecosystem engineer.</p> <p><b>Main Conclusions:</b> Natural environmental variation might be the underpinning driver of the high tolerance to OA evidenced by populations of the limpet <i>Scurria araucana </i>along the SEP.</p>
Code and data sharing for manuscript titled "Transmission heterogeneities, kinetics, and controllability of SARS-CoV-2"
<p>Code and data sharing for manuscript titled "Transmission heterogeneities, kinetics, and controllability of SARS-CoV-2".</p>
Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot
<p>As human-induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant <i>Leucadendron salignum</i> or "common sunshine conebush" as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, are characteristic of the southwestern CFR, whereas, low population structure and more recent lineage coalescence depicts the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species-level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land-usage as a significant gene flow barrier, especially in severely-threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.</p>
Spatial and temporal variation in prey colour patterns for background-matching across a continuous heterogeneous environment
<p>In heterogeneous habitats, camouflage via background-matching can be challenging because visual characteristics can vary dramatically across small spatial scales. Additionally, temporal variation in signalling functions of colouration can affect crypsis, especially when animals use colouration seasonally for intraspecific signalling (e.g. mate selection). We currently have a poor understanding of how wild prey optimise background-matching within continuously heterogeneous habitats, and whether this is affected by requirements of intraspecific signalling across biological seasons. Here, we quantified colour patterns of a wild population of shore skink (<i>Oligosoma smithi</i>), a variably coloured lizard endemic to New Zealand, to 1) investigate whether background-matching varies across a vegetation gradient; 2) assess potential signalling functions of colour; and 3) to determine whether there is a trade-off between requirements for crypsis and intraspecific signalling in colouration across seasons. Although all pattern types occurred throughout the vegetation gradient, we found evidence for background-matching in skinks across the vegetation gradient, where dorsal brightness and pattern complexity corresponded with the proportion of vegetation cover. There was also a significant disparity between ventral colour (saturation) of juveniles and adults, and also between sexes, suggestive of sex recognition. However, there was little indication that colour was condition-dependent in adults. Despite some evidence for a potential role in signalling, crypsis did not greatly differ across seasons. Our study suggests that selection favours a mix of generalist and specialist background-matching strategies across continuously heterogeneous habitats.</p>
The synthesis of SBA-Pr-3AP@Pd and its application as a highly dynamic, eco-friendly heterogeneous catalyst for Suzuki–Miyaura cross-coupling reaction
<p>The hexagonal mesoporous organic–inorganic hybrid as a new nanocatalyst was prepared by the treatment of SBA-15 with (3-chloropropyl)triethoxysilane, the 2,4,6-triamino pyrimidine ligand, and then PdCl2 to obtain the SBA-15-propyl-triamino pyrimidine@Pd called as SBA-Pr-3AP@Pd, which was examined through Suzuki–Miyaura cross-coupling reaction by several aryl halides and phenylboronic acid under mild conditions in high yield.</p>
Data from: Sex-specific heterogeneity in fixed morphological traits influences individual fitness in a monogamous bird population
Theoretical work has emphasized the important role of individual traits on population dynamics, but empirical models are often based on average or stage-dependent demographic rates. In this study on a monogamous bird, the Eurasian hoopoe (Upupa epops), we show how the interactions between male and female fixed and dynamic heterogeneity influence demographic rates and population dynamics. We built an integral projection model including individual sex, age, condition (reflecting dynamic heterogeneity) and fixed morphology (reflecting fixed heterogeneity). Fixed morphology was derived from a principal component analysis of six morphological traits. Our results revealed that reproductive success and survival were linked to fixed heterogeneity whereas dynamic heterogeneity influenced mainly the timing of reproduction. Fixed heterogeneity had major consequences for the population growth rate, but interestingly, its effect on population dynamics differed between the sexes. Female fixed morphology was directly linked to annual reproductive success whereas male fixed morphology influenced also annual survival, being twice higher in large than in small males. Even in a monogamous bird with shared parental care, large males can reach 10\% higher fitness than females. Including the dynamics of male and female individual traits in population models refines our understanding of the individual mechanisms that influence demographic rates and population dynamics and can help identifying differences in sex-specific strategies.
Data from: Invasive alien plants benefit more from clonal integration in heterogeneous environments than natives
What confers invasive alien plants a competitive advantage over native plants remains open to debate. Many of the world's worst invasive alien plants are clonal and able to share resources within clones (clonal integration), particularly in heterogeneous environments. Here, we tested the hypothesis that clonal integration benefits invasive clonal plants more than natives and thus confers invasives a competitive advantage. We selected five congeneric and naturally co-occurring pairs of invasive alien and native clonal plants in China, and grew pairs of connected and disconnected ramets under heterogeneous light, soil nutrient and water conditions that are commonly encountered by alien plants during their invasion into new areas. Clonal integration increased biomass of all plants in all three heterogeneous resource environments. However, invasive plants benefited more from clonal integration than natives. Consequently, invasive plants produced more biomass than natives. Our results indicate that clonal integration may confer invasive alien clonal plants a competitive advantage over natives. Therefore, differences in the ability of clonal integration could potentially explain, at least partly, the invasion success of alien clonal plants in areas where resources are heterogeneously distributed.
Data from: Scale-dependent role of demography and dispersal on the distribution of populations in heterogeneous landscapes
Both dispersal and local demographic processes determine a population's distribution among habitats of varying quality, yet most theory, experiments, and field studies have focused on the former. We use a generic model to show how both processes contribute to a population's distribution, and how the relative importance of each mechanism depends on scale. In contrast to studies only considering habitat-dependent dispersal, we show that predictions of ideal free distribution (IFD) theory are relevant even at landscape scales, where the assumptions of IFD theory are violated. This is because scales that inhibit one process, promote the other's ability to drive populations to the IFD. Furthermore, because multiple processes can generate IFDs, the pattern alone does not specify a causal mechanism. This is important because populations with IFDs generated by dispersal or demography respond much differently to shifts in resource distributions.
Data from: Quantitative genetic variance in experimental fly populations evolving with or without environmental heterogeneity
Heterogeneous environments are typically expected to maintain more genetic variation in fitness within populations than homogeneous environments. However, the accuracy of this claim depends on the form of heterogeneity as well as the genetic basis of fitness traits and how similar the assay environment is to the environment of past selection. Here we measure quantitative genetic variance for three traits important for fitness using replicated experimental populations of Drosophila melanogaster evolving under four selective regimes: constant salt-enriched medium (Salt), constant cadmium-enriched medium (Cad), and two heterogeneous regimes that vary either temporally (Temp) or spatially (Spatial). As theory predicts, we found that Spatial populations tend to harbor more genetic variation than Temp populations or those maintained in a constant environment that is the same as the assay environment. Contrary to expectation, Salt populations tend to have more genetic variation than Cad populations in both assay environments. We discuss the patterns for quantitative genetic (QG) variances across regimes in relation to previously reported data on genome-wide sequence diversity. For some traits, the QG patterns are similar to the diversity patterns of ecological selected SNPs whereas the QG patterns for some other traits resembled that of neutral SNPs.
Data from: The importance of individual heterogeneity for interpreting faecal glucocorticoid metabolite levels in wildlife studies
1. Being a non-invasive and inexpensive method, the analysis of faecal corticosteroid metabolites (FCM) is increasingly being applied in wildlife research. Various environmental factors have been shown to influence FCM levels, but most studies did not account for inter-individual variance, which we hypothesized may substantially affect the results. 2. We combined FCM analysis with genetic analysis to identify the sex and individual of samples collected in three consecutive winters, with repeated samples per individual, across the entire range of an endangered population of capercaillie (Tetrao urogallus) in Southwestern Germany. Using generalized additive mixed models, we modelled FCM levels as a function of sex, season and environmental covariates at two spatial scales (sampling location and home range scales). We compared two models: one including information on the individual animal, and the other excluding this information (i.e. naïve model) to assess the influence of individual effects on the results obtained. 3. Most of the variance (44.0% and 45.1% at the sampling and home range scale, respectively) was explained by the inter-individual differences, and only very little (4.0% and 5.1%, respectively) by the environmental predictors. When ignoring individual effects, the model results changed considerably, with other, previously non-informative predictors, becoming significant. 4. In the full models, accounting for inter-individual variance, no effect was found of weather conditions, at either scale. FCM levels were negatively correlated with habitat quality, at the sampling location, whereas human recreation at the home range scale led to elevated FCM levels. In the naïve models, two additional predictors appeared significant: one weather variable at local scales and two at home range scale. In all models, seasonal FCM patterns differed significantly between males and females. 5. Synthesis and applications. Our results highlight the importance of considering the effects of individual heterogeneity when studying FCM in wildlife research, as ignoring information on the individual might lead to erroneous conclusions. Combining FCM analyses with genetic analyses can be an efficient approach to adequately address this issue.21-Feb-2018
Data from: Heterogeneity in individual quality and reproductive trade-offs within species
Interspecifically, a reasonable body of evidence supports a trade-off between offspring size and number. However, at the intraspecific level, a whole manner of phenotypic correlations between offspring size and number are observed. These correlations may be predicted when heterogeneity in resource availability, or quality, is considered. Making the assumption that maternal size is a proxy for resource availability, we meta-analytically quantified four phenotypic reproductive correlations within numerous species: (1) maternal size and offspring size, (2) maternal size and offspring number, (3) offspring number and offspring size, and (4) offspring number and offspring size after controlling for maternal size. Within species, maternal size showed a positive correlation with both offspring size and number. Despite this consistency, no correlation between offspring size and number was found. After controlling for maternal size, however, offspring size and number showed a significant negative correlation. A phylogenetic component of our analysis accounted for little heterogeneity in the data, suggesting that our findings show remarkable consistency across taxa. Overall, our results support an observable phenotypic trade-off between offspring size and number. However, this analysis also highlights the importance of considering quality when examining trade-offs, a task that is not always straightforward as quality is context dependant.
Data from: Quantifying the effects of migration and mutation on adaptation and demography in spatially heterogeneous environments
How do mutation and gene flow influence population persistence, niche expansion, and local adaptation in spatially heterogeneous environments? In this article, we analyse a demographic and evolutionary model of adaptation to an environment containing two habitats in equal frequencies, and we bridge the gap between different theoretical frameworks. Qualitatively, our model yields four qualitative types of outcomes: (i) global extinction of the population (ii) adaptation to one habitat only, but also adaptation to both habitats with (iii) specialized phenotypes, or (iv) with generalized phenotypes; and we determine the conditions under which each equilibrium is reached. We derive new analytical approximations for the local densities and the distributions of traits in each habitat under a migration--selection--mutation balance, compute the equilibrium values of the means, variances and asymmetries of the local distributions of phenotypes, and contrast the effects of migration and mutation on the evolutionary outcome. We then check our analytical results by solving our model numerically, and also assess their robustness in the presence of demographic stochasticity. While increased migration results in a decrease in local adaptation, mutation in our model does not influence the values of the local mean traits. Yet, both migration and mutation can have dramatic effects on population size and even lead to metapopulation extinction when selection is strong. Niche expansion, the ability for the population to adapt to both habitats, can also be prevented by small migration rates and a reduced evolutionary potential characterised by rare mutation events of small effects; but niche expansion is otherwise the most likely outcome. Although our results are derived under the assumption of clonal reproduction, we finally show and discuss the links between our model and previous quantitative genetics models.
Data from: Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes
The spatial structure of the environment (e.g., the configuration of habitat patches) may play an important role in determining the strength of local adaptation. However, previous studies of habitat heterogeneity and local adaptation have largely been limited to simple landscapes, which poorly represent the multi-scale habitat structure common in nature. Here, we use simulations to pursue two goals: (1) we explore how landscape heterogeneity, dispersal ability, and selection affect the strength of local adaptation, and (2) we evaluate the performance of several genotype-environment association (GEA) methods for detecting loci involved in local adaptation. We found that the strength of local adaptation increased in spatially aggregated selection regimes, but remained strong in patchy landscapes when selection was moderate to strong. Weak selection resulted in weak local adaptation that was relatively unaffected by landscape heterogeneity. In general, the power of detection methods closely reflected levels of local adaptation. False positive rates (FPRs), however, showed distinct differences across GEA methods based on levels of population structure. The univariate GEA approach had high FPRs (up to 55%) under limited dispersal scenarios, due to strong isolation by distance. By contrast, multivariate, ordination-based methods had uniformly low FPRs (0-2%), suggesting these approaches can effectively control for population structure. Specifically, constrained ordinations had the best balance of high detection and low FPRs, and will be a useful addition to the GEA toolkit. Our results provide both theoretical and practical insights into the conditions that shape local adaptation and how these conditions impact our ability to detect selection.
Data from: Spatial heterogeneity in the strength of plant-herbivore interactions under predation risk: the tale of bison foraging in wolf country
Spatial heterogeneity in the strength of trophic interactions is a fundamental property of food web spatial dynamics. The feeding effort of herbivores should reflect adaptive decisions that only become rewarding when foraging gains exceed 1) the metabolic costs, 2) the missed opportunity costs of not foraging elsewhere, and 3) the foraging costs of anti-predator behaviour. Two aspects of these costs remain largely unexplored: the link between the strength of plant-herbivore interactions and the spatial scale of food-quality assessment, and the predator-prey spatial game. We modeled the foraging effort of free-ranging plains bison (Bison bison bison) in winter, within a mosaic of discrete meadows. Spatial patterns of bison herbivory were largely driven by a search for high net energy gains and, to a lesser degree, by the spatial game with grey wolves (Canis lupus). Bison decreased local feeding effort with increasing metabolic and missed opportunity costs. Bison herbivory was most consistent with a broad-scale assessment of food patch quality, i.e., bison grazed more intensively in patches with a low missed opportunity cost relative to other patches available in the landscape. Bison and wolves had a higher probability of using the same meadows than expected randomly. This co-occurrence indicates wolves are ahead in the spatial game they play with bison. Wolves influenced bison foraging at fine scale, as bison tended to consume less biomass at each feeding station when in meadows where the risk of a wolf's arrival was relatively high. Also, bison left more high-quality vegetation in large than small meadows. This behavior does not maximize their energy intake rate, but is consistent with bison playing a shell game with wolves. Our assessment of bison foraging in a natural setting clarifies the complex nature of plant-herbivore interactions under predation risk, and reveals how spatial patterns in herbivory emerge from multi-scale landscape heterogeneity.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.